Involving A Ligase (6.) Patents (Class 435/91.52)
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Publication number: 20130023011Abstract: 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.Type: ApplicationFiled: September 14, 2012Publication date: January 24, 2013Applicant: LIFE TECHNOLOGIES CORPORATIONInventors: John LEAMON, Mark ANDERSEN, Michael THORNTON
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Publication number: 20130005581Abstract: Disclosed is a composition comprising the nucleic acid and a chemical compound, said composition forming a star structure defining 3 or more stems extending from a reaction center. The stems are formed by a nucleic acid duplex and the chemical compound has been formed in the reaction center as the reaction product of 3 or more chemical groups. The advantage of the composition is that a close proximity is provided between the chemical groups in the reaction center, thereby promoting a reaction. The invention also relates to a method for preparation of the composition. The advantage of the method is that it does not require the pre-synthesis of a large number of templates and that it is not dependent upon codon/anti-codon recognition for an encoded molecule to be formed.Type: ApplicationFiled: May 17, 2012Publication date: January 3, 2013Applicant: VIPERGEN APSInventors: Nils Jokob Vest Hansen, Peter Blakskjaer, Margit Haahr Hansen, Lars Kolster Petersen, Tara Renee Heitner
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Publication number: 20120329054Abstract: A capture probe suitable for use with a method for isolating miRNAs. A method for isolating an miRNA of interest from a sample comprising the miRNA of interest comprising providing the capture probe. A method for identifying an miRNA of interest.Type: ApplicationFiled: August 29, 2012Publication date: December 27, 2012Applicant: BIOVENTURES, INC.Inventors: Elliott P. Dawson, Kristie E. Womble
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Publication number: 20120322666Abstract: Compositions, methods and systems are provided for the isolation of polymerase-nucleic acid complexes. Complexes can be separated from free enzyme by using hook molecules to target single stranded regions on the nucleic acid. Active complexes can be isolated from mixtures having both active and inactive complexes by initiating nucleic acid synthesis so as to open up a portion of a double stranded region rendering that region single stranded. Hook molecules are targeted to bind the sequences that are thus exposed. The hook molecules bound to active polymerase-nucleic acid complex are isolated, and the active polymerase-nucleic acid complexes released.Type: ApplicationFiled: March 22, 2012Publication date: December 20, 2012Applicant: Pacific Biosciences of California, Inc.Inventors: Thang Pham, Arunashree Bhamidipati, Kevin Travers, Eric Olivares, Tyson A. Clark, Jonas Korlach
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Publication number: 20120283145Abstract: 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.Type: ApplicationFiled: June 7, 2012Publication date: November 8, 2012Inventor: Yan Wang
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Publication number: 20120283144Abstract: 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.Type: ApplicationFiled: May 4, 2012Publication date: November 8, 2012Applicant: NEW ENGLAND BIOLABS, INC.Inventors: Rebecca Kucera, Thomas C. Evans, JR.
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Patent number: 8298768Abstract: Methods are provided for efficient shotgun sequencing to allow efficient selection and sequencing of nucleic acids of interest contained in a library. The nucleic acids of interest can be defined any time before or after preparation of the library. One example of nucleic acids of interest is missing or low confidence genome sequences resulting from an initial sequencing procedure. Other nucleic acids of interest include subsets of genomic DNA, RNA or cDNAs (exons, genes, gene sets, transciptomes). By designing an efficient (simple to implement, speedy, high specificity, low cost) selection procedure, a more complete sequence is achieved with less effort than by using highly redundant shotgun sequencing in an initial sequencing procedure.Type: GrantFiled: December 1, 2008Date of Patent: October 30, 2012Assignee: Complete Genomics, Inc.Inventors: Radoje Drmanac, Clifford Reid
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Publication number: 20120270754Abstract: 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.Type: ApplicationFiled: September 30, 2011Publication date: October 25, 2012Applicant: Westend Asset Clearinghouse Company, LLCInventor: William J. Blake
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Publication number: 20120270273Abstract: Provided herein are compositions, kits and methods useful in the construction of designer transcription activator-like effector (dTALE) polypeptides.Type: ApplicationFiled: January 19, 2012Publication date: October 25, 2012Applicant: PRESIDENT AND FELLOWS OF HARVARD COLLEGEInventors: Feng Zhang, Le Cong, Sriram Kosuri, George M. Church
