Entries |
Document | Title | Date |
20080214411 | Eukaryotic signal sequences for polypeptide expression and polypeptide display libraries - The present invention generally relates to methods and compositions for expressing proteins or polypeptides in prokaryotic hosts using eukaryotic signal sequences. | 09-04-2008 |
20080227661 | Mutant reverse transcriptase and methods of use - The invention relates to the generation and characterization of stable MMLV reverse transcriptase mutants. The invention also discloses methods of using stable MMLV reverse transcriptase mutants. | 09-18-2008 |
20080234142 | Random Mutagenesis And Amplification Of Nucleic Acid - A method is provided for mutagenizing nucleic acids and proteins relative to an initial nucleic acid sequence by the insertion, deletion or substitution of nucleotide(s) in the target nucleic acid during amplification. | 09-25-2008 |
20080242560 | METHODS FOR GENERATING AMPLIFIED NUCLEIC ACID ARRAYS - The present invention relates to methods for generating an array of amplified nucleic acid sequences. The methods can utilize amplicons that form nucleic acid balls that can be arrayed on a solid support. The invention additionally provides methods for obtaining targeted nucleic acid sequences. | 10-02-2008 |
20080261833 | METHODS FOR GENERATING POLYNUCLEOTIDES HAVING DESIRED CHARACTERISTICS BY ITERATIVE SELECTION AND RECOMBINATION - A method for DNA reassembly after random fragmentation, and its application to mutagenesis of nucleic acid sequences by in vitro or in vivo recombination is described. In particular, a method for the production of nucleic acid fragments or polynucleotides encoding mutant proteins is described. The present invention also relates to a method of repeated cycles of mutagenesis, shuffling and selection which allow for the directed molecular evolution in vitro or in vivo of proteins. | 10-23-2008 |
20080269074 | Methods, Kits and Compositions Pertaining to Combination Oligomers and Libraries for Their Preparation - This invention pertains to the field of combination oligomers, including the block synthesis of combination oligomers in the absence of a template, as well as related methods, kits, libraries and other compositions. | 10-30-2008 |
20080287321 | cDNA synthesis improvements - The present invention generally relates to methods of making cDNA molecules and cDNA libraries. The invention also relates to cDNA molecules and cDNA libraries produced according to these methods, as well as to vectors and host cells containing such cDNA molecules and libraries. The invention also relates to kits for making the cDNA molecules and libraries of the invention. | 11-20-2008 |
20090005268 | Compositions and Methods for Cancer Diagnostics Comprising Pan-Cancer Markers - The present invention relates to compositions and methods for cancer diagnostics, including but not limited to, so-called “pan cancer markers”. In particular, the present invention provides methods of identifying methylation patterns in genes associated with specific cancers, and their related uses. In another aspect, the present invention provides methods of selecting and combining useful sets of pan cancer markers. | 01-01-2009 |
20090011957 | Ligational encoding using building block oligonucleotides - The present invention in one aspect relates to a method for synthesizing a bifunctional complex comprising a molecule and an identifier polynucleotide identifying at least some of the chemical entities which have participated in the synthesis of the molecule in accordance with the methods of the present invention. The invention also relates to a library of different bifunctional complexes. The library of the invention can be used e.g. for identifying drug leads. Furthermore, the present invention is based on the principle that chemical entities initially provided on a building block oligonucleotide (i.e. a building block having an oligonucleotide part which is linked to a chemical entity) can be brought into reactive proximity without the use of a template comprising a set of covalently linked codons. Also, the present invention allows reaction of chemical entities when the chemical entities are linked to a single stranded identifier polynucleotide obtained by covalently linking the oligonucleotide parts (oligonucleotide identifiers) of the building blocks. The single stranded identifier polynucleotides differs from template directed synthesis methods employing codon and anti-codon hybridisation between a template and one or more transfer units, i.e. methods wherein e.g. reactive units on transfer units are reacted while the anti-codon of the transfer units are hybridised to template codons. | 01-08-2009 |
20090011958 | PROCESS FOR IMMOBILIZING ORIENTATION-CONTROLLED PROTEIN AND PROCESS FOR ARRAYING AND IMMOBILIZING PROTEIN USING THE SAME - This invention provides a process for effectively producing an immobilized protein that is immobilized only at the carboxy terminus. This is a process for immobilizing on a carrier for immobilization a protein represented by general formula (1): | 01-08-2009 |
20090018033 | Cell Aggregation and Encapsulation Device and Method - The invention is a cell aggregation device comprising a hydrogel substrate having at least one, preferably a plurality, of cell-repellant compartments recessed into the uppermost surface. Each compartment is composed of an upper cell suspension seeding chamber having an open uppermost portion and a bottom portion, and one, or more than one, lower cell aggregation recess connected to the bottom portion of the upper cell suspension seeding chamber by a port. The diameter of the port may be fully contiguous with the walls of the chambers and walls of the recesses, or the diameter of the port may be more narrow than the walls of the chamber but fully contiguous with the walls of the recesses or more narrow than both the walls of the chamber and the walls of the recesses. The upper cell suspension seeding chambers are formed and positioned to funnel the cells into the lower cell aggregation recesses through gravitational force. The aggregation recesses are formed and positioned to promote cellular aggregation by coalescing cells into a finite region of minimum gravitational energy, increasing intercellular contact and minimizing or preventing cell adherence to the substrate. A device for encapsulating aggregates of live cells is provided. The device comprises (i) a biocompatible, bio-sustainable substrate having a cell-encapsulating face composed of one or more biocompatible, bio-sustainable, spaced-apart, cell-encapsulating compartments extending therefrom and (ii) a coating layer composed of a biocompatible, bio-sustainable polymer that completely surrounds the substrate and the cell-encapsulating compartments. A method for making the device is also provided. | 01-15-2009 |
20090023603 | Methods for rapid multiplexed amplification of target nucleic acids - A fast, multiplexed PCR system is described that can rapidly generate amplified nucleic acid products, for example, a full STR profile, from a target nucleic acid. Such systems include, for example, microfluidic biochips and a custom built thermal cycler, which are also described. The resulting STR profiles can satisfy forensic guidelines for signal strength, inter-loci peak height balance, heterozygous peak height ratio, incomplete non-template nucleotide addition, and stutter. | 01-22-2009 |
20090036325 | Directed assembly of amplicons to enhance read pairing signature with massively parallel short read sequencers - The present teachings relate to improved methods, kits, and compositions for making nucleic acid libraries and sequencing nucleic acids. In some embodiments, directionally defined concatamers are generated, facilitating sequencing efforts. | 02-05-2009 |
20090062147 | Methods for synthesis of encoded libraries - The present invention provides a method of synthesizing libraries of molecules which include an encoding oligonucleotide tag. | 03-05-2009 |
20090082225 | NUCLEIC ACID ARCHIVING - This invention is directed to a process for tightly binding nucleic acid to solid phase and corresponding processes for the utilization thereof. Nucleic acid is bound to solid phase matrices exhibiting sufficient hydrophilicity and electropositivity to tightly bind the nucleic acids from a sample. These processes include nucleic acid (double or single stranded DNA and RNA) capture from high volume and/or low concentration specimens, buffer changes, washes, and volume reductions, and enable the interface of solid phase bound nucleic acid with enzyme, hybridization or amplification strategies. The tightly bound nucleic acid may be used, for example, in repeated analyses to confirm results or test additional genes in both research and commercial applications. Further, a method is described for virus extraction, purification, and solid phase amplification from large volume plasma specimens. | 03-26-2009 |
20090082226 | Gene expression analysis using array with immobilized tags of more than 25 bp (SuperSAGE-Array) - This invention provides a method of gene expression analysis that enables extensive gene expression analysis and simultaneous analysis of multiple samples of organisms for which genomic analysis has not yet been advanced. In this method, tags each comprising an oligonucleotide of more than 25 bp for identifying expressed genes, wherein the 3′-end of the tag is defined by a cleavage site of a type III restriction enzyme and the 5′-end thereof is defined by a cleavage site of another restriction enzyme located closest to the 3′-end of the cDNA of such genes, are immobilized on a solid support, gene-containing samples are hybridized to the solid support, and the signals emitted from the genes hybridized to the tags are detected to analyze the gene expression profiles in the samples. | 03-26-2009 |
20090099040 | DEGENERATE OLIGONUCLEOTIDES AND THEIR USES - The present invention provides a plurality of oligonucleotides comprising a semi-random sequence, wherein the semi-random sequence comprises degenerate nucleotides that are substantially non-complementary. Also provided are methods for using the plurality of oligonucleotides to amplify a population of target nucleic acids. | 04-16-2009 |
20090099041 | METHODS FOR MAKING NUCLEOTIDE PROBES FOR SEQUENCING AND SYNTHESIS - Compositions and methods for making a plurality of probes for analyzing a plurality of nucleic acid samples are provided. Compositions and methods for analyzing a plurality of nucleic acid samples to obtain sequence information in each nucleic acid sample are also provided. | 04-16-2009 |
20090099042 | Reverse Two-Hybrid System for Identification of Interaction Domains - The present invention provides methods for producing allele libraries and vectors for producing these libraries. The present invention also provides methods of identifying interaction domains between proteins. The vectors, kits, and methods of the present invention suitably utilize recombinational cloning to efficiently generate and screen full-length mutant alleles of target sequences of interest. | 04-16-2009 |
20090099043 | Construction of pool of interfering nucleic acids covering entire RNA target sequence and related compositions - The present invention provides a PCR based high-throughput method for preparing full-sites siRNA polynucleotide pool, comprising: DNase I random digestion; Loop-1 phosphate linker ligation; single PCR amplification; a type III restriction/modification enzyme digestion; blunt ending; Loop-2 phosphate linker ligation; double primer PCR; FokI digestion and cloning into an siRNA expression vector. The present invention enables the use of a type III restriction/modification enzyme linkers mediated PCR method for high-throughput preparing an siRNA polynucleotide pool, in which the functional length of siRNAs can be controllably distributed from 19-23 bp, thus completely mimic the natural siRNA length diversity, specially suitable for RNAi therapeutic targets screening. The present invention overcomes the bottlenecks and drawbacks of conventional siRNA polynucleotide pool construction technologies. | 04-16-2009 |
20090105094 | Error-free amplification of DNA for clonal sequencing - Methods of preparing nucleic acid templates and providing the nucleic acid templates to low copy number reaction volumes are provided. Related compositions of nucleic acid templates are also provided. | 04-23-2009 |
20090131279 | NUCLEIC ACID FLUORESCENT STAINS - The present invention provides fluorescent dye compounds and methods of using the compounds for the staining of nucleic acids. In particular, the dye compounds comprise heterocyclic molecules with hydroxy alkyl and aromatic substituents, and the dye compounds form highly fluorescent complexes upon nucleic acid binding. | 05-21-2009 |
20090137427 | Method for generating hypermutable organisms - Dominant negative alleles of human mismatch repair genes can be used to generate hypermutable cells and organisms. By introducing these genes into cells and transgenic animals, new cell lines and animal varieties with novel and useful properties can be prepared more efficiently than by relying on the natural rate of mutation. The enhanced rate of mutation can be further augmented using mutagens. Moreover, the hypermutability of mismatch repair deficient cells can be remedied to stabilize cells or mammals with useful mutations. | 05-28-2009 |
20090149349 | RECOMBINANT ADENOVIRUSES PREPARATION AND ADENOVIRUS BANKS - The invention concerns compositions and methods for preparing recombinant adenoviruses. The resulting adenoviruses can be used for transferring and/or expressing genes in cells, in vitro, ex vivo or in vivo, or also in functional genomics. More particularly, the invention concerns in particular efficient methods for producing adenovirus banks and the use of said banks in functional genomics. The invention also concerns plasmids used for constructing said adenoviruses. | 06-11-2009 |
20090156431 | Methods for Nucleic Acid Mapping and Identification of Fine Structural Variations in Nucleic Acids - An in vitro, extracellular method of juxtaposing sequence tags (GVTs) where two constituent members of a tag pair (GVT-pair) are unique positional markers of a defined separation distance and/or are markers of nucleic acid positions that demarcate adjacent cleavage sites for one or more different restriction endonucleases along the length of a plurality of target nucleic acid molecules, the method comprising: Fragmenting the target nucleic acid molecule to form target DNA insert; ligating a DNA adaptor having one or more restriction endonuclease recognition sites to both ends of a fragmented target DNA insert and the ligation of the adaptor-ligated target DNA insert to a DNA backbone to create a circular molecule; digesting the adaptor using a restriction endonuclease at the recognition site to cleave the target DNA insert at a defined distance from each end thereof to create two sequence tags (GVTs) comprising terminal sequences of the target DNA insert that are attached to the linear DNA backbone; and recircularizing the linear DNA backbone with the attached GVTs to obtain a circular DNA molecule including a GVT pair having two juxtaposed GVTs; GVT-pair DNA is recovered by nucleic acid amplification. | 06-18-2009 |
20090170727 | METHODS FOR DYNAMIC VECTOR ASSEMBLY OF DNA CLONING VECTOR PLASMIDS - A method for using cloning vector plasmids to produce DNA molecules, such as transgenes, in a single cloning step. The transgenes can be used for the purpose of gene expression or analysis of gene expression. The plasmid cloning vectors are engineered to minimize the amount of manipulation of DNA fragment components by the end user of the vectors and the methods for their use. Transgenes produced using the invention may be used in a single organism, or in a variety of organisms including bacteria, yeast, mice, and other eukaryotes with little or no further modification. | 07-02-2009 |
20090203551 | Methods and Oligonucleotide Designs for Insertion of Multiple Adaptors Employing Selective Methylation - Aspects described and claimed herein provide methods to insert multiple DNA adaptors into a population of circular target DNAs at defined positions and orientations with respect to one another. The resulting multi-adaptor constructs are then used in massively-parallel nucleic acid sequencing techniques. | 08-13-2009 |
20090253591 | METHODS FOR IDENTIFYING NEURIPOTENT CELLS - The invention is a method for using an avian embryo to identify the neuripotency of a cell population. The invention may be used for applications such as screening for candidate neuripotent cell lines for masterbanking, validation of working cell banks, and identifying agents and conditions capable of inducing neural differentiation in a cell population. | 10-08-2009 |
20090264319 | Method for the analysis of exclusive gene expression profile using a trace amount of sample - The purpose of the present invention is to prepare a cellular gene expression profile from an extremely small number of cells so as to realize its application to pathological samples, microtissues, microanimals, etc, whose handling has been infeasible because of a limited sample amount, and further to realize a gene expression profile as to cells of peripheral blood for use in pathological diagnosis, etc. There is provided a method attaining improvement of the high coverage expression profiling analysis (HiCEP) disclosed in the pamphlet of WO 02/48352, characterized in that an amount of mRNA contained in a starting material is increased through obtaining amplified RNA complementary to double-stranded cDNA sequence by the action of RNA polymerase, and that the number of double-stranded cDNAs having X primer and Y primer added thereto is increased by the use of PCR. | 10-22-2009 |
20090264320 | Methods for transforming yeast - This invention is directed to the transformation of yeast, and mutants thereof, by electroporation, which result in stably transformed yeast host cells that express recombinant products. This invention also is directed to transformed yeast cells and libraries. | 10-22-2009 |
20090275485 | Reversible Natural Product Glycosyltransferase-Catalyzed Reactions, Compounds and Related Methods - The present invention relates to methods of use of glycosyltransferases and related novel compounds. The invention exploits the reversibility of glycosyltransferases to generate new sugars, unnatural biomolecules and numerous one-pot reactions for generation of new biomolecules having varied backbones such as enediynes, vancomycins, bleomycins, anthracyclines, macrolides, pluramycins, aureolic acids, indolocarbazoles, aminglycosides, glycopeptides, polyenes, coumarins, benzoisochromanequinones, calicheamicins, erythromycin, avermectins, ivermectins, angucyclines, cardiac glycosides, steroids or flavinoids. In preferred embodiments, the invention specifically relates to biosynthesis of anticancer (the enediyne calicheamicin, CLM), anthelmintic agents (the macrolides avermectin, ivermectin and erythromycin) and antibiotic (the glycopeptide vancomycin, VCM) natural product-based drugs developed by reversible, bidirectional glycosyltransferase-catalyzed reactions. | 11-05-2009 |
20090275486 | NUCLEIC ACID SEPARATION AND PURIFICATION METHOD BASED ON REVERSIBLE CHARGE INTERACTIONS - The invention provides a method for purifying nucleic acids using a polycationic reagent and an anionic substrate to form a complex with a nucleic acid to be purified. The complex may be separated from other components of a mixture and the nucleic acid eluted from the complex with a high ionic strength solution or an anionic reagent. | 11-05-2009 |
