Acellular Preparation Of Polynucleotide Patents (Class 435/91.5)
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Patent number: 11850258Abstract: This invention claims ribonucleosides and their derivatives, including triphosphates, that have a 3?-ONH2 moiety instead of a 3?-OH moiety.Type: GrantFiled: May 29, 2020Date of Patent: December 26, 2023Inventors: Nilesh B. Karalkar, Steven A. Benner
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Patent number: 11479806Abstract: Methods of producing an amplified double stranded deoxyribonucleic acid (dsDNA) from a nucleic acid sample are provided. Aspects of the methods include amplifying using a single product nucleic acid primer and a template switch oligonucleotide to produce an amplified dsDNA product. Compositions and kits for use in performing the methods are also provided.Type: GrantFiled: November 8, 2017Date of Patent: October 25, 2022Assignee: Takara Bio USA, Inc.Inventors: Kazuo Tori, Magnolia Bostick, Andrew Farmer
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Patent number: 11261439Abstract: A nucleic acid construct is provided that encodes two or more or a plurality of spacer sequences separated by restriction endonuclease recognition site. A plurality of such nucleic acid sequences are provided as a library for making guide RNAs for use with CRISPR/Cas systems.Type: GrantFiled: September 16, 2016Date of Patent: March 1, 2022Assignee: President and Fellows of Harvard CollegeInventors: Alejandro Chavez, Johnny Hao Hu
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Patent number: 11198905Abstract: The present disclosure provides methods for determining the ploidy status of a chromosome in a gestating fetus from genotypic data measured from a mixed sample of DNA comprising DNA from both the mother of the fetus and from the fetus, and optionally from genotypic data from the mother and father. The ploidy state is determined by using a joint distribution model to create a plurality of expected allele distributions for different possible fetal ploidy states given the parental genotypic data, and comparing the expected allelic distributions to the pattern of measured allelic distributions measured in the mixed sample, and choosing the ploidy state whose expected allelic distribution pattern most closely matches the observed allelic distribution pattern. The mixed sample of DNA may be preferentially enriched at a plurality of polymorphic loci in a way that minimizes the allelic bias, for example using massively multiplexed targeted PCR.Type: GrantFiled: February 20, 2020Date of Patent: December 14, 2021Assignee: Natera, Inc.Inventors: Matthew Rabinowitz, George Gemelos, Milena Banjevic, Allison Ryan, Zachary Demko, Matthew Hill, Bernhard Zimmermann, Johan Baner, Styrmir Sigurjonsson
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Patent number: 10934583Abstract: Sequencing methods, devices, and systems are described. Arrays of nanoscale electronic elements comprising two electrodes separated by an insulating layer are used to provide sequence information about a template nucleic acid in a polymerase-template complex bound proximate to the insulating region. A sequencing reaction mixture comprising nucleotide analogs having impedance labels is introduced to the array of nanoscale electronic elements under conditions of polymerase mediated nucleic acid synthesis. The time sequence of incorporation of nucleotide analogs is determined by identifying the types of labels of the nucleotide analogs that are incorporated into the growing strand using measured impedance.Type: GrantFiled: December 8, 2017Date of Patent: March 2, 2021Assignee: Pacific Biosciences of California, Inc.Inventors: Stephen Turner, Jeremiah Hanes, Keith Bjornson
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Patent number: 10837909Abstract: [Problem] To provide a novel fluorescent probe for super-resolution imaging that uses fluorescent light emission characteristics that originate from an intermolecular nucleophilic addition-dissociation equilibrium reaction, and to provide a super-resolution fluorescent imaging method that uses the probe.Type: GrantFiled: February 23, 2016Date of Patent: November 17, 2020Assignee: The University of TokyoInventors: Yasuteru Urano, Mako Kamiya, Akihiko Morozumi, Shinnosuke Uno, Keitaro Umezawa
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Patent number: 10597648Abstract: The present disclosure provides engineered Class 1 Type I CRISPR-Cas (Cascade) systems that comprise multi-protein effector complexes, nucleoprotein complexes comprising Type I CRISPR-Cas subunit proteins and nucleic acid guides, polynucleotides encoding Type I CRISPR-Cas subunit proteins, and guide polynucleotides. Also, disclosed are methods for making and using the engineered Class 1 Type I CRISPR-Cas systems of the present invention.Type: GrantFiled: October 28, 2019Date of Patent: March 24, 2020Assignee: Caribou Biosciences, Inc.Inventors: Peter Sean Cameron, Sanne Eveline Klompe, Samuel Henry Sternberg