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Publication number: 20120266328Abstract: The invention is directed to polypeptides having any cellulolytic activity, e.g., a cellulase activity, e.g., endoglucanase, cellobiohydrolase, beta-glucosidase, xylanase, mannanse, ?-xylosidase, arabinofuranosidase, and/or oligomerase activity, including thermostable and thermotolerant activity, and polynucleotides encoding these enzymes, and making and using these polynucleotides and polypeptides. The polypeptides of the invention can be used in a variety of pharmaceutical, agricultural, food and feed processing and industrial contexts. The invention also provides compositions or products of manufacture comprising mixtures of enzymes comprising at least one enzyme of this invention.Type: ApplicationFiled: January 20, 2012Publication date: October 18, 2012Applicant: BP CORPORATION NORTH AMERICA INC.Inventors: KEVIN A. GRAY, LISHAN ZHAO, MICHELLE H. CAYOUETTE
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Patent number: 8288103Abstract: The invention is directed to a variety of multiplexing methods used to amplify and/or genotype a variety of samples simultaneously.Type: GrantFiled: May 28, 2010Date of Patent: October 16, 2012Assignee: Illumina, Inc.Inventors: Arnold Oliphant, John R. Stuelpnagel, Mark S. Chee, Scott L. Butler, Jian-Bing Fan, Min-Jui Richard Shen
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Publication number: 20120258487Abstract: This invention provides methods and compositions for assembling biological constructs (e.g., plasmids, transformed cells, etc.). In certain embodiments the methods involve encapsulating separate components of said biological construct each in a fluid droplet confined in a fluid channel; optionally mixing droplets from different fluid channels to for a sequenced order of droplets carrying different components of said biological construct in a channel or chamber; and optionally combining two or more droplets each containing different components of said biological construct to permit said components to react with each other in one or more reactions contributing to the assembly of said biological construct.Type: ApplicationFiled: April 2, 2012Publication date: October 11, 2012Applicants: THE REGENTS OF THE UNIVERSITY OF CALIFORNIA, SANDIA CORPORATIONInventors: Chieh Chang, Rajiv Bharadwaj, Anup K. Singh, Aarthi Chandrasekaran, Nathan J. Hillson
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Publication number: 20120245040Abstract: The present invention provides a method of synthesizing libraries of molecules which include an encoding oligonucleotide tag.Type: ApplicationFiled: March 4, 2011Publication date: September 27, 2012Applicant: GlaxoSmithKlineInventors: Barry Morgan, Stephen Hale, Christopher C. Arico-Muendel, Matthew Clark, Richard Wagner, David I. Israel, Malcolm L. Gefter, Dennis Benjamin, Nils Jakob Vest Hansen, Malcolm J. Kavarana, Steffen Phillip Creaser, George J. Franklin, Paolo A. Centrella, Raksha A. Acharya
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Publication number: 20120244525Abstract: Compositions are provided that include a synthetic oligonucleotide characterized by a double-stranded region, a single-stranded region, a forward primer site, a reverse primer site and one or more cleavage sites therebetween. Methods of use for these compositions include adapters for the amplification of DNA fragments.Type: ApplicationFiled: June 5, 2012Publication date: September 27, 2012Applicant: NEW ENGLAND BIOLABS, INC.Inventor: Cynthia Hendrickson
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Publication number: 20120238738Abstract: Compositions are provided that include a synthetic oligonucleotide characterized by a double-stranded region, a single-stranded region, a forward primer site, a reverse primer site and one or more cleavage sites therebetween. Methods of use for these compositions include adaptors for the amplification of DNA fragments.Type: ApplicationFiled: June 13, 2011Publication date: September 20, 2012Applicant: NEW ENGLAND BIOLABS, INC.Inventor: Cynthia Hendrickson
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Patent number: 8263367Abstract: The present invention provides at least one isolated linear composite nucleic acid molecule comprising at least one first tag from at least one first nucleic acid molecule and at least one second tag from at least one second nucleic acid molecule, wherein the first and second nucleic acids interact in a nucleic acid mixture; and wherein the first and second tags are from different nucleic acid molecules. The invention also provides a method of producing at least one isolated linear composite nucleic acid and to a method of detecting and/or identifying nucleic acid interactions.Type: GrantFiled: January 25, 2008Date of Patent: September 11, 2012Assignee: Agency for Science, Technology and ResearchInventors: Yijun Ruan, Chialin Wei, Melissa Jane Fullwood, Jun Liu