20090312199 | TRACE mRNA AMPLIFICATION METHOD AND USE THEREOF - In one embodiment of the present invention, a method for amplifying a trace amount of mRNA is disclosed which can amplify a short mRNA and a long mRNA at a same efficiency level, regardless of how long a base sequence is, and to provide a method for use of such a method, a method of the present invention for amplifying a trace amount of mRNA includes the steps of: (i) adding a dummy RNA to a solution containing the trace amount of mRNA, so as to prepare a mixed solution; (ii) synthesizing an anti-sense DNA by reverse transcription, which uses the mixed solution as a template; (iii) synthesizing a sense DNA which is complementary to the anti-sense DNA thus synthesized, so as to generate a double strand DNA made of the sense DNA and the anti-sense DNA; (iv) ligating an RNA polymerase promoter sequence to the double strand DNA thus generated, on a sense DNA 5′ end side of the double strand DNA, so as to prepare a double strand DNA for amplification; and (v) amplifying, by using RNA polymerase, an RNA from the double strand DNA for amplification. | 12-17-2009 |
20100009871 | DEVICES AND SYSTEMS FOR CREATION OF DNA CLUSTER ARRAYS - The present invention comprises systems and devices for isothermal amplification of polynucleotide sequences to produce DNA cluster arrays. | 01-14-2010 |
20100009872 | Single molecule loading methods and compositions - Methods, compositions and arrays for non-random loading of single analyte molecules into array structures are provided. | 01-14-2010 |
20100016178 | METHODS FOR RAPID PRODUCTION OF TARGET DOUBLE-STRANDED DNA SEQUENCES - It has been previously disclosed that DNA segments can be made in massively parallel chemical synthesis operations on a common substrate followed by release of the segments from the substrate and assembly of the segments into target DNA molecules. Here it is taught that if the DNA primary constructs are sufficiently long and properly designed, that the copy numbers of the primary constructs can be multiplied as needed by a PCR process using as a template regions at the ends of the primary constructs. The end regions, called flanking regions, can also be designed so that they may be cleaved easily from the amplification products. The target double-stranded DNA can then be assembled from the cleaved fragments. Hundreds of thousands of oligonucleotides can be synthesized and assembled into many different individual genes by this process in a relatively quick and efficient process. | 01-21-2010 |
20100029511 | CDNA SYNTHESIS USING NON-RANDOM PRIMERS - The present invention provides methods for selectively amplifying a target population of nucleic acid molecules in a population of RNA template molecules (e.g., all mRNA molecules expressed in a cell type except for the most highly expressed mRNA species). The invention also provides a method of generating a population of oligonucleotide primers for transcriptome profiling of total RNA from a subject of interest. | 02-04-2010 |
20100069263 | SEQUENCE TAG DIRECTED SUBASSEMBLY OF SHORT SEQUENCING READS INTO LONG SEQUENCING READS - The invention provides compositions and methods for preparing DNA sequencing libraries. In particular, the method relates to preparing DNA sequencing libraries from kilobase scale nucleic acids. The invention also provides methods for assembling short read sequencing data into longer contiguous sequences. The method is useful for various applications in genomics, including genome assembly, full length cDNA sequencing, metagenomics, and the analysis of repetitive sequences of assembled genomes. | 03-18-2010 |
20100069264 | Libraries of recombinant chimeric proteins - The provides methods for generating divergent libraries of recombinant chimeric proteins, comprising identifying a plurality of conserved amino acid sequences, selecting a plurality of consensus amino acid sequences as a backbone corresponding to said conserved amino acid sequences to serve as sites of recombination and as a backbone for recombinant chimeric proteins created, generating overlapping polynucleotides, inducing recombination between said polynucleotides to produce divergent libraries of chimeric polynucleotides wherein the recombinations intentionally take place between the sequences that correspond to the full length consensus amino acids. The advantage is that shuffling between variable regions, while maintaining the consensus backbone, increases the production of active proteins with high diversity, and better properties. | 03-18-2010 |
20100087336 | FUNCTIONAL NUCLEIC ACIDS AND METHODS - The present invention relates to methods of generating amounts of selective nucleic acids. The present invention further relates to selective nucleic acids incorporated within non-coding nucleic acids, capable of binding to or altering a target molecule. Selective nucleic acids may generally refer to, but are not limited to, deoxyribonucleic acids (DNAs), ribonucleic acids (RNAs), artificially modified nucleic acids, combinations or modifications thereof. Selective nucleic acids may also generally refer to, but are not limited to, nucleic acid aptamers, aptazymes, ribozymes, deoxyribozymes, nucleic acid probes, small interfering RNAs (siRNAs), micro RNAs (miRNAs), short hairpin RNAs (shRNAs), antisense nucleic acids, diagnostic probes or probe libraries, aptamer inhibitors, precursors of any of the above and/or combinations or modifications thereof. In one aspect, a method for generating amounts of selective nucleic acids includes incorporating a selective nucleic acid sequence into a carrier nucleic acid. In general, the carrier nucleic acid may be transcribed by a cell into a product nucleic acid which may carry an incorporated selective nucleic acid sequence. | 04-08-2010 |
20100105576 | Three Frame cDNA Expression Libraries for Functional Screening of Proteins - Compositions and methods are provided for generating three frame cDNA expression libraries for functional screening of proteins. The invention includes sets of 5′ adapters for cloning cDNA molecules in which the sets include three adapters that can be used to clone a particular cDNA in all three reading frames. The libraries so generated have greater complexity of expressed open reading frames, and thus can improve the success of functional protein screens, such as two hybrid screens. The adapters also have recombination sites for efficient cloning and transfer between systems. | 04-29-2010 |
20100120635 | SAMPLE DISPENSING - The present invention generally relates to systems and methods for mixing and dispensing a sample droplet from a microfluidic system, such as a liquid bridge system. In certain embodiments, the invention provides systems for mixing and dispensing sample droplets, including a sample acquisition stage, a device for mixing sample droplets to form sample droplets wrapped in an immiscible carrier fluid, a dispensing port, and at least one channel connecting the stage, the droplet mixing device, and the port, in which the system is configured to establish a siphoning effect for dispensing the droplets. | 05-13-2010 |
20100222237 | Methods for Generating Polynucleotides Having Desired Characteristics by Iterative Selection and Recombination - A method for DNA reassembly after random fragmentation, and its application to mutagenesis of nucleic acid sequences by in vitro or in vivo recombination is described. In particular, a method for the production of nucleic acid fragments or polynucleotides encoding mutant proteins is described. The present invention also relates to a method of repeated cycles of mutagenesis, shuffling and selection which allow for the directed molecular evolution in vitro or in vivo of proteins. | 09-02-2010 |
20100227779 | PLASMID RK2-BASED BROAD-HOST-RANGE CLONING VECTOR USEFUL FOR TRANSFER OF METAGENOMIC LIBRARIES TO A VARIETY OF BACTERIAL SPECIES - The present invention relates to a cloning vector for cloning of DNA in a broad host range of bacteria, the vector being an autonomously replicating artificial chromosome comprising: (i) the RK2 origin of replication oriV; (ii) the RK2 origin of conjugate transfer oriT; (iii) par DE from RK2; (iv) a cloning region; (v) a further origin of replication which permits replication of said vector at a copy number of no more than 1 or 2; wherein the vector is no more than 15 kb in size, does not contain trfA of RK2, and is capable of cloning inserts of at least 12 kb and wherein the content of RK2 DNA in the vector is no more than 10% of RK2. The invention also relates to host cells and a vector system having the cloning vector. Methods of cloning DNA and preparing a library and uses of the vector and the RK2 replicon in metagenomic cloning are provided. | 09-09-2010 |
20100261620 | Methods of Humanizing and Affinity-Maturing Antibodies - Methods of humanizing and affinity-maturing antibodies are disclosed. | 10-14-2010 |
20100273679 | METHODS FOR THE PREPARATION OF DNA MICROARRAYS WITH LINEAR HIGH DENSITY PROBES - A method for the realisation of DNA microarrays with linear high density probes, comprising a phase of replication of template DNA strands of a template microarray and a subsequent phase of stamping of the molecules obtained by replication on a substrate via the SuNS technique; the template strands ( | 10-28-2010 |
20100273680 | METHOD AND SYSTEM FOR THE ANALYSIS OF HIGH DENSITY CELLS SAMPLES - Methods for forming cell arrays of multiple cell samples arranged substantially in a monolayer on a single substrate particularly suited for diagnostic analysis are disclosed. The cell arrays are formed with a high-speed dispensing apparatus capable of dispensing small volumes in precise, complex patterns. Also disclosed are substrates upon which cell arrays may be formed, and methods for conducting diagnostic analyses on the formed cell arrays. | 10-28-2010 |
20100298170 | METHODS AND SYSTEMS FOR INTRODUCING FUNCTIONAL POLYNUCLEOTIDES INTO A TARGET POLYNUCLEOTIDE - A method and system is presented for introducing functional polynucleotides into a target polynucleotide using transposons. | 11-25-2010 |
20100305004 | POLYNUCLEOTIDE BACKBONES FOR COMPLEXING PROTEINS - We use the Tus-Ter interaction to enable the utilization of nucleic acid analytical methodologies for proteins. We also use the Tus-Ter interaction to make polymers and oligomers that have a nucleic acid backbone with protein functionalities. These methods are useful for molecular modeling, for efficiently running enzymatic pathway reactions, and for analyzing presence and/or amount of particular proteins. | 12-02-2010 |
20100305005 | High-throughput cell transfection device and methods of using thereof - Transfecting biology cells with nucleic acid molecules (DNA, siRNA) is an essential prerequisite in elucidating how genes function in complex cellular context and how their activities could be modulated for therapeutic intervention. Traditionally studies are carried out on a low throughput gene-by-gene scale, which has created a huge bottleneck in functional genomic study and drug discovery. Development of high-throughput cell transfection technology will permit functional analysis of massive number of genes and how their activities could be modulated by chemical or biological entities inside cells. This invention describes design, construction of device and apparatus for high throughput effective cell transfection. Procedures and protocols for using the device and apparatus are also described in the application. Novel methods of using the device in cell-based assays are also disclosed. | 12-02-2010 |
20100331216 | CELL CULTURE METHOD - To provide a cell culture method capable of sustaining in-vivo functions for a long time by suppressing dedifferentiation. A cell culture method in accordance with the present invention is to culture cells in a multi-layered state in a minute partitioned space and to obtain a tissue structure having a function resembling an in-vivo function. When the cells are mammary gland epithelial cells, a hollow acinus-like structure can be formed. The minute partitioned space is particularly preferably a micro container in a cell culture container having a plurality of such micro containers on the surface. | 12-30-2010 |
20110034350 | Protein Arrays and Methods of Use Thereof - The present invention provides human protein arrays that include at least 1000 human proteins. In another embodiment, the present invention provides a method for identifying a substrate of an enzyme, comprising contacting the enzyme with a positionally addressable array comprising at least 100 proteins immobilized on functionalized glass surface, and identifying a protein on the positionally addressable array that is bound and/or modified by the enzyme, wherein a binding or modifying of the protein by the enzyme indicates that the protein is a substrate for the enzyme. In additional embodiments, provided herein are methods for making an array of at least 1000 human proteins under non-denaturing conditions, including human proteins that are difficult to express and/or difficult to isolate in a non-denatured state. | 02-10-2011 |
20110059869 | Method for Increasing Enzymatic Reactivity - An object of the invention is to provide a method for increasing enzymatic reactivity to a target substance immobilized on a support; and a method for reducing or suppressing an inhibitory effect of a support on enzymatic reaction. The above object is achieved by a method for increasing enzymatic reactivity to a target substance immobilized on a support by allowing at least one substance selected from the group consisting of saccharides, amino acids, polyhydric alcohols and derivatives thereof to exist; and a method for reducing or suppressing an inhibitory effect of a support immobilized with a target substance on enzymatic reactivity to the target substance by allowing at least one substance selected from the group consisting of saccharides, amino acids, polyhydric alcohols and derivatives thereof to exist. | 03-10-2011 |
20110065610 | Synthetic Polypeptide Libraries and Methods for Generating Naturally Diversified Polypeptide Variants - The invention provides compositions and methods for generating libraries of DNA sequences encoding homologous polypeptides, and uses of the libraries to identify naturally diversified polypeptide variants. The invention also provides compositions and methods for generating collections of synthetic antibody fragments in which one or several complementary determining regions (CDR) are replaced by a collection of the corresponding CDR captured from a natural source. The invention further provides compositions and methods for diversifying a portion of a polypeptide by inserting a diversified sequence of synthetic or natural origin without the need for modification of the original polypeptide coding sequence. | 03-17-2011 |
20110092391 | PHAGE LAMBDA DISPLAY CONSTRUCTS - Bacteriophages in general and lambda phage in particular are powerful, flexible reagents who have yet to be exploited to their full potential. As discussed herein, the lambda phage head and/or genome comprises an easy to use and highly efficient delivery vehicle for delivering the expression products of a gene of interest systemically or to a particular tissue. | 04-21-2011 |
20110098200 | Methods using dsdna to mediate rna interference (rnai) - The present invention provides methods of producing dsDNA molecules that can be used to mediate RNA interference (RNAi). These methods include the production of hairpin DNAs including random sequences, and the use of convergent promoters to co-express sense and antisense RNAs. As such, the invention allows the production of random short hairpin RNA (shRNA) and a small interfering RNA (siRNA) expression libraries for forward genetic screening. | 04-28-2011 |
20110118149 | Synthetic Polypeptide Libraries and Methods for Generating Naturally Diversified Polypeptide Variants - The invention provides compositions and methods for generating libraries of DNA sequences encoding homologous polypeptides, and uses of the libraries to identify naturally diversified polypeptide variants. The invention also provides compositions and methods for generating collections of synthetic antibody fragments in which one or several complementary determining regions (CDR) are replaced by a collection of the corresponding CDR captured from a natural source. The invention further provides compositions and methods for diversifying a portion of a polypeptide by inserting a diversified sequence of synthetic or natural origin without the need for modification of the original polypeptide coding sequence. | 05-19-2011 |
20110136697 | METHODS FOR SYNTHESIS OF ENCODED LIBRARIES - The present invention provides a method of synthesizing libraries of molecules which include an encoding oligonucleotide tag. | 06-09-2011 |
20110143964 | FLUIDIC DEVICES AND METHODS FOR MULTIPLEX CHEMICAL AND BIOCHEMICAL REACTIONS - The present invention describes microfluidic devices that provide novel fluidic structures to facilitate the separation of fluids into isolated, pico-liter sized compartments for performing multiplexing chemical and biological reactions. Applications of the novel devices including biomolecule synthesis, polynucleotide amplification, and binding assays are also disclosed. | 06-16-2011 |
20110172127 | Methods and Devices for High Fidelity Polynucleotide Synthesis - Disclosed are methods for synthesizing and/or assembling at least one polynucleotide product having a predefined sequence from a plurality of different oligonucleotides. In exemplary embodiments, the methods involve synthesis and/or amplification of different oligonucleotides immobilized on a solid support, release of synthesized/amplified oligonucleotides in solution to form droplets, recognition and removal of error-containing oligonucleotides, moving or combining two droplets to allow hybridization and/or ligation between two different oligonucleotides, and further chain extension reaction following hybridization and/or ligation to hierarchically generate desired length of polynucleotide products. | 07-14-2011 |
20110201526 | BEAD EMULSION NUCLEIC ACID AMPLIFICATION - Disclosed are methods for nucleic acid amplification wherein nucleic acid templates, beads, and amplification reaction solution are emulsified and the nucleic acid templates are amplified to provide clonal copies of the nucleic acid templates attached to the beads. Also disclosed are kits and apparatuses for performing the methods of the invention. | 08-18-2011 |
20110207631 | METHOD FOR PRODUCTION OF cDNA LIBRARY HAVING REDUCED CONTENT OF cDNA CLONE DERIVED FROM HIGHLY EXPRESSED GENE - A method for efficiently constructing a cDNA library having a reduced content of cDNA clones derived from a highly expressed gene is provided. According to the method for constructing a cDNA library using a double-stranded DNA primer having oligo dT and mRNA as a template, the proportion of cDNA clones derived from a highly expressed gene in a cDNA library was decreased through coexistence with a probe having a property of binding to the mRNA of the highly expressed target gene so as to inhibit a cDNA extension reaction resulting from reverse transcriptase. | 08-25-2011 |