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Patent number: 10527625Abstract: One or more aqueous, near infrared emitting, high yield, highly photoluminescent, stable quantum dots conjugated to one or more biomarkers specific moieties. The conjugated quantum dots have an enhanced detection sensitivity and selectivity and may be formed using a novel and efficient method for conjugating one or more biomarker specific moieties to the quantum dots. The invention is further directed to a method for using the conjugated quantum dots for cancer detection in the margin of excised tissue.Type: GrantFiled: July 6, 2016Date of Patent: January 7, 2020Assignee: Drexel UniversityInventors: Wei-Heng Shih, Wan Y. Shih, Giang Au, Ari D. Brooks, Vanlila K. Swami
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Patent number: 10457922Abstract: The present disclosure provides engineered Class 1 Type I CRISPR-Cas (Cascade) systems that comprise multi-protein effector complexes, nucleoprotein complexes comprising Type I CRISPR-Cas subunit proteins and nucleic acid guides, polynucleotides encoding Type I CRISPR-Cas subunit proteins, and guide polynucleotides. Also, disclosed are methods for making and using the engineered Class 1 Type I CRISPR-Cas systems of the present invention.Type: GrantFiled: May 22, 2019Date of Patent: October 29, 2019Assignee: Caribou Biosciences, Inc.Inventors: Peter Sean Cameron, Sanne Eveline Klompe, Samuel Henry Sternberg
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Patent number: 10202608Abstract: 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: GrantFiled: September 30, 2011Date of Patent: February 12, 2019Assignee: Gen9, Inc.Inventor: William J. Blake
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Patent number: 9926598Abstract: The present disclosure relates to the field of molecular biology and more specifically to methods for capturing, amplifying and sequencing target polynucleotides on a solid surface.Type: GrantFiled: December 18, 2014Date of Patent: March 27, 2018Assignee: ILLUMINA, INC.Inventors: Hongxia Xu, Alex Aravanis, Shengrong Lin
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Patent number: 9856515Abstract: Provided herein is technology relating to processing and preparing samples and particularly, but not exclusively, to methods, systems, and kits for removing assay inhibitors, e.g., compounds that inhibit polymerase chain reaction, from samples comprising nucleic acids. In particular, the technology is directed toward treating crude sample preparations, such as supernatants from homogenized stool samples, with insoluble polyvinylpyrrolidone (PVP) to form PVP-assay inhibitor complexes, and filtration to separate the PVP-assay inhibitor complexes from the crude sample preparations to produce clarified samples that exhibit reduced assay inhibition.Type: GrantFiled: March 3, 2015Date of Patent: January 2, 2018Assignee: Exact Sciences CorporationInventors: Janelle J. Bruinsma, Hemanth D. Shenoi, Michael J. Domanico, James P. Light, II
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Patent number: 9803208Abstract: The present invention now provides a conditional vector comprising DNA encoding for: (i) an inducible expression cassette comprising an inducible promoter operably linked to a plasmid replication region; and (ii) a selectable marker.Type: GrantFiled: March 28, 2013Date of Patent: October 31, 2017Assignee: THE UNIVERSITY OF NOTTINGHAMInventors: Nigel Peter Minton, Ying Zhang
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Patent number: 9657330Abstract: Provided herein is technology relating to isolating nucleic acids. In particular, the technology relates to methods and kits for extracting multiple DNA targets from human stool samples.Type: GrantFiled: July 10, 2014Date of Patent: May 23, 2017Assignee: Exact Sciences CorporationInventors: Graham P. Lidgard, Janelle J. Bruinsma, Michael J. Domanico, Hemanth Shenoi
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Patent number: 9487829Abstract: Error rates in massively parallel sequencing instruments are generally too high to allow confident identification of rare variants. An approach that can substantially increase the sensitivity of massively parallel sequencing instruments for this purpose, called “Safe-SeqS” for (Safe-Sequencing System) includes (i) assignment of a unique identifier (UID) to each template molecule; (ii) amplification of each uniquely tagged template molecule to create UID-families; and (iii) redundant sequencing of the amplification products. PCR fragments with the same UID are truly mutant (“super-mutants”) if ?95% of them contain the identical mutation. We illustrate the utility of this approach for determining the fidelity of a polymerase, the accuracy of oligonucleotides synthesized in vitro, and the prevalence of mutations in the nuclear and mitochondrial genomes of normal cells.Type: GrantFiled: July 30, 2015Date of Patent: November 8, 2016Assignee: The Johns Hopkins UniversityInventors: Bert Vogelstein, Kenneth W. Kinzler, Nickolas Papadopoulos, Isaac Kinde
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Patent number: 9121046Abstract: Compositions and methods are provided for loop mediated isothermal amplification in which single stranded binding proteins are shown to protect primers from non-specific extension and to stimulate the rate of threshold amplification.Type: GrantFiled: November 7, 2012Date of Patent: September 1, 2015Assignee: New England Biolabs, Inc.Inventors: Nathan Tanner, Thomas C. Evans, Jr.