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Patent number: 8263332Abstract: A mismatched end DNA ligase is provided, which ligates two single strands to each other at a high efficiency, even if the other two single strands are not compatible. In one embodiment, the polypeptides of the ligase are Ku, Cernunnos, and XRCC4/Ligase4 (XL). This association can ligate DNA ends with a 3? overhang to a recessed 5? end, to a blunt end, or to a compatible end. In another embodiment, the proteins are Ku, Cernunnos, XRCC4/Ligase4 (XL) and DNA-PK.Type: GrantFiled: October 11, 2007Date of Patent: September 11, 2012Assignee: The Board of Trustees of the Leland Stanford Junior UniversityInventors: Chun Tsai, Seonhi Kim, Gilbert Chu
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Publication number: 20120225457Abstract: A nanoparticle-nucleic acid complex and a method of linearizing a target nucleic acid by using the nanoparticle-nucleic acid complex are disclosed. By using the nanoparticle-nucleic acid complex and the method, nucleotide sequence analysis and mapping of a target nucleic acid may be efficiently performed.Type: ApplicationFiled: November 11, 2011Publication date: September 6, 2012Applicants: SNU R&DB FOUNDATION, SAMSUNG ELECTRONICS CO., LTDInventors: June-young LEE, Jwa-min NAM, Su-hyeon KIM, Woo-chang LEE, Jae-young KIM, Joo-won RHEE, Young-kwang LEE, Dong-kwon LIM, Jae-ho HWANG
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Publication number: 20120214208Abstract: The invention relates to fusion polypeptides comprising a polynucleotide-binding domain, such as a DNA-binding domain, and a ligase domain, such as a DNA ligase domain, methods for the production of such fusion polypeptides, and uses of the fusion polypeptides, for example in a range of molecular biological techniques as well as applications in the diagnostics, protein production, pharmaceutical, nutraceutical and medical fields.Type: ApplicationFiled: September 16, 2010Publication date: August 23, 2012Applicant: MASSEY UNIVERSITYInventors: Wayne Michael Patrick, Robert Henry Wilson
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Patent number: 8236499Abstract: Provided are methods and compositions for the production of linear single-stranded nucleic acids, which can be used as templates in high-throughput sequencing systems. Also provided are methods and compositions for the production of closed single-stranded nucleic acid loops, which can be used as templates in high-throughput sequencing systems.Type: GrantFiled: March 27, 2009Date of Patent: August 7, 2012Assignee: Pacific Biosciences of California, Inc.Inventors: Pranav Patel, Keith Bjornson, Kevin Travers, Cheryl Heiner
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Publication number: 20120196279Abstract: Provided are methods and compositions for the production of double-stranded nucleic acids, which can optionally be used as templates in high-throughput sequencing systems. In certain embodiments, these templates do not require exogenous primers to facilitate initiation of polymerase-dependent nascent strand synthesis. In certain embodiments, these templates comprise a single-stranded or gapped region that serves as a polymerase priming site.Type: ApplicationFiled: January 31, 2012Publication date: August 2, 2012Applicant: Pacific Biosciences of California, Inc.Inventors: Jason Underwood, Swati Ranade, Yu-Chih Tsai
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Publication number: 20120183961Abstract: Methods and kits are provided for testing the functional effect of methylating different cytosine residues or testing patterns of DNA methylation on gene expression. Methods are also provided for site-specific methylation, as well as methylated DNA constructs.Type: ApplicationFiled: January 13, 2012Publication date: July 19, 2012Inventors: WEIGUO HAN, Simon D. Spivack, Miao Kevin Shi
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Patent number: 8222005Abstract: An isolated oligonucleotide comprising at least one ditag, wherein the ditag comprises two joined first and second sequence tags, wherein the first tag comprises the 5?-terminus sequence and the second tag comprises the 3?-terminus sequence of a nucleic acid molecule or a fragment thereof. The ditag analysis is useful for gene discovery and genome mapping.Type: GrantFiled: September 17, 2003Date of Patent: July 17, 2012Assignee: Agency for Science, Technology and ResearchInventors: Yijun Ruan, Patrick Ng, Chialin Wei
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Publication number: 20120178131Abstract: Materials and methods related to gene targeting (e.g., gene targeting with transcription activator-like effector nucleases; “TALENS”) are provided.Type: ApplicationFiled: March 22, 2012Publication date: July 12, 2012Inventors: Daniel F. Voytas, Adam J. Bogdanove, Feng Zhang