20110224104 | METHOD AND SYSTEM FOR INDENTIFICATION OF MICROORGANISMS - A method and system for identification of microorganisms in a sample. The method includes processing the sample to produce at least one group of biomarker molecules from at least one microorganism in the sample, tandem mass-analyzing biomarker fragment ions from the at least one group of biomarker molecules to obtain a sample biomarker tandem mass spectrum of the biomarker, and identifying the microorganism in the sample based on a comparison of the sample biomarker tandem mass spectrum to an experimentally-derived reference tandem mass spectrum (stored in the reference library) from a known microorganism. The system includes a sample processing unit configured to process the sample and produce at least one group of biomarker molecules from at least one microorganism in the sample. The system includes a mass-analyzer for tandem mass analysis biomarker fragment ions. The system includes a processor configured to identify the microorganism in the sample based on a comparison of a sample biomarker tandem mass spectrum to an experimentally-derived reference tandem mass spectrum from a known microorganism. | 09-15-2011 |
20110224105 | METHODS, COMPOSITIONS, AND KITS FOR GENERATING NUCLEIC ACID PRODUCTS SUBSTANTIALLY FREE OF TEMPLATE NUCLEIC ACID - Methods, kits, and compositions are provided herein for the generation of double stranded DNA products suitable for downstream analysis. | 09-15-2011 |
20110224106 | Production Of Single-Stranded Circular Nucleic Acid - A method is provided for generating single stranded circular nucleic acid from a sample of target nucleic acid. A complex comprising a transposase and a plurality of hairpin polynucleotides is formed with each of the hairpin polynucleotides having a duplex region comprising a transposase recognition sequence. The complex is mixed with the target nucleic acid, thereby fragmenting the target nucleic acid and ligating the hairpin polynucleotides to the target nucleic acid to form hairpin-linked nucleic acid fragments, each having a nucleobase segment gap between each fragment and its corresponding hairpin polynucleotide. The hairpin-linked fragments are contacted with a ligase, thereby ligating the hairpin-linked fragments together to form single-stranded circular nucleic acid comprising a pair of opposing loops and an intervening duplex region comprising a pair of nucleobase segment gaps. The single-single stranded circular nucleic acid is then contacted with a polymerase and nucleotide triphosphates, thereby filling the nucleobase segment gaps. | 09-15-2011 |
20110230374 | HIGH AFFINITY RECOMBINANT SEA LAMPREY ANTIBODIES SELECTED BY A YEAST SURFACE DISPLAY PLATFORM - The present invention relates to a Yeast Surface Display (YSD) vector for expression of VLR proteins by yeast, wherein the vector includes nucleotide sequences encoding segments of yeast flocculation proteins FloIp, such as the leader and C-terminal segments, a homologous recombinant cassette and a geneticin/kanamycin resistance gene. The vector can be used for expression of VLR that may be effective in diagnostic applications (e.g., protein chip, immunohistochemistry, flow cytometry), immunoaffinity purification, and for engineering novel fusion proteins. | 09-22-2011 |
20110257045 | METHOD FOR PREPARING HIGH-THROUGHPUT SEQUENCEABLE DNA FROM INDIVIDUAL PLAQUES OF PHAGES PRESENTING PEPTIDES - The present invention relates to a process for isolating DNA from individual plaques of peptide-presenting bacteriophages in a high-throughput capacity PCR, wherein the PCR products obtained are sequenceable and a specimen of each phage studied is retained in a replicable state. The PCR is successful despite the presence of inhibitory constituents from the growth medium or the host bacteria. | 10-20-2011 |
20110263462 | METHODS AND KITS USED IN THE DETECTION OF FUNGUS - The invention encompasses methods of using quantitative PCR to detect fungal organisms in clinical and environmental samples and to generate standards that allow the quantification of fungal organisms in the samples. | 10-27-2011 |
20110269647 | METHOD - There is described a method for identifying an interaction between an RNA and an RNA binding protein in a biological sample, comprising the steps of: a) contacting the biological sample with an agent that creates a covalent bond between the RNA and the RNA binding protein; b) fragmenting said RNA; c) ligating a first adapter to the fragmented RNA; d) hybridising a reverse transcription primer to said first adapter and reverse transcribing said cross-linked RNA; e) circularising the transcribed cDNA; f) linearising the circularised cDNA; and g) determining the sequence of one or more of the cDNAs. | 11-03-2011 |
20110275543 | DEVICE FOR STUDYING INDIVIDUAL CELLS - A device for studying individual cells including a picowell array (such as an array of microwells, dimples, depressions, tubes or enclosures) and a fluid reservoir in fluid communication with the picowells through channels is disclosed. Preferably, the device has a moveable lid that in one rest location allows loading of cells in the picowell array. Preferably the channels of the device are capillary channels. | 11-10-2011 |
20110312614 | METHODS FOR RAPID MULTIPLEXED AMPLIFICATION OF TARGET NUCLEIC ACIDS - A fast, multiplexed PCR system is described that can rapidly generate amplified nucleic acid products, for example, a full STR profile, from a target nucleic acid. Such systems include, for example, microfluidic biochips and a custom built thermal cycler, which are also described. The resulting STR profiles can satisfy forensic guidelines for signal strength, inter-loci peak height balance, heterozygous peak height ratio, incomplete non-template nucleotide addition, and stutter. | 12-22-2011 |
20110319298 | Differential detection of single nucleotide polymorphisms - This patent application claims processes and compositions of matter that enable the discovery of single nucleotide polymorphisms (SNPs) that distinguish the genomes of two individual organisms in the same species, as well as that distinguish the paternal and maternal genetic inheritance of a single individual, as well as distinguish the genomes of cells in special tissues (e.g. cancer tissues) within an individual from the genomes of the standard cells in the same individuals, as well as the SNPs that are discovered using these processes and compositions. Two steps are essential to the invention disclosed in this application. The first step provides four sets of primers, which are designated “T-extendable”, “A-extendable”, “C-extendable”, and “G-extendable”. These primers, when targeted against a reference genome as a template, add (respectively) T, A, C, and G to their 3′-ends in a template-directed primer extension reaction. The second step presents these four primer sets, separately, to a sample of the target genome DNA under conditions where they bind to their complementary segments within the target DNA. Once bound, members of each primer set serve as primers for a template-directed primer extension reaction using the target genome as the template. If the template from the target genome presents the same templating nucleotide for the first nucleotide added in the extension reaction as the reference genome, then the T-extendable, A-extendable, C-extendable, and G-extendable primers will be extended (respectively) by T, A, C, and G. If, however, the template from the target genome presents a nucleotide different from the reference genome, then the T-extendable, A-extendable, C-extendable, and G-extendable primers will be extended (respectively) by not T, not A, not C, and not G (referred to here as “3N” or “3”, to indicate the other three nucleotides, where which of the other three is understood by context). In these cases, the primers have discovered a SNP, a difference between the target and reference genomes. Then, the T-extendable, A-extendable, C-extendable, and G-extendable primers that add (respectively) not-T, not-A, not-C, and not-G are separated or made otherwise physically distinct (through, for example, the use of irreversible terminators, such as 2′,3′-dideoxynucleosides) from those that added T, A, C, and G (respectively). Those that added T, A, C, and G (respectively) did not discover a SNP, and are discarded. The primers that added “not-T”, “not-A”, “not-C”, and “not-G” discovered a SNP, and presented in a mixture enriched (relative to those primers that did not discover a SNP) in a useful deliverable. Following these steps, the SNPs discoveries are realized by sequencing the extracted species. The information obtained from this sequencing allows the identification of the locus of the SNP in the in silico genome. | 12-29-2011 |
20110319299 | METHODS AND COMPOSITIONS FOR POLYNUCLEOTIDE LIBRARY PRODUCTION, IMMORTALIZATION AND REGION OF INTEREST EXTRACTION - Aspects of the present invention are drawn to methods and compositions for the genetic analysis of regions of interest (ROI) from one or more starting polynucleotide sample(s). In certain aspects, adapter tagged polynucleotide fragments from a plurality of initial polynucleotide samples are pooled, circularized and amplified to produce an immortalized library. Multiple ROI's from this immortalized library are amplified (e.g., in independent iPCR reactions) to generate amplicons, and, in some embodiments, pooled to form a pooled ROI amplicon sample. In certain embodiments, the amplicons for each ROI amplicon in the pooled ROI amplicon sample are present at known molar or mass ratios. The pooled ROI amplicon sample can be analyzed/processed as desired, e.g., sequenced using next generation sequencing technology. | 12-29-2011 |
20120004142 | METHOD FOR CONSTRUCTING MUTAGENESIS LIBRARIES IN SITU - Method and kit for constructing a random mutagenesis library. The method comprises providing a first expression vector comprising a target polynucleotide fragment, providing a pair of Vector-primers that are complementary to the vector portion of the first expression vector, wherein the Vector-primers comprise a second selection marker gene, and wherein the Vector-primers allow PCR amplification of the target polynucleotide; and performing a PCR reaction using the first expression vector as the template with the Vector-primers under error-prone PCR conditions in the presence of a thermostable DNA ligase, generating a second expression vector which comprises the second selection marker gene and a mutated target polynucleotide. | 01-05-2012 |
20120028843 | Methods and Apparatuses for Chip-Based DNA Error Reduction - Methods and apparatus relate to reduction of sequence errors generated during synthesis of nucleic acids on a microarray chip. The error reduction can include synthesis of complementary stands (to template strands), using a short universal primer complementary to the template strands and polymerase. Heteroduplex can be formed be melting and re-annealing complementary stands and template strands. The heteroduplexes containing a mismatch can be recognized and cleaved by a mismatch endonuclease. The mismatch-containing cleaved heteroduplexes can be removed from the microarray chip using a global buffer exchange. The error free synthetic nucleic acids generated therefrom can be used for a variety of applications, including synthesis of biofuels and value-added pharmaceutical products. | 02-02-2012 |
20120040869 | SEQUENCE PRESERVED DNA CONVERSION - Described herein are inexpensive high throughput methods to convert a target single stranded DNA (ssDNA) such that each nucleotide (or base) adenine (A), thymine (T), guanine (G) and cytosine (C) is converted to a pre-determined oligonucleotide code, with the sequential order preserved in the converted ssDNA, or RNA. The method does not require the use of DNA polymerases during the cycles and involves the use of an oligonucleotide probe library with repeated cycles of ligation and cleavage. At each cycle, one or more nucleotides on one end (e.g., either the 5′ end or the 3′ end) of a target, e.g., ssDNA, are cleaved and then ligated with the corresponding oligonucleotide code at the other end of the target ssDNA. | 02-16-2012 |
20120040870 | Method For Assembly Of Polynucleic Acid Sequences - The present invention provides a method for the assembly of a polynucleic acid sequence from a plurality of nucleic acid sequences in which the polynucleic acid sequence is of a formula N | 02-16-2012 |
20120040871 | OLIGONUCLEOTIDE MEDIATED NUCLEIC ACID RECOMBINATION - Methods of recombining nucleic acids, including homologous nucleic acids, are provided. Families of gene shuffling oligonucleotides and their use in recombination procedures, as well as polymerase and ligase mediated recombination methods are also provided. | 02-16-2012 |
20120071358 | Fluidic devices and methods for multiplex chemical and biochemical reactions - The present invention describes microfluidic devices that provide novel fluidic structures to facilitate the separation of fluids into isolated, pico-liter sized compartments for performing multiplexing chemical and biological reactions. Applications of the novel devices including biomolecule synthesis, polynucleotide amplification, and binding assays are also disclosed. | 03-22-2012 |
20120071359 | PURIFIED EXTENDED POLYMERASE/TEMPLATE COMPLEX FOR SEQUENCING - Methods, Compositions, and Systems are provided for obtaining polymerase-template complex mixtures with improved levels of active polymerase. In some aspects, methods are described in which a polymerase-template complex is exposed to reaction conditions in which a complementary strand to the template is produced. The extended reaction mixture is purified, for example by gel filtration chromatography to produce a mixture of polymerase-template complex having a higher active fraction. This purified mixture can be used for further analyses including single molecule sequencing. | 03-22-2012 |
20120071360 | ALKALINE SHOCK-BASED METHOD OF PROCESSING A BIOLOGICAL SAMPLE - Method of processing a biological sample to yield nucleic acid appropriate for use in a subsequent in vitro nucleic acid amplification reaction. The method involves a rapid, transient exposure to alkaline conditions which can be achieved by mixing an alkaline solution with a pH-buffered solution that includes a detergent and the biological sample to be tested for the presence of particular nucleic acid species using in vitro amplification. The invented method advantageously can improve detection of some target nucleic acids without substantially compromising detectability of others. The method is particularly useful for simultaneously preparing RNA and DNA templates that can be used in multiplex amplification reactions. | 03-22-2012 |
20120077716 | SYSTEM AND METHOD FOR PRODUCING FUNCTIONALLY DISTINCT NUCLEIC ACID LIBRARY ENDS THROUGH USE OF DEOXYINOSINE - An embodiment of a nucleic acid adaptor is described that comprises a double stranded nucleic acid element that comprises a plurality of deoxyinosine species positionally located in a spaced relationship from each other on a first strand and base pair to an A, T, or G nucleotide species on a second strand, where a first end of the double stranded nucleic acid element is constructed and arranged to preferentially ligate to each end of a double stranded target nucleic acid molecule. | 03-29-2012 |
20120088695 | Method and Device for Protein Delivery into Cells - Methods for performing surface-mediated protein delivery into living cells, and fabricating protein-transfected cell cluster arrays are provided. The method comprises providing a protein-containing mixture; depositing said protein-containing mixture onto a surface at defined locations; affixing the protein-containing mixture to the surface as microspots; and plating cells onto the surface in sufficient density and under conditions for the proteins to be delivered into the cells. The protein-containing mixture comprises any suitable amino acid sequence, including peptides, proteins, protein-domains, antibodies, or protein-nucleic acid conjugates, etc., with a carrier reagent. Protein-transfected cell arrays may be used for rapid and direct, screening of protein or enzymatic functions or any given intracellular protein interaction in the natural environment of a living cell, as well as for high-throughput screening of other biological and chemical analytes, which affect the functions of these proteins. | 04-12-2012 |
20120094875 | PRODUCTION PROCESS OF HIGH AFFINITY AND HIGH SPECIFICITY OLIGONUCLEOTIDES FOR ORGANIC AND INORGANIC MOLECULES - The object of this patent advances the State of the Art by the following innovations: | 04-19-2012 |
20120122737 | METHODS FOR SELECTING AND AMPLIFYING POLYNUCLEOTIDES - The invention provides methods for controlling the density of different molecular species on the surface of a solid support. A first mixture of different molecular species is attached to a solid support under conditions to attach each species at a desired density, thereby producing a derivatized support having attached capture molecules. The derivatized support is treated with a second mixture of different molecular species, wherein different molecular species in the second mixture bind specifically to the different capture molecules attached to the solid support. One or more of the capture molecules can be reversibly modified such that the capture molecules have a different activity before and after the second mixture of molecular species are attached. In particular embodiments, the different molecular species are nucleic acids that are reversibly modified to have different activity in an amplification reaction. | 05-17-2012 |
20120129731 | Design and construction of diverse synthetic peptide and polypeptide libraries - The present invention concerns the design and construction of diverse peptide and polypeptide libraries. In particular, the invention concerns methods of analytical database design for creating datasets using multiple relevant parameters as filters, and methods for generating sequence diversity by directed multisyntheses oligonucleotide synthesis. The present methods enable the reduction of large complex annotated databases to simpler datasets of related sequences, based upon relevant single or multiple key parameters that can be individually directly defined. The methods further enable the creation of diverse libraries based on this approach, using multisynthetic collections of discrete and degenerate oligonucleotides to capture the diverse collection of sequences, or portions thereof. | 05-24-2012 |
20120149602 | METHOD FOR MAKING POPULATIONS OF DEFINED NUCLEIC ACID MOLECULES - The present invention provides methods of making a population of nucleic acid molecules, wherein each nucleic acid molecule comprises a predetermined nucleic acid sequence, each of said methods comprising the steps of: (a) synthesizing, on a substrate, a population of nucleic acid molecules wherein: i) each synthesized nucleic acid molecule comprises a predetermined nucleic acid sequence; and ii) each synthesized nucleic acid molecule is localized to a defined area of said substrate; (b) harvesting said population of synthesized nucleic acid molecules from said substrate to yield harvested nucleic acid molecules; and (c) introducing said harvested nucleic acid molecules into vector molecules. | 06-14-2012 |