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Publication number: 20150147785Abstract: The present invention relates to methods for generating a labelled nucleic acid from an RNA comprising a 5? protecting group, said method comprises the steps of obtaining a mixture of template strands of nucleic acids, said mixture comprising said RNA and further potentially other nucleic acids without a 5? protecting group, annealing at least one oligonucleotide primer to the template strand of said RNA and potentially other nucleic acids, and template sequence dependent extending said primer, thereby obtaining a complementary nucleic acid strand annealed to its template strand, or providing the RNA in duplex with a complementary nucleic acid strand annealed to its template strand, and optionally modifying the extension product of said nucleic acids without 5? protecting group either on the 5? end of the template strand or on the 3? end of the complementary strand, or both, and labelling a complementary nucleic acid of a double stranded nucleic acid not modified, wherein therefore the labelled nucleic acid dType: ApplicationFiled: July 10, 2013Publication date: May 28, 2015Inventors: Alexander Seitz, Irmlind Gabler, Lukas Paul
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Publication number: 20150133317Abstract: Disclosed herein are compositions and methods for sequencing, analyzing, and utilizing samples such as single samples. Also disclosed herein are compositions and methods for matching together two or more sequences from a sample. Also disclosed herein are compositions and methods for expressing and screening molecules of interest.Type: ApplicationFiled: April 27, 2012Publication date: May 14, 2015Applicants: Department of Veterans Affairs, The Board of Trustees of the Leland Stanford Junior UniversityInventors: William H. Robinson, Yann Chong Tan, Jeremy Sokolove
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Patent number: 9017973Abstract: The invention provides methods and compositions, including, without limitation, algorithms, computer readable media, computer programs, apparatus, and systems for determining the identity of nucleic acids in nucleotide sequences using, for example, data obtained from sequencing by synthesis methods. The methods of the invention include correcting one or more phenomena that are encountered during nucleotide sequencing, such as using sequencing by synthesis methods. These phenomena include, without limitation, sequence lead, sequence lag, spectral crosstalk, and noise resulting from variations in illumination and/or filter responses.Type: GrantFiled: November 28, 2011Date of Patent: April 28, 2015Assignee: Intelligent BioSystems, Inc.Inventors: Steven Gordon, Jerzy Olejnik
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Patent number: 9005930Abstract: The present invention relates to kits and methods for efficiently generating 5? capped RNA having a modified cap nucleotide and for use of such modified-nucleotide-capped RNA molecules. In particular, the present invention provides kits and methods for capping RNA using a modified cap nucleotide and a capping enzyme system, such as poxvirus capping enzyme. The present invention finds use for in vitro production of 5?-capped RNA having a modified cap nucleotide and for in vitro or in vivo production of polypeptides by in vitro or in vivo translation of such modified-nucleotide-capped RNA. The invention also provides methods and kits for capturing or isolating uncapped RNA comprising primary RNA transcripts or RNA having a 5?-diphosphate, and methods and kits for using a capping enzyme system and modified cap nucleotides for labeling uncapped RNA comprising primary RNA transcripts or RNA having a 5?-diphosphate with detectable dye or enzyme moieties.Type: GrantFiled: August 28, 2014Date of Patent: April 14, 2015Assignee: Cellscript, LLCInventors: Jerome Jendrisak, Ronald Meis, Gary Dahl
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Patent number: 9005935Abstract: The present invention provides new compositions for transposase-mediated fragmenting and tagging DNA targets. The invention relates to the surprising discovery that use of manganese ions (Mn2+) in transposase reactions improves the transposase reaction. It also relates to the surprising discovery that Mg2+ ions can be used in a transposase reaction with wild-type and/or engineered transposases at levels much higher than previously thought. The invention provides for the use of naturally-occurring transposases in in vitro reactions, as well as improved schemes for cleaving, tagging, and amplifying target DNA.Type: GrantFiled: May 11, 2012Date of Patent: April 14, 2015Assignee: Agilent Technologies, Inc.Inventor: Alexander S. Belyaev