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Publication number: 20120164693Abstract: Methods for discriminating between fully complementary hybrids and those that differ by one or more base pairs and libraries of unimolecular, double-stranded oligonucleotides on a solid support. In one embodiment, the present invention provides methods of using nuclease treatment to improve the quality of hybridization signals on high density oligonucleotide arrays. In another embodiment, the present invention provides methods of using ligation reactions to improve the quality of hybridization signals on high density oligonucleotide arrays. In yet another embodiment, the present invention provides libraries of unimolecular or intermolecular, double-stranded oligonucleotides on a solid support. These libraries are useful in pharmaceutical discovery for the screening of numerous biological samples for specific interactions between the double-stranded oligonucleotides, and peptides, proteins, drugs and RNA.Type: ApplicationFiled: December 4, 2007Publication date: June 28, 2012Applicant: Affymetrix, INC.Inventors: David J. Lockhart, Mark S. Chee, Dirk Vetter, Martin Digglemann
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Publication number: 20120156731Abstract: Disclosed are methods and materials for assembling long polynucleotides from synthetic oligonucleotides. The use of synthetic oligonucleotides permits non-natural design of sequences. The oligonucleotides used for construction may be relatively short, according to practicalities of nucleotide synthesis. They are assembled using a ligase which is operative over a range of temperatures, i.e., is thermostable. The method and oligonucleotides are designed such that the melting temperature of the strands to be hybridized is set at a number of selected specific temperatures for each group of oligonucleotides to be hybridized and ligated. Hybridization and ligation take place at or near the melting temperature, so that each succeeding ligation is governed by a temperature that will prevent hybridization if any mismatches are present.Type: ApplicationFiled: March 20, 2008Publication date: June 21, 2012Applicant: The Board of Trustees of the Leland Stanford Junior UniversityInventors: Yanyi Huang, James Berger, Stephen Quake
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Publication number: 20120142060Abstract: 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.Type: ApplicationFiled: November 1, 2011Publication date: June 7, 2012Applicant: Rubicon Genomics, Inc.Inventors: VLADIMIR L. MAKAROV, Emmanuel Kamberov, Brendan J. Tarrier
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Publication number: 20120107806Abstract: Methods and kits for DNA repair are provided. The methods and kits described herein repair multiple types of DNA damage. The kit may include a plurality of enzymes to repair a greater variety of lesions than any single enzyme is capable of repairing. Repair of damaged DNA may include releasing damaged bases from the DNA strand, nicking the DNA at the damaged sites, translating the nicks via 5?-3? exonuclease activity, and sealing the nicks. The enzymes employed in the repair process may then be heat-inactivated, thereby obviating a purification process. The repaired DNA may then be analyzed using a variety of DNA analysis methods.Type: ApplicationFiled: January 5, 2012Publication date: May 3, 2012Applicant: General Electric CompanyInventors: John Richard Nelson, Wei Gao
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Publication number: 20120088235Abstract: Nucleic acid sequencing methods and related products and methods for detection and presentation of the same are disclosed. Methods for sequencing a target nucleic acid comprise providing a daughter strand produced by a template-directed synthesis, the daughter strand comprising a plurality of subunits coupled in a sequence corresponding to a contiguous nucleotide sequence of all or a portion of the target nucleic acid.Type: ApplicationFiled: January 29, 2010Publication date: April 12, 2012Applicant: STRATOS GENOMICS, INC.Inventors: Mark Stamatios Kokoris, Robert N. McRuer
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Publication number: 20120070862Abstract: Disclosed herein are uniquely distinct nucleic acid tags and methods for their use and production. The disclosed tags do not hybridize to a genome of interest and thus can be used as labels without generating background signal associated with unintended hybridization. In one example, tag sequences are derived from a genome divergent to the genome of interest. The divergent genome provides a vast library of potential tag sequences. These potential tag sequences can be screened using a bioinformatics-based approach against the genome of interest. These potentially distinct sequences can then be synthesized and tested empirically against the genome of interest to identify those sequences that are uniquely distinct. The tags can then be produced, for example by oligonucleotide synthesis techniques.Type: ApplicationFiled: November 4, 2011Publication date: March 22, 2012Inventors: Nelson Alexander, Stacey Stanislaw
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Publication number: 20120058521Abstract: Methods and compositions for making and using pre-adenylated oligonucleotide sequences are provided.Type: ApplicationFiled: November 2, 2011Publication date: March 8, 2012Applicant: President and Fellows of Harvard CollegeInventors: George M. Church, François Vigneault, A. Michael Sismour