20120172258 | NUCLEIC ACID SAMPLE PREPARATION METHODS AND COMPOSITIONS - The present invention provides compositions and methods for preparing a nucleic acid library in a multi-purpose buffer (e.g., employing whole genome amplification), where nucleic acid purification is not required between or during steps. In certain embodiments, small amounts of starting nucleic acid (e.g., genomic DNA) are employed and the steps are accomplished in a single container. In some embodiments, the nucleic acid library is subjected to sequencing methodologies or rolling circle amplification. | 07-05-2012 |
20120172259 | USING POPULATIONS OF BEADS FOR THE FABRICATION OF ARRAYS ON SURFACES - The present invention provides a method of creating an array of features. The method can include steps of (a) providing a plurality of beads, wherein each bead in the plurality of beads includes probe content; (b) contacting the plurality of beads with a surface to produce a layer of beads on the surface; and (c) transferring the probe content from the beads to the surface to create an array of spatially discrete features on the surface, wherein each spatially discrete feature includes probe content from a bead in the plurality of beads. | 07-05-2012 |
20120184466 | PARTHENOGENIC ACTIVATION OF HUMAN OOCYTES FOR THE PRODUCTION OF HUMAN EMBRYONIC STEM CELLS - Methods of producing human stem cells are disclosed for parthenogenetically activating human oocytes by manipulation of O | 07-19-2012 |
20120190587 | Global Amplification Using A Randomly Primed Composite Primer - The invention relates to the field of polynucleotide amplification. More particularly, the invention provides methods, compositions and kits for amplification of (i.e., making multiple copies of) a multiplicity of different polynucleotide template sequences using a randomly primed RNA/DNA composite primer. | 07-26-2012 |
20120208724 | LINKING SEQUENCE READS USING PAIRED CODE TAGS - Artificial transposon sequences having code tags and target nucleic acids containing such sequences. Methods for making artificial transposons and for using their properties to analyze target nucleic acids. | 08-16-2012 |
20120252701 | METHODS FOR GENERATING POLYNUCLEOTIDES HAVING DESIRED CHARACTERISTICS BY ITERATIVE SELECTION AND RECOMBINATION - A method for DNA reassembly after random fragmentation, and its application to mutagenesis of nucleic acid sequences by in vitro or in vivo recombination is described. In particular, a method for the production of nucleic acid fragments or polynucleotides encoding mutant proteins is described. The present invention also relates to a method of repeated cycles of mutagenesis, shuffling and selection which allow for the directed molecular evolution in vitro or in vivo of proteins. | 10-04-2012 |
20120252702 | PROCESSING OF AMPLIFIED DNA FRAGMENTS FOR SEQUENCING - A processing method to trim ends of DNA fragments, exposing the internal DNA part to give original DNA sequence information enabling application of next generation sequencing for DNA samples to be amplified by DOP-PCR or other primer dependent amplification methods. Specifically, nucleic acids are amplified using primers comprising a recognition site for a restriction enzyme, for example Bpml or Mmel. Primer sequences are removed by cleavage with the restriction enzyme. | 10-04-2012 |
20120264653 | Methods for High Fidelity Production of Long Nucleic Acid Molecules - In a method for synthesizing a pool of nucleic acid molecules, a first nucleic acid has a first 5′ region and a first 3′ region and a second nucleic acid has a second 5′ region and a second 3′ region. The second 3′ region and the first 5′ region have identical nucleic acid sequences. The first 3′ region is hybridized with an oligonucleotide, extending the hybridized oligonucleotide and producing a first extension product having a 3′ region complementary to the first 5′ region. The second nucleic acid is hybridized with the first extension product to hybridize the 3′ region of the first extension product to the second 3′ region, extending the 3′ region of the first extension product and producing a second extension product having a 3′ region complementary to the second 5′ region. Error-containing molecules are separated from error-free molecules by a component that selects for a sequence error. | 10-18-2012 |
20120270754 | Iterative Nucleic Acid Assembly Using Activation of Vector-Encoded Traits - Certain aspects of the present invention provide methods for assembling nucleic acid molecules using iterative activation of one or more vector-encoded traits to progressively assemble a longer nucleic acid insert. Aspects of the invention also provide kits, compositions, devices, and systems for assembling synthetic nucleic acids using iterative activation of one or more vector-encoded traits. | 10-25-2012 |
20120270755 | METHOD FOR PREPARING A SUBSTRATE FOR ARRANGING ANIMAL CELLS IN AN ARRAY AND METHOD FOR PREPARING A SUBSTRATE ON WHICH ANIMAL CELLS ARE ARRANGED IN AN ARRAY - A new means of separately arranging individual animal cells on a substrate surface is provided. A method for preparing a substrate for arranging animal cells in an array, comprising steps (1) to (3): (1) preparing a substrate having adsorption surfaces in an array on an electrode substrate surface; (2) causing an extracellular matrix to adsorb to the electrode surface and the adsorption surfaces of the substrate; and (3) applying a weak potential to the electrode to cause the extracellular matrix on the electrode surface to separate to obtain a substrate with the extracellular matrix adhered to the adsorption surfaces thereof. A method for preparing a substrate on which animal cells have been arranged in an array, comprising steps (1) to (4): (1) preparing a substrate having adsorption surfaces in an array on an electrode substrate surface; (2) causing an extracellular matrix to adsorb to the electrode surface and the adsorption surfaces of the substrate; (3) applying a weak potential to the electrode to cause the extracellular matrix on the electrode surface to separate to obtain a substrate with extracellular matrix adhered to the adsorption surfaces thereof; and (4) culturing the animal cells on the surface of the substrate obtained in (3) to obtain a substrate on which the animal cells have adhered to the adsorption surface. | 10-25-2012 |
20120283144 | Ligation Enhancement - Compositions and methods are provided for enhancing enzymatic ligation between nucleic acid fragments that relies on one or more small molecule enhancers having a size of less than 1000 daltons. For example, enhancement of ligation efficiencies are observed for double-stranded nucleic acid fragments that are blunt-ended, have a single nucleotide overhang at the ligation end, or have staggered ends compared to ligation under similar conditions in the absence of the one or more small molecule ligation enhancer. The use of small molecule enhancers for ligating nucleic acids results in an increased number of transformed host cells after transformation with the ligated molecules. This enhancement can be observed with chemically transformed host cells and with host cells transformed by electroporation. | 11-08-2012 |
20120283145 | Methods of Making Di-Tagged DNA Libraries from DNA or RNA Using Double-tagged Oligonucleotides - Disclosed are methods, compositions and kits related to making double-tagged DNA libraries from RNA/DNA samples. A double-tagged oligonucleotide (DTO) is employed to efficiently add two different tags to ends of DNAs to make a double-tagged DNA libraries. Also disclosed are methods to make mate pair libraries using the double-tagged oligonucleotide, and methods to make double-tagged single stranded DNA. The double-tagged DNA libraries of the invention are ready to be used on next generation sequencing machines. | 11-08-2012 |
20120295819 | METHODS AND COMPOSITIONS FOR MULTIPLEX PCR - The present invention provides methods, compositions, kits, systems and apparatus that are useful for multiplex PCR of one or more nucleic acids present in a sample. In particular, various target-specific primers are provided that allow for the selective amplification of one or more target sequences. In one aspect, the invention relates to target-specific primers useful for the selective amplification of one or more target sequences associated with cancer or inherited disease. In some aspects, amplified target sequences obtained using the disclosed methods, kits, systems and apparatuses can be used in various downstream processes including nucleic acid sequencing and used to detect the presence of genetic variants. | 11-22-2012 |
20120302467 | Patterned substrates for cell applications - The present invention relates to a method for making arrays or patterns comprising hydrophilic areas and hydrophobic background surrounding the hydrophilic areas, methods of cultivating cells using these arrays or patterns, and uses of these arrays or patterns in cell cultivation methods, e.g. for cell patterning, cell screenings, cell transfection and cell co-culturing. | 11-29-2012 |
20120316086 | PATTERNED FLOW-CELLS USEFUL FOR NUCLEIC ACID ANALYSIS - Provided is a surface having metal regions and an interstitial region having a composition that differs from the metal regions, wherein a continuous gel layer coats the surface across the metal regions and the interstitial regions. Nucleic acids or other analytes can be attached to the continuous gel layer such that a greater amount is attached over the metal regions than over the interstitial region. Also provided are methods for making such surfaces. Methods are also provided for making an array of nucleic acids or other analytes using such surfaces. | 12-13-2012 |
20120322692 | LOADING MOLECULES ONTO SUBSTRATES - Disclosed are compositions, devices, and methods for loading molecules of interest onto a substrate by contacting beads having molecules of interest attached to them with the substrate, for example by providing a field that brings the beads into proximity or contact with the substrate and moves the beads with respect to the substrate. Such molecules of interest can be deposited onto substrates for single-molecule analysis. | 12-20-2012 |
20120329679 | EUKARYOTIC CELL DISPLAY SYSTEMS - The present invention provides expression vectors and helper display vectors which can be used in various combinations as vector sets for display of polypeptides on the outer surface of eukaryotic host cells. The expression vector of the invention can be used alone for soluble expression without having to change or reengineer the display vectors. The display systems of the invention are particularly useful for displaying a genetically diverse repertoire or library of polypeptides on the surface of yeast cells, and mammalian cells. | 12-27-2012 |
20130005612 | Methods for High Fidelity Production of Long Nucleic Acid Molecules with Error Control - A method for synthesizing a nucleic acid having a desired sequence and length comprises providing a solid support having an immobilized nucleic acid, performing a nucleic acid addition reaction to elongate the immobilized nucleic acid by adding a nucleotide or an oligonucleotide attached to a protecting group to the nucleic acid, determining whether the nucleotide or the oligonucleotide is added to the nucleic acid, removing the protecting group, and continuing until the immobilized nucleic acid has a desired sequence and length. | 01-03-2013 |
20130005613 | METHODS AND COMPOSITIONS FOR MULTIPLEX PCR - The present invention provides methods, compositions, kits, systems and apparatus that are useful for multiplex PCR of one or more nucleic acids present in a sample. In particular, various target-specific primers are provided that allow for the selective amplification of one or more target sequences. In one aspect, the invention relates to target-specific primers useful for the selective amplification of one or more target sequences associated with cancer or inherited disease. In some aspects, amplified target sequences obtained using the disclosed methods, kits, systems and apparatuses can be used in various downstream processes including nucleic acid sequencing and used to detect the presence of genetic variants. | 01-03-2013 |
20130017978 | METHODS AND TRANSPOSON NUCLEIC ACIDS FOR GENERATING A DNA LIBRARY - A method for the generation of DNA fragmentation library based on a transposition reaction in the presence of a transposon end with an engineered cleaveage site providing facilitated downstream handling of the produced DNA fragments, e.g., in the generation of sequencing templates. Transposon nucleic acids comprising a transposon end sequence and an engineered cleaveage site located in the sequence, e.g., in Mu transposon end sequence, are disclosed. | 01-17-2013 |
20130029880 | METHODS OF SYNTHESIZING HETEROMULTIMERIC POLYPEPTIDES IN YEAST USING A HAPLOID MATING STRATEGY - Methods are provided for the synthesis and secretion of recombinant hetero-multimeric proteins in mating competent yeast. A first expression vector is transformed into a first haploid cell; and a second expression vector is transformed into a second haploid cell. The transformed haploid cells, each individually synthesizing a non-identical polypeptide, are identified and then genetically crossed or fused. The resulting diploid strains are utilized to produce and secrete fully assembled and biologically functional hetero-multimeric protein. | 01-31-2013 |
20130029881 | SELECTIVE TERMINAL TAGGING OF NUCLEIC ACIDS - Methods are provided for adding a terminal sequence tag to nucleic acid molecules for use in RNA or DNA amplification. The tag introduced may be used as a primer binding site for subsequent amplification of the DNA molecule and/or sequencing of the DNA molecule and therefore provides means for identification and cloning of the 5′-end or the complete sequence of mRNAs. | 01-31-2013 |
20130029882 | Nucleic Acids and Libraries - The invention relates to a nucleic acid comprising the following contiguous elements arranged in the 5 prime to 3 prime direction; a promoter; a selectable marker; a cloning site for receipt of a nucleic acid segment, said segment comprising a candidate miRNA target sequence; and a poly adenylation signal, said elements arranged such that a transcript directed by said promoter comprises said selectable marker, said candidate miRNA target sequence, and said poly adenylation signal in that order. Suitably the miRNA test sequence is or is derived from a 3′UTR. The invention also relates to methods for making and screening libraries. | 01-31-2013 |
20130040863 | SOLID-PHASE CLONAL AMPLIFICATION AND RELATED METHODS - The present invention provides methods and compositions for analyzing nucleic acid sequences. In some aspects, the methods utilize clonal objects, such as DNA balls, that have been captured on beads. Using the methods described here, compositions are fabricated wherein a bead and one clonal object are affinity bound or hybridized to each other through an affinity binding patch or hybridization patch on the surface of the bead. The invention also provides a population of beads having affinity bound or hybridized clonal objects at a ratio of 1:1. The invention additionally provides methods for amplifying a target nucleic acid molecule utilizing the compositions described herein. | 02-14-2013 |
20130059761 | Assembly of High Fidelity Polynucleotides - Methods and apparatus relate to the synthesis of high fidelity polynucleotides and to the reduction of sequence errors generated during synthesis of nucleic acids on a solid support. Specifically, design of support-bound template oligonucleotides is disclosed. Assembly methods include cycles of annealing, stringent wash and extension of polynucleotides comprising a sequence region complementary to immobilized template oligonucleotides. The error free synthetic nucleic acids generated therefrom can be used for a variety of applications, including synthesis of biofuels and value-added pharmaceutical products. | 03-07-2013 |
20130059762 | METHODS AND COMPOSITIONS FOR MULTIPLEX PCR - The present invention provides methods, compositions, kits, systems and apparatus that are useful for multiplex PCR of one or more nucleic acids present in a sample. In particular, various target-specific primers are provided that allow for the selective amplification of one or more target sequences. In one aspect, the invention relates to target-specific primers useful for the selective amplification of one or more target sequences associated with cancer or inherited disease. In some aspects, amplified target sequences obtained using the disclosed methods, kits, systems and apparatuses can be used in various downstream processes including nucleic acid sequencing and used to detect the presence of genetic variants. | 03-07-2013 |
20130065795 | ARRAY OF MICROMOLDED STRUCTURES FOR SORTING ADHERENT CELLS - An apparatus for collecting or culturing cells or cell colonies includes: a common substrate formed from a flexible resilient polymeric material and having a plurality of wells formed therein; and a plurality of rigid cell carriers releasably connected to said common substrate, with said carriers arranged in the form of an array, and with each of the carriers resiliently received in one of the wells. A method of collecting or culturing cells or cell colonies with such an apparatus is carried out by depositing a liquid media carrying cells on the apparatus so that said cells settle on or adhere to said the carriers; and then (c) releasing at least one selected carrier having said cells thereon by gradual application of release energy to each carrier from the cavity in which it is received (e.g., by pushing with a probe). | 03-14-2013 |
20130079251 | Systems and Methods for Processing Fluids - Systems and methods for processing fluid samples are disclosed. Fluid sample processing is accomplished using a series of microfluidic bump arrays include an automated and integrated system for sorting particles from a biological sample, lysing those particles to expose total RNA or DNA, purifying the RNA or DNA, processing the RNA or DNA by chemical or enzymatic modification, to select RNA or DNA molecules by size, or to generate, optionally, a sequencing library. The sequencing library is suitable for use in next generation sequencing (“NGS”). | 03-28-2013 |
20130090267 | TEMPERATURE CONTROL DEVICE WITH A FLEXIBLE TEMPERATURE CONTROL SURFACE - A device for controlling temperature in a reaction chamber is disclosed. The device comprises: a bladder assembly comprising a housing dimensioned to hold a reaction chamber disposed within an interior volume of the housing; and a first temperature-control bladder disposed within the housing, the first temperature-control bladder is configured to receive a temperature-control fluid and comprises a flexible, heat conductive surface that comes in contact with at least a portion of an exterior surface of the reaction chamber after receiving the temperature-control fluid. Also disclosed are a bladder thermal cycler, a temperature-control bladder assembly and methods for producing a thermal cycle in a reaction chamber. | 04-11-2013 |
20130096033 | METHODS FOR MANUFACTURING MOLECULAR ARRAYS - The methods of the present invention provide methods for manufacturing a master substrate and methods for manufacturing replica arrays from the master substrate. The methods may be used, for example, directly to manufacture or “print” peptide arrays from a DNA array; however, the methods are applicable to a wide range of manufacturing applications for use any time multiple copies of an array needs to be printed. | 04-18-2013 |