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Publication number: 20150094211Abstract: The present disclosure provides compositions, methods, kits, systems and apparatus that are useful for nucleic acid polymerization. In particular, modified polymerases and biologically active fragments thereof are provided that allow for nucleic acid amplification. In some aspects, the disclosure provides modified polymerases having lower systematic error as compared to a reference polymerase. In one aspect, the disclosure relates to modified polymerases useful for nucleic acid sequencing, genotyping, copy number variation analysis, paired-end sequencing and other forms of genetic analysis. In some aspects, the disclosure relates to modified polymerases useful for the generation of nucleic acid libraries or nucleic acid templates. In some aspects, the disclosure relates to the identification of homologous amino acid mutations that can be transferred across classes or families of polymerases to provide novel polymerases with altered properties.Type: ApplicationFiled: September 30, 2014Publication date: April 2, 2015Inventors: Peter VANDER HORN, Daniel MAZUR, Theo NIKIFOROV, Mindy LANDES, Eileen TOZER
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Publication number: 20150087528Abstract: The present invention is directed to methods to prepare a DNA molecule or a plurality of DNA molecules by random fragmentation. In some embodiments, the present invention regards preparing a template for DNA sequencing by random fragmentation. In specific embodiments, the random fragmentation comprises chemical fragmentation, mechanical fragmentation, or enzymatic fragmentation. In further specific embodiments, a universal sequence is attached to the 3? end of the DNA fragments, such as by ligation of an adaptor sequence or by homopolymeric tailing with terminal deoxynucleotidyltransferase. In other embodiments, a library is prepared with methods of the present invention.Type: ApplicationFiled: August 4, 2014Publication date: March 26, 2015Applicant: RUBICON GENOMICS, INC.Inventors: Vladimir L. MAKAROV, Irina SLEPTSOVA, Emmanuel KAMBEROV, Eric BRUENING
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Publication number: 20150087027Abstract: The present invention is directed to methods and compositions for adding tails of specific lengths to a substrate polynucleotide. The invention also contemplates methods and compositions for immobilization of tailed substrates to a solid support. The disclosure contemplates that the attenuator molecule is any biomolecule that associates with a tail sequence added to a substrate polynucleotide and controls the addition of a tail sequence to the 3? end of the substrate polynucleotide. The sequence that is added to the substrate polynucleotide is referred to herein as a tail sequence, or simply a tail, and the process of adding a nucleotide to a substrate polynucleotide is referred to herein as tailing.Type: ApplicationFiled: March 13, 2013Publication date: March 26, 2015Inventors: Vladimir Makarov, Laurie Kurihara
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Publication number: 20150072351Abstract: The present invention relates to a method for preparing a nucleic acid with high sensitivity, wherein a nucleic acid polymerase is used to add a terminator to the nucleic acid to be used for analysis prior to a nucleic acid polymerization reaction such as a PCR reaction, a real time quantitative PCR reaction, or the like, for detecting a trace of nucleic acid, such that a non-specific priming occurring competitively with an amplification reaction of a target nucleic acid may be basically eliminated, thereby precisely detecting only the trace of target nucleic acid and precisely measuring a concentration of the target nucleic acid.Type: ApplicationFiled: April 8, 2013Publication date: March 12, 2015Inventors: Han Oh Park, Jun Hee Lee, Hyun Seo Kim, Sora Choi, Jong Hoon Kim
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Patent number: 8962281Abstract: Disclosed herein are engineered cleavage half-domains; fusion polypeptides comprising these engineered cleavage half-domains; polynucleotides encoding the engineered cleavage half-domains and fusion proteins; and cells comprising said polynucleotides and/or fusion proteins. Also described are methods of using these polypeptides and polynucleotides, for example for targeted cleavage of a genomic sequence.Type: GrantFiled: February 7, 2011Date of Patent: February 24, 2015Assignee: Sangamo BioSciences, Inc.Inventors: Yannick Doyon, Jeffrey C. Miller