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Publication number: 20120053087Abstract: The present invention relates to methods of joining two or more double-stranded (ds) or single-stranded (ss) DNA molecules of interest in vitro, wherein the distal region of the first DNA molecule and the proximal region of the second DNA molecule of each pair share a region of sequence identity. The method allows the joining of a large number of DNA fragments, in a predetermined order and orientation, without the use of restriction enzymes. It can be used, e.g., to join synthetically produced sub-fragments of a gene or genome of interest. Kits for performing the method are also disclosed. The methods of joining DNA molecules may be used to generate combinatorial libraries useful to generate, for example, optimal protein expression through codon optimization, gene optimization, and pathway optimization.Type: ApplicationFiled: February 25, 2011Publication date: March 1, 2012Applicant: Synthetic Genomics, Inc.Inventors: Daniel G. Gibson, Hamilton O. Smith, Clyde A. Hutchison, Lei Young, J. Craig Venter
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Publication number: 20120040870Abstract: 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 Nn+1, in which N represents a nucleic acid sequence and where n is 1 or greater than 1 and each N may be the same or a different nucleic acid sequence, in which the method comprises: (i) providing a first nucleic acid sequence N1 which has an oligonucleotide linker sequence L13 at the 3?-end of the nucleic acid sequence; (ii) providing a second nucleic acid sequence N2 which optionally has an oligonucleotide linker sequence L23? at the 3?-end of the nucleic acid sequence and which has an oligonucleotide linker sequence L25? at the 5?-end of the nucleic acid sequence, wherein the 5?-end linker sequence L25? of nucleic acid sequence N2 is complementary to the 3?-end linker sequence L13? of nucleic acid sequence N1; (iii) optionally providing one or more additional nucleic acid sequences N, wherein nucleic acid sequence N2 has anType: ApplicationFiled: December 18, 2009Publication date: February 16, 2012Applicant: ITI SCOTLAND LIMITEDInventors: Austin Che, Tom Knight, Barry Canton, Jason Kelly, Reshma Shetty
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Patent number: 8114596Abstract: The described method provides, methods, and kits to produce, identify, catalog and classify a comprehensive collection of nucleic acid targets produced from a nucleic acid sample. The method, referred to as Cataloging and Classification of Sequence Tags, involves generating a set of target nucleic acid fragments; coupling the target nucleic acid fragments to a nucleic acid bridge comprising, for example, two or more primer binding sites and two recognition sites for cleavage at a site offset from the recognition site to the fragment's end; and cleaving the fragments to generate chimeric nucleic acids of known length. The nucleic acid bridge is thus disposed between the two nucleic acid fragments in the chimeric nucleic acid. The resulting duplex nucleic acids comprise a set of sequence tags (i.e., by amplification using universal primers), comprising an addressable portion, a target nucleic portion and a portion of the nucleic acid bridge.Type: GrantFiled: October 9, 2009Date of Patent: February 14, 2012Inventor: Joseph C. Kaufman
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Publication number: 20120028313Abstract: The present invention relates to a linker or population of linkers that include an oligonucleotide fixed portion and an oligonucleotide variable portion represented by formula (N)n, wherein N is A, C, G, T or U, or their derivatives, and n is an integer equal to or higher than 1. A linker-polynucleotide or a population of linker-polynucleotides of the invention may be constituted by said linker or population of linkers and a target first strand polynucleotide bound to said linker. The invention also encompasses a method of preparing said linker or population of linkers and a method of preparing a linker-polynucleotide using said linker or population of linkers. The linkers or polynucleotide-linkers of the invention can be used in a method of preparing a cDNA library.Type: ApplicationFiled: October 4, 2010Publication date: February 2, 2012Applicant: RIKENInventor: Yoshihide Hayashizaki
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Publication number: 20120003699Abstract: Methods of separating tagged nucleic acid fragments from populations of fragments are provided. The fragments are produced from a population of tagged nucleic acids. In some cases, the population of tagged nucleic acids comprises a population of clonal nucleic acids.Type: ApplicationFiled: June 29, 2011Publication date: January 5, 2012Applicant: Pacific Biosciences of CaliforniaInventors: Cheryl Heiner, Stephen Turner, Kevin Travers