20130096034 | MICROFABRICATION METHODS FOR THE OPTIMAL PATTERNING OF SUBSTRATES - A method of fabricating a microarray including the steps of: (a) contacting a substrate having wells with a reagent reactive with said substrate to produce a surface modification within said wells and a surface modification surrounding said wells; (b) polishing said substrate to produce a polished surface modification surrounding said wells, wherein said surface modification surrounding said wells is removed and said surface modification within said wells is retained, and (c) depositing a biopolymer onto said substrate, wherein different affinities of said surface modification within said wells and said polished surface facilitate localization of said biopolymer within said wells. | 04-18-2013 |
20130109596 | HIGH EFFICIENCY, SMALL VOLUME NUCLEIC ACID SYNTHESIS | 05-02-2013 |
20130130940 | MULTI-TARGETED PRIMING FOR GENOME-WIDE GENE EXPRESSION ASSAYS - The present invention is a method of generating a library of expressed cDNA sequences using multi-targeted primers that are complementary to degenerate motifs present in a large proportion of corresponding mRNA sequences. Multi-targeting priming (MTP) for genome-wide gene expression assays provides selective targeting of multiple sequences and counter-selection against undesirable sequences. Priming with MTPs in addition to oligo-dT can result in higher sensitivity, a greater number of genes whose expression is well measured, a greater number of genes whose differences in gene expression are detected to be statistically, and a greater power to detect meager differences in expression. | 05-23-2013 |
20130137605 | SEQUENCE TAG DIRECTED SUBASSEMBLY OF SHORT SEQUENCING READS INTO LONG SEQUENCING READS - The invention provides methods for preparing DNA sequencing libraries by assembling short read sequencing data into longer contiguous sequences for genome assembly, full length cDNA sequencing, metagenomics, and the analysis of repetitive sequences of assembled genomes. | 05-30-2013 |
20130143773 | HIGH-SPEED MATURATION METHOD FOR AN OLIGONUCLEOTIDE LIBRARY FOR THE PURPOSE OF PREPARING A PROTEIN LIBRARY - The present invention provides a method of producing a maturated oligonucleotide library, including a step of obtaining a terminal-modified product of a maturation target oligonucleotide library, including adding a tag sequence to the 5′ terminus of the maturation target oligonucleotide library and an arrest sequence, which stalls translation elongation on a ribosome, to the 3′ terminus of the maturation target oligonucleotide library, a step of transcribing the terminal-modified sequence product to give a transcript, and a step of in vitro translation for translating the transcript in vitro, wherein the maturation target oligonucleotide library is a random oligonucleotide library. | 06-06-2013 |
20130172216 | Arrays and Methods of Use - Methods are provided for producing a molecular array comprising a plurality of molecules immoblised to a solid substrate at a density which allows individual immobilised molecules to be individually resolved, wherein each individual molecule in the array is spatially addressable and the identity of each molecule is known or determined prior to immobilisation. The use of spatially addressable low density molecular arrays in single molecule detection and analysis techniques is also provided. Novel assays and methods are also provided. | 07-04-2013 |
20130184185 | METHODS FOR INCREASING THE DIVERSITY OF MONOCLONAL ANTIBODIES PRODUCED AGAINST AN ANTIGEN - The present invention relates to methods for increasing the diversity of monoclonal antibodies produced against an antigen. The methods of the invention utilize immunization of a murine host defective in one or more enzymes involved in a post-translational modification of a polypeptide or a modification of a lipid, wherein said modification is exposed on a cell surface. The invention also relates to monoclonal antibodies produced by these methods and which are not produced when a normal mouse is immunized with the same antigen. The invention further relates to compositions comprising these monoclonal antibodies, as well as to such monoclonal antibodies bound or conjugated to a toxin, a detectable marker or to a solid support. | 07-18-2013 |
20130203634 | INTEGRATED ANALYSIS SYSTEM - The invention provides systems, devices, methods, and kits for performing an integrated analysis. The integrated analysis can include sample processing, library construction, amplification, and sequencing. The integrated analysis can be performed within one or more modules that are fluidically connected to each other. The one or more modules can be controlled and/or automated by a computer. The integrated analysis can be performed on a tissue sample, a clinical sample, or an environmental sample. The integrated analysis system can have a compact format and return results within a designated period of time. | 08-08-2013 |
20130203635 | NUCLEIC ACID LIGATION METHOD - Methods and kits for covalently joining a 3′ nucleic acid fragment having a 5′-hydroxyl terminus to a 5′ nucleic acid fragment having a 3′-phosphate terminus are disclosed. The methods include the step of contacting the 3′-phosphate terminus of a first nucleic acid molecule and the 5′-hydroxyl terminus of a second nucleic acid molecule with an isolated 2′,3′-cyclic phosphate RNA ligase (RtcB) and a purine triphosphate in the presence of manganese (II) ion, whereby the 3′-phosphate terminus of the first nucleic acid molecule and the 5′-hydroxyl terminus of the second nucleic acid molecule are covalently joined. | 08-08-2013 |
20130210680 | SYSTEMS AND METHODS FOR AMPLIFICATION AND PHAGE DISPLAY - The present invention generally relates to amplification of biological entities, for example, for phage display. In one aspect, members of a library of biological entities are encapsulated in separate compartments (e.g., in separate microfluidic droplets) and amplified. As a specific example, by putting members of a phage display library into microfluidic droplets such that no droplet contains more than one member of the library, the library can be amplified without any substantial changes in growth rates or population distributions, or other artifacts created due to differences in growth rates or amplification between different members of the library. In some cases, the volume of the compartments can be used to control the copy number of a biological entity during amplification. In certain cases, biological entities with different amplification rates can be amplified independently of each other. In some embodiments, the ratio of a rapidly amplifying biological entity to a slowly amplifying biological entity can be controlled. This can be advantageous, for example, in preserving diversity within a library by preventing rapidly amplifying biological entities from outcompeting slowly amplifying biological entities. For example, certain methods and systems of the invention can be useful in situations where preferential amplification of library members can present a problem. | 08-15-2013 |
20130210681 | Direct Cloning - A method for performing homologous recombination between at least a first nucleic acid molecule and a second nucleic acid molecule which share at least one region of sequence homology. A method for improving the efficiency of homologous recombination. | 08-15-2013 |
20130225450 | Method of Ligating a Nucleic Acid - A method of preparing a nucleic acid library in droplets in contact with oil, including: (a) blunt-ending nucleic acid fragments in a droplet in the oil to yield blunt-ended nucleic acid fragments;
| 08-29-2013 |
20130225451 | MATERIALS AND METHODS FOR THE SYNTHESIS OF ERROR-MINIMIZED NUCLEIC ACID MOLECULES - The present invention provides materials and methods useful for error correction of nucleic acid molecules. In one embodiment of the invention, a first plurality of double-stranded nucleic acid molecules having a nucleotide mismatch are fragmented by exposure to a molecule having unidirectional mismatch endonuclease activity. The nucleic acid molecules are cut at the mismatch site or near the mismatch site, leaving a double-stranded nucleic acid molecule having a mismatch at the end or near end of the molecule. The nucleic acid molecule is then exposed to a molecule having unidirectional exonuclease activity to remove the mismatched nucleotide. The missing nucleotides can then be filled in by the action of, e.g., a molecule having DNA polymerase activity. The result is double-stranded nucleic acid molecules with a decreased frequency of nucleotide mismatches. Also provided are novel nucleic acid sequences encoding mismatch endonucleases, polypeptides encoded thereby, as well as nucleic acid constructs, transgenic cells, and various compositions thereof. | 08-29-2013 |
20130237458 | Method of adding a DBR by primer extension - Aspects of the present invention include methods and compositions for determining the number of individual polynucleotide molecules originating from the same genomic region of the same original sample that have been sequenced in a particular sequence analysis configuration or process. In these aspects of the invention, a degenerate base region (DBR) is attached to the starting polynucleotide molecules that are subsequently sequenced (e.g., after certain process steps are performed, e.g., amplification and/or enrichment). The number of different DBR sequences present in a sequencing run can be used to determine/estimate the number of different starting polynucleotides that have been sequenced. DBRs can be used to enhance numerous different nucleic acid sequence analysis applications, including allowing higher confidence allele call determinations in genotyping applications. | 09-12-2013 |
20130244907 | METHOD FOR PREPARING B CELL WHICH PRODUCES HUMAN-TYPE ANTIBODY - Provided is a method for preparing B cells which produce a human-type antibody, comprising substituting an antibody gene of B cells with a human antibody gene, wherein the B cells are non-human vertebrate B cells capable of inducing or halting AID (activation induced cytidine deaminase) expression with the induction of the expression of an exogenous Cre recombinase gene through extracellular stimulation followed by the inversion of the direction of the exogenous AID gene by expressed Cre recombinase. | 09-19-2013 |
20130261027 | NUCLEIC ACID ADAPTORS AND USES THEREOF - Provided herein are compositions, systems, methods, and kits for joining together the ends of one or more polynucleotides using at least one pair of blocking oligonucleotide adaptors. Blocking oligonucleotide adaptors can be used to reduce the formation of adaptor dimers or trimers (or higher-order concatemers) which can improve the yield of desirable polynucleotide-adaptor products in any recombinant nucleic acid workflow. Blocking oligonucleotide adaptors can comprise a double-stranded oligonucleotide adaptor (duplex) having an overhang cohesive portion that anneals with a blocking oligonucleotide which can be a separate single-stranded oligonucleotide. A blocking oligonucleotide, when annealed to an overhang portion, can prevent undesirable hybridization of the overhang portion to another nucleic acid, such as the overhang portion from another blocking oligonucleotide adaptor or a polynucleotide of interest. | 10-03-2013 |
20130274146 | CAPTURE REACTIONS - The invention generally relates to methods of performing a capture reaction. In certain embodiments, the method involves obtaining a nucleic acid, fragmenting the nucleic acid, and capturing a target sequence on the nucleic acid fragment using a capture moiety, such as a molecular inversion probe. | 10-17-2013 |
20130281323 | DEVICE AND METHOD FOR CELL-EXCLUSION PATTERNING - This disclosure relates to devices and methods for cell-exclusion patterning. Specifically, this disclosure provides a device and method to exclude cells in selected areas during cell seeding and create cell-free arrays that can be used for cell migration and related studies and assays. | 10-24-2013 |
20130281324 | BI-FUNCTINAL COMPLEXES AND METHODS FOR MAKING AND USING SUCH COMPLEXES - The present invention is directed to a method for the synthesis of a bi-functional complex comprising a molecule part and an identifier oligonucleotide part identifying the molecule part. A part of the synthesis method according to the present invention is preferably conducted in one or more organic solvents when a nascent bi-functional complex comprising an optionally protected tag or oligonucleotide identifier is linked to a solid support, and another part of the synthesis method is preferably conducted under conditions suitable for enzymatic addition of an oligonucleotide tag to a nascent bi-functional complex in solution. | 10-24-2013 |
20130288929 | Method for Making an Enriched Library - A method for making an enriched library comprising specific nucleic acid sequence information allowing to identifying at least one binding entity that binds to at least one target wherein the specific binding entity has been present in an in vitro display library. | 10-31-2013 |
20130288930 | EFFICIENT METHOD FOR DISPLAYING PROTEIN MULTIMER - The invention provides a method of producing a protein multimer-nucleic acid complex comprising a protein multimer and any one target component of the protein multimer. A nucleic acid encoding the target component is subjected to in vitro translation to provide a translation product containing a target component-nucleic acid complex of the target component and the nucleic acid encoding the target component. A nucleic acid encoding a non-target component constituting the protein multimer together with the target component is translated into the non-target component by adding the nucleic acid encoding the non-target component to the previously provided translation product to provide the non-target component. The non-target component then is associated with the target component contained in the target component-nucleic acid complex to form a protein multimer, thus affording the protein multimer-nucleic acid complex of the protein multimer and the nucleic acid encoding the target component. | 10-31-2013 |
20130296196 | METHODS, SYSTEMS AND DEVICES FOR MULTIPLE SINGLE-CELL CAPTURING AND PROCESSING USING MICROFLUIDICS - Methods, systems, and devices are described for multiple single-cell capturing and processing utilizing microfluidics. Tools and techniques are provided for capturing, partitioning, and/or manipulating individual cells from a larger population of cells along with generating genetic information and/or reactions related to each individual cell. Different capture configurations may be utilized to capture individual cells and then processing each individual cell in a multi-chamber reaction configuration. Some embodiments may provide for specific target amplification, whole genome amplification, whole transcriptome amplification, real-time PCR preparation, copy number variation, preamplification, mRNA sequencing, and/or haplotyping of the multiple individual cells that have been partitioned from the larger population of cells. Some embodiments may provide for other applications. Some embodiments may be configured for imaging the individual cells or associated reaction products as part of the processing. Reaction products may be harvested and/or further analyzed in some cases. | 11-07-2013 |
20130296197 | Device for Nucleic Acid Analysis and Nucleic Acid Analyzer - Sample nucleic acids are prevented from removing from a sample-immobilizing layer during a sequencing reaction. A reaction device for nucleic acid analysis is provided that enables high throughput analysis by increasing the number of nucleic acid samples that can be analyzed. The reaction device for nucleic acid analysis comprises a substrate, a sample-immobilizing layer on the substrate, nucleic acid samples or carriers having nucleic acid samples on their surfaces, which are immobilized on the sample-immobilizing layer, and a blocking layer that covers areas other than areas where the nucleic acid samples or the carriers are bound to the sample-immobilizing layer, wherein the immobilizing layer is formed of an inorganic oxide. | 11-07-2013 |
20130303407 | COMPOSITIONS AND METHODS FOR PROCESSING AND AMPLIFICATION OF DNA, INCLUDING USING MULTIPLE ENZYMES IN A SINGLE REACTION - The present invention concerns preparation of DNA molecules, such as a library, using a stem-loop oligonucleotide. In particular embodiments, the invention employs a single reaction mixture and conditions. In particular, at least part of the inverted palindrome is removed during the preparation of the molecules to facilitate amplification of the molecules. Thus, in specific embodiments, the DNA molecules are suitable for amplification and are not hindered by the presence of the palindrome. | 11-14-2013 |
20130338042 | KINETIC EXCLUSION AMPLIFICATION OF NUCLEIC ACID LIBRARIES - A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated. | 12-19-2013 |
20130338043 | Efficient, Expansive, User-Defined DNA Mutagenesis - The presently disclosed subject matter provides methods for the creation of one or more user-defined mutations that can be located anywhere in a target sequence, such as in a gene. These mutations can comprise single mutations, multiple mutations, or a comprehensive codon mutagenesis library, in which all possible single codon substitutions in a gene are created. These methods can be used on a single-stranded or double-stranded template. | 12-19-2013 |
20140005077 | Methods for Identifying and Isolating Cells Expressing a Polypeptide | 01-02-2014 |
20140018263 | Formation Of Droplet Or Hydrogel Arrays Using Hydrophilic-Hydrophobic Patterned Surfaces For High-Throughput Screening Applications - The present invention relates to a method of forming an array of separated homogenous fluid microdroplets or hydrogel micropads of a desired shape and size in a desired spatial pattern, comprising the steps of providing a patterned substrate with a solid support coated with a porous polymer layer or film comprising hydrophilic areas having the desired shape and size, surrounded by hydrophobic areas separating the hydrophilic areas into the desired spatial pattern, and applying the fluid to a multitude of the hydrophilic areas at the same time. | 01-16-2014 |
20140038854 | DEVICE AND METHOD FOR THE GENERATION OF MOLECULAR MICROARRAYS - The invention relates to a device and a method for the generation of molecular microarrays. The invention relates therefore to a universal approach for the generation of protein microarrays, DNA microarrays and RNA microarrays (in general nucleic acid microarrays), by production of an output molecule from a template molecule microarray via enzymatic or chemical processes and transfer of the output molecule onto the desired molecular microarray. | 02-06-2014 |
20140045728 | Orthogonal Amplification and Assembly of Nucleic Acid Sequences - Methods and compositions for synthesizing nucleic acid sequences of interest from heterogeneous mixtures of oligonucleotide sequences are provided. | 02-13-2014 |
20140094392 | METHODS OF GENERATING LIBRARIES AND USES THEREOF - This invention relates to methods for the generation of humanized antibodies, particularly a humanized antibody heavy chain protein and a humanized antibody light chain protein. The method comprises using cells that express or can be induced to express Activation Induced Cytidine Deaminase (AID). | 04-03-2014 |