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Publication number: 20150050658Abstract: Disclosed methods pertain to nucleic acid shuffling techniques that employ repeated short extension cycles. In each such cycle, strand extension along a template fragment is limited such that the strand extends only for a relatively short length (e.g., a few base pairs). Repeated short extension cycles cause many template switches during shuffling and thereby produce chimeric products with many crossovers. The methods may employ a pre-shuffling truncation or excision operation in which one or more parent nucleic acids has a portion of its full-length sequence truncated or excised. Shuffling with truncated parent nucleic acids introduces crossovers at the location of the truncation. Apparatus for implementing the disclosed methods may include appropriately configured thermocycling tools.Type: ApplicationFiled: March 12, 2013Publication date: February 19, 2015Applicant: Codexix, Inc.Inventor: Catherine M. Cho
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Publication number: 20150050696Abstract: The present invention relates to a method based on the use of restriction enzyme digestion and ligation via cleavage sites, thereby to prepare two or more standardized expression cassettes.Type: ApplicationFiled: March 27, 2013Publication date: February 19, 2015Inventors: Johannes Andries Roubos, Herman Jan Pel, Bernard Meijrink
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Publication number: 20150050697Abstract: Provided herein is technology relating to the manipulation and detection of nucleic acids, including but not limited to compositions, methods, and kits related to nucleotides comprising a chemically reactive linking moiety.Type: ApplicationFiled: August 19, 2014Publication date: February 19, 2015Inventor: Dae Hyun Kim
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Publication number: 20150045546Abstract: Isolation or in vitro assembly of the Cas9-crRNA complex of the Streptococcus thermophilus CRISPR3/Cas system and use for cleavage of DNA bearing a nucleotide sequence complementary to the crRNA and a proto-spacer adjacent motif. Methods for site-specific modification of a target DNA molecule using an RNA-guided DNA endonuclease comprising at least one RNA sequence and at least one of an RuvC active site motif and an HNH active site motif; for conversion of Cas9 polypeptide into a nickase cleaving one strand of double-stranded DNA by inactivating one of the active sites (RuvC or HNH) in the polypeptide by at least one point mutation; for assembly of active polypeptide-polyribonucleotides complex in vivo or in vitro; and for re-programming a Cas9-crRNA complex specificity in vitro or using a cassette containing a single repeat-spacer-repeat unit.Type: ApplicationFiled: March 15, 2013Publication date: February 12, 2015Applicant: Vilnius UniversityInventors: Virginijus Siksnys, Giedrius Gasiunas, Tautvydas Karvelis
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Publication number: 20150037787Abstract: A mixed polynucleotide includes a first double stranded (ds) portion, a second portion including at least one single stranded (ss) portion, and a third ds portion. The second portion connects the first ds portion and the third ds portion to provide a modified polynucleotide.Type: ApplicationFiled: July 31, 2013Publication date: February 5, 2015Applicant: INTERNATIONAL BUSINESS MACHINES CORPORATIONInventors: Binquan Luan, Ajay K. Royyuru, Gustavo A. Stolovitzky, Chao Wang, Deqiang Wang
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Patent number: 8940092Abstract: The present invention relates generally to nanocomposite materials. The present invention relates more particularly to hybrid fibers as well as devices including them and methods for making them. Accordingly, one aspect of the invention is a hybrid fiber including a plurality of nanowires, each nanowire having a length, a width, and a thickness, the length being at least 10 times the width and at least 10 times the thickness; and a plurality of binder elements, each binder element having a length, a width, and a thickness, each substantially smaller than the average length of the nanowires and at least one of which is less than about 10 nm in dimension, the binder elements being arranged to intercouple individual nanowires. In certain embodiments, the binder elements are carbon nanotubes, and the nanowires are formed from silicon carbide.Type: GrantFiled: September 26, 2012Date of Patent: January 27, 2015Assignee: University of Washington through its Center for CommercializationInventors: Woon-Hong Yeo, Kieseok Oh, Kyong-Hoon Lee, Fong-Li Chou, Jae-Hyun Chung
