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Biochemical method (e.g., using an enzyme or whole viable micro-organism, etc.)

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506 - Combinatorial chemistry technology: method, library, apparatus

506023000 - METHOD OF CREATING A LIBRARY (E.G., COMBINATORIAL SYNTHESIS, ETC.)

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DocumentTitleDate
20090005268Compositions 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
20100120635SAMPLE 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
20110201526BEAD 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
20130029882Nucleic 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
20130029881SELECTIVE 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
20130029880METHODS 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
20120172258NUCLEIC 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
20120184466PARTHENOGENIC 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 O07-19-2012
20130079251Systems 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
20130040863SOLID-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
20100105576Three 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
20130090267TEMPERATURE 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
20130059761Assembly 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
20130059762METHODS 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
20130065795ARRAY 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
20090011958PROCESS 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
20090011957Ligational 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
20120270754Iterative 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
20100273680METHOD 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
20090275486NUCLEIC 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
20090099040DEGENERATE 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
20090099041METHODS 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
20090149349RECOMBINANT 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
20100009872Single 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
20100009871DEVICES 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
20100273679METHODS 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
20110172127Methods 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
20090170727METHODS 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
20110207631METHOD 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
20080287321cDNA 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
20120295819METHODS 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
20090264319Method 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
20090264320Methods 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
20080261833METHODS 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
20110269647METHOD - 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
20090137427Method 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
20110224105METHODS, 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
20110224104METHOD 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
20090023603Methods 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
20090062147Methods 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
20110143964FLUIDIC 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
20090082225NUCLEIC 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
20120077716SYSTEM 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
20090105094Error-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
20090253591METHODS 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
20110059869Method 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
20100298170METHODS 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
20100305004POLYNUCLEOTIDE 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
20100305005High-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
20130137605SEQUENCE 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
20090036325Directed 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
20100222237Methods 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
20110034350Protein 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
20110118149Synthetic 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
20090312199TRACE 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
20100016178METHODS 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
20100069263SEQUENCE 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
20110098200Methods 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
20080269074Methods, 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
20100331216CELL 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
20090203551Methods 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
20090082226Gene 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
20080242560METHODS 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
20080214411Eukaryotic 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
20110257045METHOD 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
20110136697METHODS 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
20120208724LINKING 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
20120302467Patterned 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
20110263462METHODS 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
20100261620Methods of Humanizing and Affinity-Maturing Antibodies - Methods of humanizing and affinity-maturing antibodies are disclosed.10-14-2010
20100227779PLASMID 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
20090099042Reverse 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
20090099043Construction 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
20120040869SEQUENCE 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
20120172259USING 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
20110065610Synthetic 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
20120040870Method 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 N02-16-2012
20090275485Reversible 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
20120040871OLIGONUCLEOTIDE 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
20090156431Methods 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
20110319299METHODS 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
20110319298Differential 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
20120004142METHOD 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
20120252702PROCESSING 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
20100029511CDNA 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
20120122737METHODS 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
20120071359PURIFIED 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
20120071360ALKALINE 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
20120071358Fluidic 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
20110092391PHAGE 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
20090131279NUCLEIC 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
20120129731Design 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
20120316086PATTERNED 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
20130172216Arrays 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
20120190587Global 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
20090018033Cell 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
20120264653Methods 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
20120270755METHOD 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
20120322692LOADING 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
20110230374HIGH 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
20120088695Method 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
20120329679EUKARYOTIC 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
20120149602METHOD 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
20130017978METHODS 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
20080227661Mutant 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
20080234142Random 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
20100087336FUNCTIONAL 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
20100069264Libraries 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
20120252701METHODS 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
20130096034MICROFABRICATION 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
20130096033METHODS 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
20130130940MULTI-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
20130143773HIGH-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
20110224106Production 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
20110275543DEVICE 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
20120283145Methods 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
20120283144Ligation 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
20130184185METHODS 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
20110312614METHODS 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
20120028843Methods 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
20130203635NUCLEIC 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
20130203634INTEGRATED 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
20120094875PRODUCTION 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
20130210680SYSTEMS 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
20130210681Direct 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

Patent applications in class Biochemical method (e.g., using an enzyme or whole viable micro-organism, etc.)