20140128291 | OLIGONUCLEOTIDES AND METHODS FOR THE PREPARATION OF RNA LIBRARIES - Disclosed are compositions and methods for the preparation of RNA libraries for sequencing, gene expression profiling, microarray and other uses and for simplification of the library preparation process. The disclosure provides blocking oligonucleotides which bind to byproduct nucleic acid molecules formed during the ligation of adapters to nucleic acid segments prior to sequencing and inhibit or block amplification of the byproduct nucleic acid molecules in subsequent amplification reactions. Methods for library preparation using blocking oligonucleotides are also provided. | 05-08-2014 |
20140128292 | METHODS FOR IMPROVING LIGATION STEPS TO MINIMIZE BIAS DURING PRODUCTION OF LIBRARIES FOR MASSIVELY PARALLEL SEQUENCING - Described herein is a thermostable enzyme capable of efficient ligation of two oligomers at high temperature. The embodiments herein have led to the development of an optimized ligation step used in library preparation for sequencing reactions. | 05-08-2014 |
20140179564 | COMPOSITIONS AND METHODS FOR SELECTION OF NUCLEIC ACIDS CONTAINING MODIFIED BASES - Methods are provided for reducing the complexity of a population of nucleic acids prior to performing an analysis of the nucleic acids, e.g., sequence analysis. The methods result in a subset of the initial population enriched for a desired property, or lacking nucleic acids having an undesired property. The methods are particularly useful for analyzing populations having a high degree of complexity, e.g., chromosomal-derived DNA, whole genomic DNA, or mRNA populations. In addition, such methods allow for analysis of pooled samples. | 06-26-2014 |
20140187447 | Ligation Enhancement - Compositions and methods are provided for enhancing enzymatic ligation between nucleic acid fragments that relies on one or more small molecule enhancers having a size of less than 1000 daltons. For example, enhancement of ligation efficiencies are observed for double-stranded nucleic acid fragments that are blunt-ended, have a single nucleotide overhang at the ligation end, or have staggered ends compared to ligation under similar conditions in the absence of the one or more small molecule ligation enhancer. The use of small molecule enhancers for ligating nucleic acids results in an increased number of transformed host cells after transformation with the ligated molecules. This enhancement can be observed with chemically transformed host cells and with host cells transformed by electroporation. | 07-03-2014 |
20140200165 | NOVEL FAB FRAGMENT LIBRARIES AND METHODS FOR THEIR USE - The present invention provides Fab libraries and methods for using the Fab libraries to obtain antibodies against a target. The Fab library of the invention contains at least 10 | 07-17-2014 |
20140206581 | Methods of Making Di-Tagged DNA Libraries from DNA or RNA Using Double-tagged Oligonucleotides - Disclosed are methods, compositions and kits related to making double-tagged DNA libraries from RNA/DNA samples. A double-tagged oligonucleotide (DTO) is employed to efficiently add two different tags to ends of DNAs to make a double-tagged DNA libraries. Also disclosed are methods to make mate pair libraries using the double-tagged oligonucleotide, and methods to make double-tagged single stranded DNA. The double-tagged DNA libraries of the invention are ready to be used on next generation sequencing machines. | 07-24-2014 |
20140213485 | Methods For Preparing cDNA From Low Quantities of Cells - Methods for preparing cDNA libraries from single and low quantities of cells are disclosed. The methods are based on the principles of multi-strand displacement amplification or semi-random primed polymerase chain reaction. The methods typically include a step of reverse transcription and subsequent amplification of cDNA. The methods can be adapted for preparation of cDNA libraries that are representative of mRNA or whole RNA expressed by the cell or cells. The cDNA is suitable for sequencing or microarray analysis. | 07-31-2014 |
20140221254 | Chromosome Conformation Analysis - Disclosed herein are compositions, methods and kits for analyzing three-dimensional chromatin and/or chromosome conformation. Method are also disclosed for using the methods disclosed herein for diagnosing diseases such as cancer. | 08-07-2014 |
20140221255 | Method for Large-Scale Synthesis of Long-Chain Nucleic Acid Molecule - Systems and methods for synthesizing long-chain nucleic acids molecules are disclosed. The systems and methods described in this application use a Ligation- Purification-Amplification (“LPA”) technique. The LPA technique requires first producing nucleotide sequences with the length of at least 500 bp-1 kbp by assembling smaller oligonucleotide fragments (30 bp-200 bp). The assembled nucleotide sequences are then purified and amplified. This technology can be used to achieve parallel amplification of three or more nucleotide sequences at the same time. In embodiments of the invention, a solid-phase ligation-purification method is adopted, in which nucleic acid molecules are fixed on the surface of beads or other solid particles in order to rapidly purify products obtained from the ligation reaction. | 08-07-2014 |
20140235509 | TEMPLATE DIRECTED SPLIT AND MIX SYNTHESIS OF SMALL MOLECULE LIBRARIES - The invention combines the advantages of split and mix synthesis with the advantages of template directed synthesis. The method comprises the steps of a) adding a linker molecule L to one or more reaction wells; b) adding a molecule fragment to each of said reaction wells; c) adding an oligonucleotide identifier to each of said reaction wells; d) subjecting said wells to conditions sufficient to allow said molecule fragments and said oligonucleotide identifiers to become attached to said linker molecule, or conditions sufficient for said molecule fragments to bind to other molecule fragments and sufficient for said oligonucleotide identifiers to bind to other oligonucleotide identifiers; e) combining the contents of said one or more reaction wells; and f) contacting the resulting bifunctional molecule(s) of step e) with one or more (oligonucleotide) templates each capable of hybridizing to at least one of the oligonucleotide identifiers added step c). | 08-21-2014 |
20140243243 | DEVICE AND METHOD FOR CELL-EXCLUSION PATTERNING - This disclosure relates to devices and methods for cell-exclusion patterning. Specifically, this disclosure provides a device and method to exclude cells in selected areas during cell seeding and create cell-free arrays that can be used for cell migration and related studies and assays. | 08-28-2014 |
20140256597 | Method of amplifying and labeling the mRNA sample for mRNA microarray - Disclosed is method of amplifying and labeling mRNA sample for the mRNA microarray. The invention utilizes the specific synthesized single strand oligonucleotide (ssDNA) poly-T to hybridize the complementary poly-A in the tail of the mRNA; converts the hybridized mRNA to the cDNA; hybridizes the mRNA detection probe on the mRNA microarray chip with the cDNA; amplifies the hybridized cDNA through extending the polymer based on the ssDNA; labels the amplified cDNA by integrating the fluorescent modified nucleotide into the amplified duplex oligonucleotide during polymer extension; verifies the amplified labeled cDNA through detecting the fluorescent signal. The fluorescent signal from the mRNA detection probe spot on the mRNA microarray chip will indicate the presence of the detected mRNA and the quantity of the fluorescent signal from the mRNA detection probe sport will be directly proportional to the amount of the fluorescent modified nucleotide in the amplified duplex oligonucleotide. | 09-11-2014 |
20140274807 | METHODS FOR PRODUCING STRANDED cDNA LIBRARIES - The present system provides novel methods and compositions for selecting a particular strand of RNA and/or producing a cDNA library that results in an unbiased representation of RNA in a sample. | 09-18-2014 |
20140274808 | DIGITAL TO BIOLOGICAL CONVERTER - The present invention provides a system for receiving biological sequence information and activating the synthesis of a biological entity. The system has a receiving unit for receiving a signal encoding biological sequence information transmitted from a transmitting unit. The transmitting unit can be present at a remote location from the receiving unit. The system also has an assembly unit connected to the receiving unit, and the assembly unit assembles the biological entity according to the biological sequence information. Thus, according to the present invention biological sequence information can be digitally transmitted to a remote location and the information converted into a biological entity, for example a protein useful as a vaccine, immediately upon being received by the receiving unit and without further human intervention after preparing the system for receipt of the information. The invention is useful, for example, for rapidly responding to viral and other biological threats that are specific to a particular locale. | 09-18-2014 |
20140274809 | MULTI-WELL MANIFOLD ASSEMBLY SYSTEM FOR OLIGONUCLEOTIDE SYNTHESIS - A multi-well manifold assembly and method for reducing cross-contamination in continuous synthesis reactions in channels of microfluidic devices, for example oligonucleotide synthesis. | 09-18-2014 |
20140274810 | Methods for Amplification of Nucleic Acids Utilizing Hairpin Loop or Duplex Primers - The present invention provides methods of amplifying a target nucleic acid utilizing duplex primer. The first strand of the primer comprises a random nucleotide sequence of about 6 to about 9 nucleotides in length that is able to hybridize to the target nucleic acid and a tag sequence. The second strand of the primer comprises a sequence complementary to the tag sequence allowing the primer to form a duplex and the ability to bind the tag sequence of the product nucleic acid for further amplification. The resulting nucleic acid produced contains tag sequences on both the 3′- and 5′-termini. | 09-18-2014 |
20140274811 | Methods for Amplifying a Complete Genome or Transcriptome - The present invention provides methods for amplifying a complete genome or transcriptome. The genome or transcriptome is prepared as a set of target nucleic acids and mixed with a first primer. The first primer comprises a target-binding region having a first random sequence of about 6 to about 9 nucleotides and a tag sequence that contains one or more non-natural nucleotides. The first primer is annealed to the target nucleic acids and extended by polymerase to produce a first duplex nucleic acid. The target nucleic acid is removed from the first nucleic acid. A second primer is annealed to the first nucleic acid having a second random sequence of about 6 to about 9 nucleotides and a tag sequence that contains one or more non-natural nucleotides. The second primer is extended by polymerase to produce a second duplex nucleic acid. The second nucleic acid contains a tag sequence on one terminus and a complement of the tag sequence on the other. The first nucleic acid is removed from the second nucleic acid. A third primer is annealed to the second nucleic acid having the same sequence as the tag sequence or a portion thereof and at least one of the non-natural nucleotides of the tag sequence. The third primer is extended by polymerase to produce a third duplex nucleic acid. The second nucleic acid is removed from the third nucleic acid. The third primer is annealed to the second nucleic acid and the third nucleic acid. The third primer is extended by polymerase. Repeating these last three steps thereby results in amplification of the genome or transcriptome. | 09-18-2014 |
20140274812 | Methods of Transcription Activator Like Effector Assembly - The disclosure describes methods that include providing a first nucleic acid having a sequence encoding a first set comprising one or more transcription activator-like effector (TALE) repeat domains and/or one or more portions of one or more TALE repeat domains; contacting the first nucleic acid with a first enzyme, wherein the first enzyme creates a first ligatable end; providing a second nucleic acid having a sequence encoding a second set comprising one or more TALE repeat domains and/or one or more portions of one or more TALE repeat domains; contacting the second nucleic acid with a second enzyme, wherein the second enzyme creates a second ligatable end, and wherein the first and second ligatable ends are compatible; and ligating the first and second nucleic acids through the first and second ligatable ends to produce a first ligated nucleic acid, wherein the first ligated nucleic acid is linked to a solid support, and wherein the first ligated nucleic acid encodes a polypeptide comprising said first and second sets. | 09-18-2014 |
20140309145 | HIGH THROUGHPUT METHOD FOR ASSEMBLY AND CLONING POLYNUCLEOTIDES COMPRISING HIGHLY SIMILAR POLYNUCLEOTIDIC MODULES - The present invention relates to a method for the assembly and cloning of polynucleotides comprising highly similar polynucleotidic modules, that is highly versatile, does not require intermediate amplification step and can be easily automated for high throughput production of customized polynucleotidic modules. | 10-16-2014 |
20140315762 | METHODS FOR TAGGING DNA-ENCODED LIBRARIES - The present invention relates to oligonucleotide-encoded libraries and methods of tagging such libraries. In particular, the methods and oligonucleotides can include one or more 2′-substituted nucleotides, such as 2′-O-methyl or 2′-fluoro nucleotides, and other conditions or reagents to enhance enzyme ligation or one or more chemical functionalities to support chemical ligation. | 10-23-2014 |
20140323357 | MICROFLUIDIC CARTRIDGE AND METHOD OF MAKING SAME - The present technology provides for a microfluidic substrate configured to carry out PCR on a number of polynucleotide-containing samples in parallel. The substrate can be a single-layer substrate in a microfluidic cartridge. Also provided are a method of making a microfluidic cartridge comprising such a substrate. Still further disclosed are a microfluidic valve suitable for use in isolating a PCR chamber in a microfluidic substrate, and a method of making such a valve. | 10-30-2014 |
20140342948 | METHODS FOR MULTIPLEX AMPLIFICATION - Methods for multiplex amplification of target nucleic acid sequences are provided. | 11-20-2014 |
20140349890 | Multiplex Amplification Methods - Compositions and methods for amplifying selected polynucleotides, including DNA and RNA, particularly in multiplex amplification reactions using common primers amplification. Generally, methods of the invention employ multiple steps such as template-specific hybridization, a linear amplification, partial degradation of nucleic acid, and ligation. At the end of the process the sequences of selected polynucleotides are flanked by the common sequences which can be used for exponential amplification using common primers. In some aspects the polynucleotides are associated with a barcode and the presence of the barcode is detected to measure the amount of the polynucleotide. | 11-27-2014 |
20140357531 | METHOD FOR PRODUCING A NUCLEIC ACID LIBRARY HAVING AT LEAST TWO ADJACENT VARIABLE CODON TRIPLETS - The invention relates to a method for producing a DNA sequence for a nucleic acid library having a plurality of elements. The synthesized DNA sequence comprises at least three sections. The first section and the third section in each element have defined sequences (D1, D2) that are identical in each element of the nucleic acid library. In a middle second section, at least two adjoining variable codon triplets are arranged. | 12-04-2014 |
20140371107 | BIOMOLECULE ISOLATION - Methods, devices and systems for handling sample liquids, encapsulating liquids and magnetic particles are disclosed. | 12-18-2014 |
20140378349 | COMPOSITIONS AND METHODS FOR SAMPLE PROCESSING - This disclosure provides methods and compositions for sample processing, particularly for sequencing applications. Included within this disclosure are bead compositions, such as diverse libraries of beads attached to large numbers of oligonucleotides containing barcodes. Often, the beads provides herein are degradable. For example, they may contain disulfide bonds that are susceptible to reducing agents. The methods provided herein include methods of making libraries of barcoded beads as well as methods of combining the beads with a sample, such as by using a microfluidic device. | 12-25-2014 |
20140378350 | COMPOSITIONS AND METHODS FOR SAMPLE PROCESSING - This disclosure provides methods and compositions for sample processing, particularly for sequencing applications. Included within this disclosure are bead compositions, such as diverse libraries of beads attached to large numbers of oligonucleotides containing barcodes. Often, the beads provides herein are degradable. For example, they may contain disulfide bonds that are susceptible to reducing agents. The methods provided herein include methods of making libraries of barcoded beads as well as methods of combining the beads with a sample, such as by using a microfluidic device. | 12-25-2014 |
20150011434 | METHOD FOR THE SYNTHESIS OF A BIFUNCTIONAL COMPLEX - Disclosed is a method for obtaining a bifunctional complex comprising a display molecule part and a coding part, wherein a nascent bifunctional complex comprising a chemical reaction site and a priming site for enzymatic addition of a tag is reacted at the chemical reaction site with one or more reactants, and provided with respective tag(s) identifying the reactant(s) at the priming site is using one or more enzymes. | 01-08-2015 |
20150018253 | Methods and Compositions for Selective Labeling of Different Biotinylated Targets within Multicolor or Multilabel Assays - Disclosed are compositions and methods for the labeling of two or more targets with different labels. Specifically, disclosed are compositions for biotin and the protection of biotin within multilabel assays which employ the biotin-biotin binding protein binding relationship for each distinct label in relation to targets such as nucleic acids, polypeptides, antibodies or cells. These multilabel assays are enabled through the use of biotin with desthiobiotin, orthogonal protecting schemes for biotin, or a combination of the approaches. | 01-15-2015 |
20150045258 | CASCADED ADDITION OF TARGET SPECIFIC UNIVERSAL ADAPTERS TO NUCLEIC ACIDS - The present invention generally pertains to methods for the addition of one or more nucleic acid adaptors to a PCR product. The present invention generally relates to a method for the cascaded, highly specific addition of universal nucleic acid adapters to one or more target nucleic acids in a single PCR amplification reaction, as well as a kit encompassing the same. | 02-12-2015 |
20150051116 | NEXT-GENERATION SEQUENCING LIBRARIES - Provided herein is technology relating to next-generation sequencing and particularly, but not exclusively, to methods and compositions for preparing a next-generation sequencing library comprising short overlapping DNA fragments and using the library to sequence one or more target nucleic acids. | 02-19-2015 |