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Publication number: 20150010953Abstract: Provided herein is a method for producing a population of oligonucleotides that has reduced synthesis errors. In certain embodiments, the method comprises: a) obtaining an initial population of hairpin oligonucleotide molecules that each comprise a double-stranded stem region and a loop region; b) contacting the double-stranded region of the hairpin oligonucleotide molecules with a mismatch binding protein; and c) eliminating any molecules that bind to the mismatch binding protein, thereby producing a population of oligonucleotides that has reduced synthesis errors. A kit and a composition for performing the method are also provided.Type: ApplicationFiled: July 3, 2013Publication date: January 8, 2015Inventors: Derek Lee Lindstrom, Jeffrey R. Sampson, Daniel E. Ryan
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Publication number: 20150004618Abstract: The invention relates to a method for linking at least two target nucleic acid molecules from a single biological compartment, comprising the steps of isolating a fraction from a sample, wherein the fraction comprises the compartment comprising at least two nucleic acid molecules; diluting said fraction and aliquoting the dilution in multiple separate reaction vessels such that each reaction vessel comprises preferably one compartment, or encapsulating said compartment in emulsion droplets such that each droplet comprises preferably one compartment; linking said at least two target nucleic acid molecules, preferably by overlap extension PCR. The method may be employed in the analysis of mutations present in a single cell and in the production of antibodies which are present in a single hybridoma.Type: ApplicationFiled: February 6, 2013Publication date: January 1, 2015Applicant: MAX-PLANCK GESELLSCHAFT ZUR FOERDERUNG DER WISSENSCHAFTEN E.V.Inventors: Hans-Joerg Warnatz, Joern Gloekler, Hans Lehrach
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Publication number: 20140377810Abstract: Fusion proteins comprising a single strand DNA binding protein and a nucleic acid polymerase (e.g. DNA polymerase or reverse transcriptase). These high fidelity proteins are suitable for use in nucleic acid amplification methods, including the polymerase chain reaction (PCR).Type: ApplicationFiled: August 4, 2014Publication date: December 25, 2014Inventors: Jun LEE, Robert Potter, David Mandelman
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Publication number: 20140363852Abstract: The invention provides improved methods for synthesizing polynucleotides, such as DNA and RNA, using enzymes and specially designed nucleotide analogs. Using the methods of the invention, specific sequences of polynucleotides can be synthesized de novo, base by base, in an aqueous environment, without the use of a nucleic acid template. Because the nucleotide analogs have an unmodified 3? OH, i.e., as found in “natural” deoxyribose and ribose molecules, the analogs result in natural polynucleotides suitable for incorporation into biological systems.Type: ApplicationFiled: August 13, 2014Publication date: December 11, 2014Inventors: J. William Efcavitch, Suhaib Siddiqi
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Publication number: 20140363849Abstract: Provided are the following: a method, for improving reactivity of a nucleic acid synthesis reaction, comprising a step for adding an ?-amino acid to a reaction solution; a composition, for a nucleic acid synthesis reaction, comprising DNA polymerase, reaction buffer, at least one primer, at least one deoxyribonucleotide triphosphate, and an ?-amino acid; and a reaction buffer, for a nucleic acid synthesis reaction, comprising an ?-amino acid.Type: ApplicationFiled: January 24, 2013Publication date: December 11, 2014Applicant: Takara Bio Inc.Inventors: Kiyoyuki Matsumura, Takashi Uemori, Hiroyuki Mukai
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Publication number: 20140363851Abstract: The invention provides improved methods for synthesizing polynucleotides, such as DNA and RNA, using enzymes and specially designed nucleotide analogs. Using the methods of the invention, specific sequences of polynucleotides can be synthesized de novo, base by base, in an aqueous environment, without the use of a nucleic acid template. Because the nucleotide analogs have an unmodified 3? OH, i.e., as found in “natural” deoxyribose and ribose molecules, the analogs result in natural polynucleotides suitable for incorporation into biological systems.Type: ApplicationFiled: July 28, 2014Publication date: December 11, 2014Inventors: J. William Efcavitch, Suhaib Siddiqi