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Publication number: 20110318821Abstract: The present invention relates the use of broad range primer (e.g., as broad range capture olignucleotides) immobilized in a SCODA method gel to allow, for example, selective concentration of target nucleic acids. Such concentrated target nucleic acids may, for example, be: i) eluted from the gel and analyzed (e.g., by broad range primer methods); ii) subject to in situ (e.g., in gel) PCR methods; and/or iii) analyzed in the gel (e.g., by fluorescent detection methods).Type: ApplicationFiled: March 8, 2010Publication date: December 29, 2011Applicant: IBIS BIOSCIENCES INC.Inventor: Steven A. Hofstadler
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Publication number: 20110318789Abstract: The present invention relates to the cloning and characterisation of a prokaryotic DNA repair ligase, which is shown to possess a range of activities that allow the ligation and repair of non-compatible DNA ends and double strand breaks (DSBs). The enzyme has a range of applications in the manipulation and cloning of nucleic acids.Type: ApplicationFiled: September 6, 2011Publication date: December 29, 2011Inventors: Aidan Doherty, Marina Della, Geoffrey Weller, Stephen Jackson
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Publication number: 20110312507Abstract: A novel reaction discovery system that does not depend on DNA duplex formation is provided. The advantages of this system include exploring reactions conditions not possible where DNA hybridization is required. For example, the inventive reaction discovery system allows for reaction conditions using organic solvents, higher temperatures, and water-insoluble reagents, catalysts, and ligands. The invention also provides single-stranded oligonucleotide templates with substrate pairs covalently attached and methods of screening for reaction conditions that result in a direct covalent bond between the substrates. Kits are also provided for practicing this novel reaction discovery system.Type: ApplicationFiled: January 9, 2008Publication date: December 22, 2011Applicant: President and Fellows of Harvard CollegeInventors: David R. Liu, Matthew William Kanan, Mary M. Rozenman
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Publication number: 20110306653Abstract: This invention is intended to enhance and improve the resistance of a single- or double-stranded nucleic acid fragment comprising a base sequence of a functional nucleic acid to degradation by nucleolytic enzymes in a simple and cost-effective manner. The single- or double-stranded nucleic acid fragment comprises, ligated to at least one end thereof, hairpin-shaped DNA comprising: (A) a nucleic acid region comprising 2 to 5 arbitrary nucleotides; (B) a nucleic acid region comprising a “gna” or “gnna” base sequence, wherein each “n” represents “g”, “t”, “a”, or “c”, a base analogue, or a modified base; and (C) a nucleic acid region comprising a base sequence complementary to the nucleic acid region (A), sequentially from the 5? end toward the 3? end.Type: ApplicationFiled: May 13, 2011Publication date: December 15, 2011Applicants: TAGCYX BIOTECHNOLOGIES, RIKENInventors: Ichiro HIRAO, Michiko HIRAO, Shuang LIU, Iwao NOZAWA
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Publication number: 20110306098Abstract: The present invention relates generally to recombinant genetic technology. More particularly, the present invention relates to compositions and methods for use in selection and isolation of nucleic acid molecules. The invention further relates to methods for the preparation of individual nucleic acid molecules and populations of nucleic acid molecules, as well as nucleic acid molecules produced by these methods. The invention also relates to screening and/or selection methods for identifying and/or isolating nucleic acid molecules which have one or more common features (e.g., characteristics, activities, etc) and populations of nucleic acid molecules which share one or more features.Type: ApplicationFiled: May 5, 2011Publication date: December 15, 2011Applicant: Invitrogen CorporationInventors: Michael A. Brasch, David Cheo, Xiao Li, Dominic Esposito, Devon R.N. Byrd
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Patent number: 8067556Abstract: The present invention provides compositions and improved methods for multi-site directed mutagenesis and DNA shuffling. The present compositions and methods provide increased mutation frequency and increased number of transformants which allow one to sequence only a few clones in order to identify the correct mutants and to obtain the desired mutant by screening large number of transformants in a short time. Moreover, the inclusion of FEN-1, PEF and optimized buffer and cycling conditions provided in the present invention should also facilitate random mutagenized library construction and the mutagenesis of large or difficult templates.Type: GrantFiled: July 18, 2002Date of Patent: November 29, 2011Assignee: Agilent Technologies, Inc.Inventors: Holly H. Hogrefe, Janice M. Cline