20150057192 | Methods for Dynamic Vector Assembly of DNA Cloning Vector Plasmids - A method for using cloning vector plasmids to produce DNA molecules, such as transgenes, in a single cloning step. The transgenes can be used for the purpose of gene expression or analysis of gene expression. The plasmid cloning vectors are engineered to minimize the amount of manipulation of DNA fragment components by the end user of the vectors and the methods for their use. Transgenes produced using the invention may be used in a single organism, or in a variety of organisms including bacteria, yeast, mice, and other eukaryotes with little or no further modification. | 02-26-2015 |
20150065396 | MICROFLUIDIC DEVICES AND METHODS OF THEIR USE - Methods and systems for manipulating drops in microfluidic channels are provided. | 03-05-2015 |
20150072898 | Broad Host Range Expression Vector for Diverse Prokaryotes - The invention relates to a synthetic nucleic acid molecule for expressing at least one nucleotide sequence of interest in at least one prokaryotic host cell, comprising, amongst others, at least one replication module comprising at least one replication cassette for promoting replication of the nucleic acid molecule in Gram-negative organisms and at least one replication cassette for promoting replication of the nucleic acid molecule in Gram-positive organisms, and at least one expression module for promoting expression of the nucleotide sequence of interest in the host cell, wherein each module is flanked at both ends by at least one unique restriction site. The invention further concerns a method for producing a shuttle vector comprising several modules, wherein said shuttle vector is designed by selecting each of said modules such that the vector is optimized for its intended use. | 03-12-2015 |
20150072899 | DEGENERATE OLIGONUCLEOTIDES AND THEIR USES - The present invention provides a plurality of oligonucleotides comprising a semi-random sequence, wherein the semi-random sequence comprises degenerate nucleotides that are substantially non-complementary. Also provided are methods for using the plurality of oligonucleotides to amplify a population of target nucleic acids. | 03-12-2015 |
20150080267 | METHOD FOR IMMUNIZING AN AVIAN SPECIES - The present invention relates to a method for generating a plurality of different IgY antibodies, by immunizing each of a plurality of avian organisms of the same or different species with a composition comprising a plurality of different antigens, thereby generating a plurality of different IgY antibodies. | 03-19-2015 |
20150087556 | COMPOSITIONS AND METHODS FOR MAKING cDNA LIBRARIES FROM SMALL RNAs - This disclosure provides methods and compositions for generating cDNA libraries. | 03-26-2015 |
20150087557 | ENZYME COMPOSITION FOR DNA END REPAIR, ADENYLATION, PHOSPHORYLATION - Enzyme compositions and their method of use that provide ready-to-use master mixtures. The compositions comprise a modified thermophilic DNA polymerase lacking 5′-3′ and 3′-5′ exonuclease activity premixed with T4 DNA polymerase, Klenow fragment and T4 polynucleotide kinase and all other necessary components, including reaction buffer and nucleoside triphosphates, required to perform DNA blunting, phosphorylation, and single nucleotide extension reactions in one tube and in two steps. Among other benefits, the mixture of different enzymes, buffers and nucleoside triphosphates is stable during prolonged storage. | 03-26-2015 |
20150099670 | Method of preparing post-bisulfite conversion DNA library - The invention relates to a method of preparing bisulfite-treated DNA library by ligation of adaptors to DNA after bisulfite conversion. The prepared library is suitable for use in sequencing reactions to analyze genome-wide DNA methylation status. | 04-09-2015 |
20150099671 | Compositions and Methods for Constructing cDNA Libraries that Allow for Mapping the 5' and 3' Ends of RNAs - This disclosure provides methods and compositions for preparing and constructing cDNA libraries. | 04-09-2015 |
20150099672 | BEAD EMULSION NUCLEIC ACID AMPLIFICATION - Disclosed are methods for nucleic acid amplification wherein nucleic acid templates, beads, and amplification reaction solution are emulsified and the nucleic acid templates are amplified to provide clonal copies of the nucleic acid templates attached to the beads. Also disclosed are kits and apparatuses for performing the methods of the invention. | 04-09-2015 |
20150105299 | Method for Differentiation of Polynucleotide Strands - Objective of the present invention is to provide a method for keeping of directional information in double-stranded DNA. We suggest to convert polynucleotide into a hybrid double-stranded DNA. One particular strand of this hybrid double-stranded DNA should be synthesised using at least one modified nucleotide. Thus, this particular strand would contain modified nucleotides along the whole length. Density of directional markers would not depend on the length of polynucleotides. Any internal fragments of the hybrid double-stranded DNA would have directional information. When it is necessary the modified strand may be easily degraded or separated from the other strand. It was found that such hybrid double-stranded DNA may be easily generated in a number of molecular biology tasks and may be used for molecular cloning, library preparation and strand separation. | 04-16-2015 |
20150105300 | Sample Processing Methods - A method of processing a sample may include introducing a sample into a vessel, the vessel having proximal and distal ends, the sample being introduced into the proximal end of the vessel; incubating the sample in the vessel with a substance capable of specific binding to a preselected component of the sample; propelling components of the incubated sample, other than the preselected component, toward the proximal end of the vessel by clamping the vessel distal to the incubated sample and compressing the vessel where the incubated sample is contained; propelling the preselected component toward a distal segment of the vessel by clamping the vessel proximal to the preselected component and compressing the vessel where the preselected component is contained; and mixing the preselected component with a reagent in the distal segment of the vessel. | 04-16-2015 |
20150111788 | MULTIPLEX ISOLATION OF PROTEIN-ASSOCIATED NUCLEIC ACIDS - The invention provides novel methods and materials for genetic and genomic analysis using single or multiplex isolation of protein-associated nucleic acids, including transposase-assisted chromatin immunoprecipitation (TAM-ChIP) and antibody-oligonucleotide proximity ligation. These methods comprise tagging and isolating chromatin or other protein-associated nucleic acids and using antibody-oligonucleotide complexes that recognize the proteins associated with such nucleic acids. | 04-23-2015 |
20150111789 | METHODS FOR ADDING ADAPTERS TO NUCLEIC ACIDS AND COMPOSITIONS FOR PRACTICING THE SAME - Provided are methods of adding adapters to nucleic acids. The methods include combining in a reaction mixture a template ribonucleic acid (RNA), a template switch oligonucleotide including a 3′ hybridization domain and a sequencing platform adapter construct, a polymerase, and dNTPs. The reaction mixture components are combined under conditions sufficient to produce a product nucleic acid that includes the template RNA and the template switch oligonucleotide each hybridized to adjacent regions of a single product nucleic acid that includes a region polymerized from the dNTPs by the polymerase. Aspects of the invention further include compositions and kits. | 04-23-2015 |
20150119290 | Digital Counting of Individual Molecules by Stochastic Attachment of Diverse Labels - Compositions, methods and kits are disclosed for high-sensitivity single molecule digital counting by the stochastic labeling of a collection of identical molecules by attachment of a diverse set of labels. Each copy of a molecule randomly chooses from a non-depleting reservoir of diverse labels. Detection may be by a variety of methods including hybridization based or sequencing. Molecules that would otherwise be identical in information content can be labeled to create a separately detectable product that is unique or approximately unique in a collection. This stochastic transformation relaxes the problem of counting molecules from one of locating and identifying identical molecules to a series of binary digital questions detecting whether preprogrammed labels are present. The methods may be used, for example, to estimate the number of separate molecules of a given type or types within a sample. | 04-30-2015 |
20150119291 | NUCLEIC ACID AMPLIFICATION - The present invention provides methods for the amplification of nucleic acid molecules. Methods for amplifying target polynucleotides, including mRNA, using oligonucleotides, DNA and RNA polymerases are provided. The invention further provides compositions and kits for practicing the methods, as well as methods which use the amplification products. | 04-30-2015 |
20150119292 | METHOD FOR RETAINING EVEN COVERAGE OF SHORT INSERT LIBRARIES - The invention relates to a method of preparing a library of template polynucleotides with uniform sequence representation and to use of a library of templates prepared using this method for solid-phase nucleic acid amplification. In particular, the invention relates to a method of preparing a library of template polynucleotides which have common sequences at their 5′ ends and at their 3′ ends, which contains even representation of all the fragments present in a starting sample of nucleic acid before fragmentation. The invention is especially applicable to the preparation of short insert libraries, where the sample fragments are less than 150 base pairs in length. | 04-30-2015 |
20150119293 | SYNTHETIC LIGATION REASSEMBLY IN DIRECTED EVOLUTION - A directed evolution process for rapid and facilitated production from a progenitor polynucleotide template, of a library of mutagenized progeny polynucleotides wherein each of the 20 naturally encoded amino acids is encoded at each original codon position. This method, termed site-saturation mutagenesis, or simply saturation mutagenesis, is preferably based on the use of the degenerate N,N,G/T sequence. Also, a method of non-stochastically producing a library of chimeric nucleic acid molecules having an overall assembly order that is chosen by design. Accordingly, a set of progenitor templates, such as genes (e.g. a family of esterase genes) or genes pathways (e.g. encoding antibiotics) can be shuffled to generate a sizable library of distinct progeny polynucleotide molecules (e.g. 10 | 04-30-2015 |
20150119294 | SYNTHETIC POLYPEPTIDE LIBRARIES AND METHODS FOR GENERATING NATURALLY DIVERSIFIED POLYPEPTIDE VARIANTS - The invention provides compositions and methods for generating libraries of DNA sequences encoding homologous polypeptides, and uses of the libraries to identify naturally diversified polypeptide variants. The invention also provides compositions and methods for generating collections of synthetic antibody fragments in which one or several complementary determining regions (CDR) are replaced by a collection of the corresponding CDR captured from a natural source. The invention further provides compositions and methods for diversifying a portion of a polypeptide by inserting a diversified sequence of synthetic or natural origin without the need for modification of the original polypeptide coding sequence. | 04-30-2015 |
20150126410 | MEANS AND METHODS TO INCREASE ADENOVIRUS PRODUCTION - The invention relates in a first embodiment to a method for increasing the yield of replication-incompetent adenoviruses having at least a partial deletion in the E1-region, wherein said adenoviruses are generated in a production cell, the method comprising the steps of: (a) expressing in said production cell an adenoviral pIX polypeptide from a nucleic acid sequence encoding said adenoviral pIX polypeptide under the control of (i) at least a minimal endogenous pIX promoter and a heterologous promoter; or (ii) a heterologous promoter; and (b) expressing in said production cell the elements necessary for the production and assembly of said adenoviruses from corresponding coding sequences, thereby increasing the yield of said adenoviruses generated in said production cell in comparison to the yield of replication-incompetent adenoviruses having at least a partial deletion in the E1-region generated in said production cell in the absence of said nucleic acid sequence encoding said adenoviral pIX polypeptide. In another embodiment, the invention relates to a method for constructing an adenovirus library, a production cell as well as the use of an adenoviral pIX polypeptide for increasing the yield of replication-incompetent adenoviruses having at least a partial deletion in the E1-region. | 05-07-2015 |
20150133344 | SEQUENCE TAG DIRECTED SUBASSEMBLY OF SHORT SEQUENCING READS INTO LONG SEQUENCING READS - The invention provides methods for preparing DNA sequencing libraries by assembling short read sequencing data into longer contiguous sequences for genome assembly, full length cDNA sequencing, metagenomics, and the analysis of repetitive sequences of assembled genomes. | 05-14-2015 |
20150141294 | REVERSIBLE NATURAL PRODUCT GLYCOSYLTRANSFERASE-CATALYZED REACTIONS, COMPOUNDS AND RELATED METHODS - The present invention relates to methods of use of glycosyltransferases and related novel compounds. The invention exploits the reversibility of glycosyltransferases to generate new sugars, unnatural biomolecules and numerous one-pot reactions for generation of new biomolecules having varied backbones such as enediynes, vancomycins, bleomycins, anthracyclines, macrolides, pluramycins, aureolic acids, indolocarbazoles, aminglycosides, glycopeptides, polyenes, coumarins, benzoisochromanequinones, calicheamicins, erythromycin, avermectins, ivermectins, angucyclines, cardiac glycosides, steroids or flavinoids. In preferred embodiments, the invention specifically relates to biosynthesis of anticancer (the enediyne calicheamicin, CLM), anthelmintic agents (the macrolides avermectin, ivermectin and erythromycin) and antibiotic (the glycopeptide vancomycin, VCM) natural product-based drugs developed by reversible, bidirectional glycosyltransferase-catalyzed reactions. | 05-21-2015 |
20150141295 | SOLID-PHASE CLONAL AMPLIFICATION AND RELATED METHODS - The present invention provides methods and compositions for analyzing nucleic acid sequences. In some aspects, the methods utilize clonal objects, such as DNA balls, that have been captured on beads. Using the methods described here, compositions are fabricated wherein a bead and one clonal object are affinity bound or hybridized to each other through an affinity binding patch or hybridization patch on the surface of the bead. The invention also provides a population of beads having affinity bound or hybridized clonal objects at a ratio of 1:1. The invention additionally provides methods for amplifying a target nucleic acid molecule utilizing the compositions described herein. | 05-21-2015 |
20150148263 | METHODS FOR SELECTING AND AMPLIFYING POLYNUCLEOTIDES - The invention provides methods for controlling the density of different molecular species on the surface of a solid support. A first mixture of different molecular species is attached to a solid support under conditions to attach each species at a desired density, thereby producing a derivatized support having attached capture molecules. The derivatized support is treated with a second mixture of different molecular species, wherein different molecular species in the second mixture bind specifically to the different capture molecules attached to the solid support. One or more of the capture molecules can be reversibly modified such that the capture molecules have a different activity before and after the second mixture of molecular species are attached. In particular embodiments, the different molecular species are nucleic acids that are reversibly modified to have different activity in an amplification reaction. | 05-28-2015 |
20150291953 | METHODS AND KITS FOR NUCLEIC ACID SAMPLE PREPARATION FOR SEQUENCING - The present disclosure relates to methods and kits for DNA library construction, particularly for consistent and reproducible DNA sequencing. | 10-15-2015 |
20150299729 | ULTRAHIGH THROUGHPUT MICROINJECTION DEVICE - Many applications in cell biology, genetic engineering, cell-based therapeutics, and drug discovery require precise and safe methods for introducing membrane-impermeable molecules into cells. This can be implemented satisfactorily by microinjection. However, disadvantages of traditional manual microinjection include high degree of operator skill, low throughput and labor-intensiveness. Many studies have focused on developing automated and high-throughput systems for microinjection to address these limitations. However, none have provided sufficient throughput for applications such as ex vivo cell therapy, where manipulation of many cells is helpful. | 10-22-2015 |
20150299785 | METHOD OF MEASURING ADAPTIVE IMMUNITY - Compositions and methods for measuring adaptive immune receptor (T cell receptor and immunoglobulin) diversity are described, and find uses for assessing immunocompetence and other purposes. Means are provided for assessing the effects of diseases or conditions that compromise the immune system and of therapies aimed to reconstitute it. Lymphoid (B- and T-cell) adaptive immune receptor diversity is quantified by calculating the number of uniquely rearranged. CDR3-containing immunoglobulin (Ig) or T-cell receptor (TCR) variable region-encoding genes from sample cells such as blood cells. | 10-22-2015 |
20150307929 | METHODS AND COMPOSITIONS FOR MULTIPLEX PCR - The present invention provides methods, compositions, kits, systems and apparatus that are useful for multiplex PCR of one or more nucleic acids present in a sample. In particular, various target-specific primers are provided that allow for the selective amplification of one or more target sequences. In one aspect, the invention relates to target-specific primers useful for the selective amplification of one or more target sequences associated with cancer or inherited disease. In some aspects, amplified target sequences obtained using the disclosed methods, kits, systems and apparatuses can be used in various downstream processes including nucleic acid sequencing and used to detect the presence of genetic variants. | 10-29-2015 |
20150322503 | Reagents and Methods of PCR - Modified double-stranded oligonucleotides that have terminal regions on each of their strands, that have a hybrid length of 6-50 nucleotides long, that have a melting temperature Tm of at least 32° C., and that include 2-4 modifying groups, each covalently attached to a different terminal region, preferably to a terminal nucleotide, said modifying groups being polycyclic substituents that do not have bulky portions that are non-planar, said modified oligonucleotide being capable of binding to the 5′ exonuclease domains of DNA polymerases and, when included in a PCR or other primer-dependent DNA amplification reaction at a concentration, generally not more than 2000 nM, that is effective for at least one of the functions of suppressing mispriming, increasing polymerase selectivity against 3′ terminal mismatches. increasing polymerase selectivity against AT-rich 3′ ends, reducing scatter among replicates, suppressing polymerase 5′ exonuclease activity, and inhibiting polymerase activity; as well as amplification reaction mixtures containing such modified double-stranded oligonucleotides, and amplification reactions, amplification assays and kits that include such modified double-stranded oligonucleotides. | 11-12-2015 |