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Publication number: 20140350074Abstract: The invention provides compositions and methods for reducing expression of a target gene in a cell, involving contacting a cell with an isolated double stranded nucleic acid (dsNA) in an amount effective to reduce expression of a target gene in a cell. The dsNAs of the invention possess a pattern of deoxyribonucleotides (in most embodiments, the pattern comprises at least one deoxyribonucleotide-deoxyribonucleotide base pair) designed to direct the site of Dicer enzyme cleavage within the dsNA molecule. Deoxyribonucleotides of the dsNA molecules of the invention are located within a region of the dsNA that can be excised via Dicer cleavage to generate an active siRNA agent that no longer contains the deoxyribonucleotide pattern (e.g., deoxyribonucleotide-deoxyribonucleotide base pairs). Such DNA-extended Dicer-substrate siRNAs (DsiRNAs) were demonstrated to be more effective RNA inhibitory agents than corresponding double stranded RNA-extended DsiRNAs.Type: ApplicationFiled: July 10, 2014Publication date: November 27, 2014Inventor: Bob Dale Brown
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Publication number: 20140350089Abstract: The present invention is directed to a synthetic nucleic acid sequence which encodes a protein wherein at least one non-common codon or less-common codon is replaced by a common codon. The synthetic nucleic acid sequence can include a continuous stretch of at least 90 codons all of which are common codons.Type: ApplicationFiled: March 3, 2014Publication date: November 27, 2014Applicant: SHIRE HUMAN GENETIC THERAPIES, INC.Inventors: Richard F. Selden, Allan M. Miller, Douglas A. Treco
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Publication number: 20140343265Abstract: In some embodiments, the present teachings provide compositions, systems, methods and kits for generating a population of nucleic acid fragments. In some embodiments, nucleic acids can be fragmented enzymatically. For example, methods for generating a population of nucleic acid fragments can include a nucleic acid nicking reaction. In one embodiment, the methods can include a nick translation reaction. A nicking reaction can introduce nicks at random positions on either strand of a double-stranded nucleic acid. A nick translation reaction can move the position of nicks to a new position so that the new positions of two of the nicks are aligned to create a double-stranded break. In some embodiments, methods for generating a population of nucleic acid fragments can include joining at least one end of a fragmented nucleic acid to one or more oligonucleotide adaptors.Type: ApplicationFiled: June 25, 2014Publication date: November 20, 2014Inventors: Zhoutao CHEN, Xiaoping DUAN, Kyusung PARK
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Publication number: 20140342409Abstract: Disclosed are mutant DNA polymerases having increased 3?-mismatch discrimination relative to a corresponding, unmodified polymerase. The mutant polymerases are useful in a variety of disclosed primer extension methods. Also disclosed are related compositions, including recombinant nucleic acids, vectors, and host cells, which are useful, e.g., for production of the mutant DNA polymerases.Type: ApplicationFiled: April 21, 2014Publication date: November 20, 2014Applicant: Roche Molecular Systems, Inc.Inventors: Fred Reichert, Keith Bauer, Thomas W. Myers
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Publication number: 20140322753Abstract: The present invention relates to isolated polypeptides having endoglucanase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods for producing and using the polypeptides.Type: ApplicationFiled: June 30, 2014Publication date: October 30, 2014Inventors: Paul Harris, Elena Vlasenko, Marcus Sakari Kauppinnen, Elizabeth Zaretsky, Sarah Teter, Kimberly Brown
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Patent number: 8846348Abstract: The present invention relates to kits and methods for efficiently generating 5? capped RNA having a modified cap nucleotide and for use of such modified-nucleotide-capped RNA molecules. In particular, the present invention provides kits and methods for capping RNA using a modified cap nucleotide and a capping enzyme system, such as poxvirus capping enzyme. The present invention finds use for in vitro production of 5?-capped RNA having a modified cap nucleotide and for in vitro or in vivo production of polypeptides by in vitro or in vivo translation of such modified-nucleotide-capped RNA. The invention also provides methods and kits for capturing or isolating uncapped RNA comprising primary RNA transcripts or RNA having a 5?-diphosphate, and methods and kits for using a capping enzyme system and modified cap nucleotides for labeling uncapped RNA comprising primary RNA transcripts or RNA having a 5?-diphosphate with detectable dye or enzyme moieties.Type: GrantFiled: February 20, 2014Date of Patent: September 30, 2014Assignee: CellScript, LLCInventors: Jerome Jendrisak, Ronald Meis, Gary Dahl