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Publication number: 20110288147Abstract: The invention features compositions and methods that are useful for reducing the expression or activity of a specified gene in a eukaryotic cell.Type: ApplicationFiled: September 17, 2009Publication date: November 24, 2011Inventor: Bob Dale Brown
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Publication number: 20110287492Abstract: The present invention relates to a method for the reduction of repetitive sequences (or the improvement in low-copy sequences) in DNA samples by a combination of restriction endonuclease treatment, followed by adapter ligation, renaturation kinetics-based fractionation, optionally coupled with duplex sequence nucleases and further restriction endonuclease treatment, followed by adapter ligation. The low-copy enriched fractions can be used in further DNA analysis.Type: ApplicationFiled: November 25, 2009Publication date: November 24, 2011Inventors: Daniele Trebbi, Michael Josephus Theresia van Eijk
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Publication number: 20110251089Abstract: The present invention provides a method of synthesizing libraries of molecules which include an encoding oligonucleotide tag.Type: ApplicationFiled: March 18, 2011Publication date: October 13, 2011Applicant: GlaxoSmithKlineInventors: Barry Morgan, Stephen Hale, Christopher C. Arico-Muendel, Matthew Clark, Richard Wagner, David I. Israel, Malcolm L. Gefter, Dennis Benjamin, Nils Jakob Vest Hansen, Malcolm J. Kavarana, Steffen Phillip Creaser, George J. Franklin, Paolo A. Centrella, Raksha A. Acharya
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Patent number: 8034587Abstract: The present invention relates to the cloning and characterization of a prokaryotic DNA repair ligase, which is shown to possess a range of activities that allow the ligation and repair of non-compatible DNA ends and double strand breaks (DSBs). The enzyme has a range of applications in the manipulation and cloning of nucleic acids.Type: GrantFiled: August 2, 2004Date of Patent: October 11, 2011Assignee: Cambridge Enterprise LimitedInventors: Aidan Doherty, Marina Della, Geoffrey Weller, Stephen Jackson
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Publication number: 20110224106Abstract: 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.Type: ApplicationFiled: March 9, 2011Publication date: September 15, 2011Applicant: Ibis Biosciences, Inc.Inventors: Mark W. Eshoo, John Picuri
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Patent number: 8013134Abstract: The present invention relates to sensitive, rapid and convenient assays for detection and or quantification of one or more analyte(s) in solution using multivalent proximity probes. The proximity probes each comprise several binding moieties, such as antibodies, and associated nucleic acid(s). When the binding moieties have bound to their analyte(s), the nucleic acids on opposite proximity probes interact with each other and a signal is generated based on this interaction. The multivalent proximity probes are especially valuable for highly sensitive and specific protein detection.Type: GrantFiled: November 22, 2002Date of Patent: September 6, 2011Assignee: Olink ABInventor: Simon Fredriksson
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Patent number: 8003357Abstract: The present invention relates to enzymes having catalytic activity at a pH below 5.0. The present invention provides hydrolyzing enzymes obtainable from archaeobacteria, in detail to hydrolytic enzymes obtainable from the archaeobacterium Ferroplasma acidiphilum. In general, the present invention provides enzymes which are active and stable at acidic pH values, especially at pH values from 1 to 4, especially in the range of pH 2 to 3, obtainable from Ferroplasma acidiphilum, especially to an esterase, glycosidases and a DNA ligase. In addition to stability and activity at low pH values, the enzymes according to the present invention are all dependent on Fe2+ for their catalytic activity.Type: GrantFiled: March 3, 2006Date of Patent: August 23, 2011Assignee: Helmholtz-Zentrum Fuer Infektionsforschung GmbHInventors: Olga Golyshina, Peter Golyshin, Kenneth Timmis, Manuel Ferrer
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Patent number: RE43097Abstract: The invention provides a method of nucleic acid sequence analysis based on the ligation of one or more sets of encoded adaptors to the terminus of a target polynucleotide. Encoded adaptors whose protruding strands form perfectly matched duplexes with the complementary protruding strands of the target polynucleotide are ligated, and the identity of the nucleotides in the protruding strands is determined by an oligonucleotide tag carried by the encoded adaptor. Such determination, or “decoding” is carried out by specifically hybridizing a labeled tag complement to its corresponding tag on the ligated adaptor.Type: GrantFiled: May 18, 2010Date of Patent: January 10, 2012Assignee: Illumina, Inc.Inventors: Glenn Albrecht, Sydney Brenner, Robert B. DuBridge, David H. Lloyd, Michael C. Pallas