20150329853 | COMPOSITIONS AND METHODS FOR CREATING ALTERED AND IMPROVED CELLS AND ORGANISMS - The present invention provides compositions comprising randomized in-frame fusion polynucleotides and methods for introducing them into a host organism to identify desirable phenotypic changes that disrupt or alter existing genetic or biochemical mechanisms or pathways, thus creating novel characteristics of the transformed organism. Methods for using the compositions for increasing diversity within populations of organisms are also presented. | 11-19-2015 |
20150337290 | METHODS AND PRODUCTS FOR MUTATING NUCLEOTIDE SEQUENCES - Described herein are products and methods directed to introducing deletions, insertions and substitutions into nucleotide sequences using transposons. Described herein are isolated transposons comprising first and second outside cutter recognition sequences and first and second terminal inverted repeat sequences, wherein the first and second outside cutter restriction recognition sequences are located at least partially internally to the first and second inverted repeat sequences. | 11-26-2015 |
20150337292 | METHOD OF PRODUCING SECRETABLE ANTIBODIES BY EXPRESSION IN SACCHAROMYCES CEREVISIAE - The invention relates to a method for the production and non-covalent surface display of antibodies and derived fragments as well as molecule libraries based thereon on the surface of | 11-26-2015 |
20150343410 | Preparation of Templates for Nucleic Acid Sequencing - The invention relates to methods of generating templates for a nucleic acid sequencing reaction which comprise: providing at least one double-stranded nucleic acid molecule, wherein both strands of the double-stranded nucleic acid molecule are attached to a solid support at the 5′ end, cleaving one or both strands of the double-stranded nucleic acid molecule, and subjecting the cleaved strand(s) to denaturing conditions to remove the portion of the cleaved strand(s) not attached to the solid support, thereby generating a partially or substantially single-stranded template for a nucleic acid sequencing reaction. | 12-03-2015 |
20150344876 | HIGH EFFICIENCY, SMALL VOLUME NUCLEIC ACID SYNTHESIS - The disclosure generally relates to compositions and methods for the production of nucleic acid molecules. In some aspects, the invention allows for the microscale generation of nucleic acid molecules, optionally followed by assembly of these nucleic acid molecules into larger molecules. In some aspects, the invention allows for efficient production of nucleic acid molecules (e.g., large nucleic acid molecules such as genomes). | 12-03-2015 |
20150344943 | METHODS AND SYSTEMS FOR NUCLEIC ACID AMPLIFICATION - The disclosure provides methods and systems for nucleic acid amplification including isothermal nucleic acid amplification. | 12-03-2015 |
20150353989 | SAMPLE PREPARATION FOR NUCLEIC ACID AMPLIFICATION - Presented are methods and compositions for preparing samples for amplification and sequencing. Particular embodiments relate to methods of obtaining nucleic acids material directly from tissues such as whole blood or FFPE samples. | 12-10-2015 |
20150353993 | COMPOSITIONS, METHODS, SYSTEMS AND KITS FOR TARGET NUCLEIC ACID ENRICHMENT - The present invention provides methods, compositions, kits, systems and apparatus that are useful for isolating nucleic acid molecules from a sample. In particular, the methods generally relate to normalizing the concentration of target nucleic acid molecules from a sample. In one aspect, the invention relates to purifying a primer extension product from a primer extension reaction mixture. In some aspects, nucleic acid molecules obtained using the disclosed methods, kits, systems and apparatuses can be used in various downstream processes including nucleic acid sequencing. | 12-10-2015 |
20150360193 | COMPOSITIONS AND METHODS FOR THE AMPLIFICATION OF NUCLEIC ACIDS - The present disclosure relates to systems and methods for the amplification of nucleic acids, including, but not limited to, the amplification of nucleic acid libraries and whole genome amplification. | 12-17-2015 |
20150360226 | SINGLE CELL CAPTURE WITH POLYMER CAPTURE FILMS - The present invention provides methods, systems, assemblies, and articles for capturing single cells with a polymer capture film. In certain embodiments, the polymer capture films comprise a plurality of individual channels with top and bottom openings, where the channels are dimensioned such that a single cell is: i) is captured inside the channel, partially or substantially occluding the channel, when negative pressure is provided to the bottom opening; or ii) is captured by the top opening, but does not enter the channel, when negative pressure is provided to the bottom opening. In some embodiments, the channels of the polymer capture film align with the wells of a multi-well chip such that the cell, or the contents of the single cell, may be transferred to a corresponding well. | 12-17-2015 |
20150361481 | MULTIPLEX NUCLEIC ACID AMPLIFICATION - In some embodiments, the disclosure relates generally to compositions, comprising a single reaction mixture containing a plurality of different populations of discrete supports, and a plurality of different populations of target nucleic acids. The single reaction mixture can contain a first population of beads; a second population of beads; a first population of target nucleic acids, where at least two different target nucleic acids in the first population of target nucleic acids can bind to a bead in the first population of beads; and a second population of target nucleic acids, where at least two different target nucleic acids in the second population of target nucleic acids can bind to a bead in the second population of beads. The single reaction mixture can be employed to monoclonally amplify the first target nucleic acids on the first beads, and monoclonally amplify the second target nucleic acids on the second beads. | 12-17-2015 |
20150368687 | Compositions and Methods for Synthesis of High Fidelity Oligonucleotides - Aspects of the invention relate to methods, compositions for synthesizing high fidelity oligonucleotides. | 12-24-2015 |
20150372182 | RADIATION MICRODOSIMETERS CORRELATED WITH BIOLOGICAL CELLS AND CELL COMPONENTS - One feature pertains to a radiation dosimeter comprising a microdosimeter cell array that includes a first microdosimeter cell having a first semiconductor volume configured to generate a first current in response to incident radiation. The first semiconductor volume may have at least one of a first size, a first shape, a first semiconductor type, and/or a first semiconductor doping type and concentration that is associated with a first biological cell type or a first biological cell component type. The dosimeter may further comprise a processing circuit communicatively coupled to the microdosimeter cell array and configured to generate a signal based on the first current. The signal generated may be indicative of an amount of radiation absorbed by the microdosimeter cell array. A display may be utilized by the dosimeter to show a radiation level reading based on the signal generated. | 12-24-2015 |
20150376608 | LIBRARY PREPARATION OF TAGGED NUCLEIC ACID USING SINGLE TUBE ADD-ON PROTOCOL - A method of preparing a library of tagged nucleic acid fragments including contacting a population of cells directly with a lysis reagent having one or more protease to generate a cell lysate; inactivating the protease to generate an inactivated cell lysate, and applying a transposase and a transposon end composition containing a transferred strand to the inactivated cell lysate under conditions wherein the target nucleic acid and the transposon end composition undergo a transposition reaction. | 12-31-2015 |
20160001249 | Methods for Loading a Sensor Substrate - A method of loading beads on a sensor substrate includes applying a suspension including beads to a flow cell defined over a sensor substrate. The sensor substrate includes a plurality of wells. The beads at least partially deposit into the plurality of wells. The method also includes removing liquid from the flow cell, evaporating liquid from the flow cell, for example, by drawing air through the flow cell; and applying a hydrating solution to the flow cell. | 01-07-2016 |
20160010078 | Two-Dimensional Cell Array Device and Apparatus for Gene Quantification and Sequence Analysis | 01-14-2016 |
20160016169 | MICROFLUIDIC DEVICES FOR THE RAPID AND AUTOMATED PROCESSING OF SAMPLE POPULATIONS - Microfluidic devices for the rapid and automated processing of sample populations are provided. Described are multiplexer tiplexer microfluidic devices configured to serially deliver a plurality of distinct sample populations to a sample processing element rapidly and automatically, without cross-contaminating the distinct sample populations. Also provided are microfluidic sample processing elements that can be used to rapidly and automatically manipulate and/or interrogate members of a sample population. The microfluidic devices can be used to improve the throughput and quality of experiments involving model organisms, such as | 01-21-2016 |
20160017391 | cDNA Synthesis Improvements - The present invention generally relates to methods of making cDNA molecules and cDNA libraries. The invention also relates to cDNA molecules and cDNA libraries produced according to these methods, as well as to vectors and host cells containing such cDNA molecules and libraries. The invention also relates to kits for making the cDNA molecules and libraries of the invention. | 01-21-2016 |
20160017410 | HIGHLY MULTIPLEX SINGLE AMINO ACID MUTAGENESIS FOR MASSIVELY PARALLEL FUNCTIONAL ANALYSIS - Disclosed is a method for multiplexed mutagenesis of a target nucleotide sequence. The method entails generating, in parallel, a set of mutagenic oligonucleotide primers designed to cover all or part of the target nucleotide sequence, and reacting the set of mutagenic oligonucleotide primers with the target sequence in the presence of a polymerase to generate a mutant nucleotide sequence library, wherein each member of the mutant nucleotide sequence library comprises a full-length copy of the target nucleotide sequence having a unique programmed mutation derived from one member of the set of mutagenic oligonucleotide primers. Also disclosed are methods for generating a mutant nucleotide sequence library and for generating a mutant protein library. | 01-21-2016 |
20160024490 | METHOD FOR SEPARATING DNA BY SIZE - The present invention provides method for isolating DNA molecules having a size above a certain cut-off value from a DNA containing sample, comprising a) contacting the sample with a binding buffer which comprises a chaotropic agent and a buffering agent to provide a binding mixture and binding DNA molecules having a size above the cut-off value to a binding matrix which has a silicon containing surface, wherein the cut-off value is determined by the pH value of the binding mixture; b) separating the bound DNA from the remaining sample; c) optionally washing the bound DNA; and d) optionally eluting the bound DNA from the binding matrix. Said method allows the size selective purification of DNA molecules. | 01-28-2016 |
20160032359 | Methods for Generating Nucleic Acid Molecule Fragments Having a Customized Size Distribution - The invention provides methods for generating nucleic acid molecule fragments having a customized distribution. In one aspect, a method of generating nucleic acid fragments having a customized fragment size distribution is provided comprising obtaining a master pool of nucleic acid molecules to be fragmented; fragmenting at least two independent aliquots of the master pool of nucleic acid molecules in separate reactions, wherein the fragmentation conditions are identical except for a single variable. | 02-04-2016 |
20160045883 | STABILISATION FEATURES - Devices, systems and methods for making and handling liquid samples are disclosed. | 02-18-2016 |
20160045884 | SINGLE CELL CAPTURE WITH CAPTURE CHIPS - The present invention provides methods, systems, assemblies, and articles for capturing single cells with a capture chip. In certain embodiments, the capture chip comprises a substrate comprising a plurality of cell-sized dimples or wells that each allow a single cell to be captured from a cell suspension. In some embodiments, the dimples or wells of the capture chip align with the holes or wells of a multi-well through-hole chip, and/or a multi-well chip, such that the cell, or the contents of the single cell, may be transferred to a corresponding well of the multi-well chip. In particular embodiments, the bottom of each dimple or well of the capture chip has a positive electrical charge sufficient to attract cells from a cell suspension flowing over the dimples or wells. | 02-18-2016 |
20160051958 | HIGH-SPEED ON DEMAND MICROFLUIDIC DROPLET GENERATION AND MANIPULATION - Methods and devices for the formation and/or merging of droplets in microfluidic systems are provided. In certain embodiments a microfluidic droplet merger component is provided that comprises a central channel comprising a plurality of elements disposed and spaced to create a plurality of lateral passages that drain a carrier fluid out of a fluid stream comprising droplets of a first fluid contained in the carrier fluid; and a deformable lateral membrane valve disposed to control the width of said center channel. | 02-25-2016 |
20160051959 | NUCLEIC ACID SAMPLE PREPARATION METHODS AND COMPOSITIONS - The present invention provides compositions and methods for preparing a nucleic acid library in a multi-purpose buffer (e.g., employing whole genome amplification), where nucleic acid purification is not required between or during steps. In certain embodiments, small amounts of starting nucleic acid (e.g., genomic DNA) are employed and the steps are accomplished in a single container. In some embodiments, the nucleic acid library is subjected to sequencing methodologies or rolling circle amplification. | 02-25-2016 |
20160059203 | METHOD OF FABRICATING CELL ARRAYS AND USES THEREOF - The present disclosure provides a fabrication process that results in creating large arrays of living cells, such as stem cells, which are subsequently exposed to nanoliter quantities of compounds to test the efficacy on cellular metabolism. | 03-03-2016 |
20160108461 | TARGETED WHOLE GENOME AMPLIFICATION METHOD FOR IDENTIFICATION OF PATHOGENS - The methods disclosed herein relate to methods and compositions for amplifying nucleic acid sequences, more specifically, from nucleic acid sequences of pathogens by targeted whole genome amplification. | 04-21-2016 |
20160138013 | SUBSTANTIALLY UNBIASED AMPLIFICATION OF GENOMES - Methods and manufactures for substantially unbiased amplification of genomes are provided herein. Some embodiments include methods of producing a substantially unbiased amplification library of a genome of a single cell. Some embodiments include methods of producing a substantially unbiased amplification of a genome by multiple strand displacement amplification (MDA). Some embodiments include a substrate for substantially unbiased amplification a genome of each of a plurality of single cells | 05-19-2016 |
20160138082 | Thermo-controllable high-density chips for multiplex analyses - The present invention provides miniaturized instruments for conducting chemical reactions where control of the reaction temperature is desired or required. Specifically, this invention provides chips and optical systems for performing and monitoring temperature-dependent chemical reactions. The apparatus and methods embodied in the present invention are particularly useful for high-throughput and low-cost amplification of nucleic acids. | 05-19-2016 |
20160144333 | Assembly of High Fidelity Polynucleotides - Methods and apparatus relate to the synthesis of high fidelity polynucleotides and to the reduction of sequence errors generated during synthesis of nucleic acids on a solid support. Specifically, design of support-bound template oligonucleotides is disclosed. Assembly methods include cycles of annealing, stringent wash and extension of polynucleotides comprising a sequence region complementary to immobilized template oligonucleotides. The error free synthetic nucleic acids generated therefrom can be used for a variety of applications, including synthesis of biofuels and value-added pharmaceutical products. | 05-26-2016 |
20160145603 | COMPOSITIONS FOR MAKING RANDOM CODON-MUTANT LIBRARIES AND USES THEREOF - The present disclosure relates to compositions and methods for randomly introducing codon-mutations in a target nucleic acid molecule and, more particularly, using wild-type and triplet-randomized oligonucleotides to introduce mutations uniformly across a target nucleotide of interest in a controlled fashion and with a low rate of insertions or deletions. | 05-26-2016 |
20160153001 | METHODS FOR TRANSFORMING YEAST | 06-02-2016 |
20160160210 | RNA-Guided Human Genome Engineering - A method of altering a eukaryotic cell is provided including transfecting the eukaryotic cell with a nucleic acid encoding RNA complementary to genomic DNA of the eukaryotic cell, transfecting the eukaryotic cell with a nucleic acid encoding an enzyme that interacts with the RNA and cleaves the genomic DNA in a site specific manner, wherein the cell expresses the RNA and the enzyme, the RNA binds to complementary genomic DNA and the enzyme cleaves the genomic DNA in a site specific manner | 06-09-2016 |
20160168578 | METHODS AND DEVICES FOR ELECTROMAGNETIC LIGATION OF NUCLEIC ACIDS AND ELECTROMAGNETIC TRANSFORMATION OF CELLS | 06-16-2016 |
20160177293 | MODIFIED PEPTIDE DISPLAY | 06-23-2016 |
20160177374 | Integrated Capture and Amplification of Target Nucleic Acid for Sequencing | 06-23-2016 |
20160193607 | TRANSPORTABLE COMPOSITE LIQUID CELLS | 07-07-2016 |
20160194695 | NUCLEIC ACID AMPLIFICATION METHOD USING ALLELE-SPECIFIC REACTIVE PRIMER | 07-07-2016 |
20160201105 | STEP-UP METHOD FOR COLD-PCR ENRICHMENT | 07-14-2016 |
20160251700 | NUCLEIC ACID SAMPLE PREPARATION | 09-01-2016 |
20160376584 | METHOD AND APPARATUS FOR DUAL SOLID PHASE NUCLEIC ACID SYNTHESIS - Provided herein are methods and apparatuses for synthesizing nucleic acids having a predefined sequence through enzymatic elongation. In some embodiments, the methods and/or apparatuses comprise controlled manipulation of solid objects with respect to a solid substrate comprising an oligonucleotide template array. | 12-29-2016 |
20170233722 | COMBINATORIAL PHOTO-CONTROLLED SPATIAL SEQUENCING AND LABELING | 08-17-2017 |
20170233725 | Scavenger Compounds for Improved Sequencing-by-Synthesis | 08-17-2017 |
20170233728 | LINKER ELEMENT AND METHOD OF USING SAME TO CONSTRUCT SEQUENCING LIBRARY | 08-17-2017 |
20180023089 | Methods for Dynamic Vector Assembly of DNA Cloning Vector Plasmids | 01-25-2018 |
20180023112 | HIGH RESOLUTION SYSTEMS, KITS, APPARATUS, AND METHODS USING MAGNETIC BEADS FOR HIGH THROUGHPUT MICROBIOLOGY APPLICATIONS | 01-25-2018 |
20180023131 | METHODS TO AMPLIFY HIGHLY UNIFORM AND LESS ERROR PRONE NUCLEIC ACID LIBRARIES | 01-25-2018 |
20190144855 | FOCUSED ACOUSTICS MEDIATED NUCLEIC ACID LIGATION | 05-16-2019 |