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Publication number: 20140273100Abstract: A cDNA synthesis method includes: mixing a lysis solution containing a chaotropic substance and a nucleic acid-binding solid-phase carrier in a sample containing a ribonucleic acid (RNA), thereby adsorbing the RNA on the carrier; reverse-transcribing the RNA adsorbed on the carrier while keeping the RNA adsorbed on the carrier in a reverse transcription reaction mixture, thereby synthesizing cDNA; and eluting the synthesized cDNA with an eluent.Type: ApplicationFiled: March 11, 2014Publication date: September 18, 2014Applicant: Seiko Epson CorporationInventors: Yuji Saito, Fumio Takagi
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Patent number: 8822146Abstract: The present invention relates to a use of non-cofactor compounds, represented by formulas (I) or (II) wherein R and Z are independently selected from H, D, C1-C12-alkyl, preferably C1-C4-alkyl, alkenyl, alkinyl, phenyl or -LX, wherein X represents a functional group or a reporter group attached via a linker group L, and QH is selected from —SH, —SeH, —NHNH2 or —ONH2, for a targeted modification or derivatization of a biomolecule by covalent coupling to the biomolecule in the presence of a directing methyltransferase. Further development of the method of targeted modification and derivatization are the method for targeted labeling a biomolecule and method for detecting unmethylated target sites in a biomolecule comprising modification of the biomolecule according to the present invention.Type: GrantFiled: April 1, 2010Date of Patent: September 2, 2014Assignee: Vilnius UniversityInventors: Saulius Klimasauskas, Zita Liutkeviciute, Edita Kriukiene
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Publication number: 20140227691Abstract: The present invention provides methods for selectively enriching a biological sample for short nucleic acids, such as fetal DNA in a maternal sample or apoptic DNA in a biological sample from a cancer patient and for subsequently analyzing the short nucleic acids for genotype, mutation, and/or aneuploidy.Type: ApplicationFiled: May 16, 2011Publication date: August 14, 2014Applicant: FLUIDIGM, INC.Inventors: Andrew May, Alain Mir, Ramesh Ramakrishnan, Bernhard G. Zimmermann
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Publication number: 20140220639Abstract: Disclosed are mutant DNA polymerases having increased 3?-mismatch discrimination relative to a corresponding, unmodified polymerase. The mutant polymerases are useful in a variety of disclosed primer extension methods. Also disclosed are related compositions, including recombinant nucleic acids, vectors, and host cells, which are useful, e.g., for production of the mutant DNA polymerases.Type: ApplicationFiled: March 28, 2014Publication date: August 7, 2014Applicant: ROCHE MOLECULAR SYSTEMS, INC.Inventors: FRED REICHERT, KEITH BAUER, THOMAS W. MYERS
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Publication number: 20140221454Abstract: The invention provides compositions and methods for reducing expression of a target gene in a cell, involving contacting a cell with an isolated double stranded nucleic acid (dsNA) in an amount effective to reduce expression of a target gene in a cell. The dsNAs of the invention possess a pattern of deoxyribonucleotides (in most embodiments, the pattern comprises at least one deoxyribonucleotide-deoxyribonucleotide base pair) designed to direct the site of Dicer enzyme cleavage within the dsNA molecule. Deoxyribonucleotides of the dsNA molecules of the invention are located within a region of the dsNA that can be excised via Dicer cleavage to generate an active siRNA agent that no longer contains the deoxyribonucleotide pattern (e.g., deoxyribonucleotide-deoxyribonucleotide base pairs). Such DNA-extended Dicer-substrate siRNAs (DsiRNAs) were demonstrated to be more effective RNA inhibitory agents than corresponding double stranded RNA-extended DsiRNAs.Type: ApplicationFiled: August 20, 2013Publication date: August 7, 2014Applicant: Dicerna Pharmaceuticals, Inc.Inventor: Bob Dale Brown
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Publication number: 20140212929Abstract: Disclosed are mutant DNA polymerases having increased 3?-mismatch discrimination relative to a corresponding, unmodified polymerase. The mutant polymerases are useful in a variety of disclosed primer extension methods. Also disclosed are related compositions, including recombinant nucleic acids, vectors, and host cells, which are useful, e.g., for production of the mutant DNA polymerases.Type: ApplicationFiled: March 28, 2014Publication date: July 31, 2014Applicant: Roche Molecular Systems, Inc.Inventors: Fred Reichert, Keith Bauer, Thomas W. Myers