Acellular Preparation Of Polynucleotide Patents (Class 435/91.5)
  • Patent number: 10202608
    Abstract: 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: Grant
    Filed: September 30, 2011
    Date of Patent: February 12, 2019
    Assignee: Gen9, Inc.
    Inventor: William J. Blake
  • Patent number: 9926598
    Abstract: 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: Grant
    Filed: December 18, 2014
    Date of Patent: March 27, 2018
    Assignee: ILLUMINA, INC.
    Inventors: Hongxia Xu, Alex Aravanis, Shengrong Lin
  • Patent number: 9856515
    Abstract: 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: Grant
    Filed: March 3, 2015
    Date of Patent: January 2, 2018
    Assignee: Exact Sciences Corporation
    Inventors: Janelle J. Bruinsma, Hemanth D. Shenoi, Michael J. Domanico, James P. Light, II
  • Patent number: 9803208
    Abstract: 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: Grant
    Filed: March 28, 2013
    Date of Patent: October 31, 2017
    Assignee: THE UNIVERSITY OF NOTTINGHAM
    Inventors: Nigel Peter Minton, Ying Zhang
  • Patent number: 9657330
    Abstract: 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: Grant
    Filed: July 10, 2014
    Date of Patent: May 23, 2017
    Assignee: Exact Sciences Corporation
    Inventors: Graham P. Lidgard, Janelle J. Bruinsma, Michael J. Domanico, Hemanth Shenoi
  • Patent number: 9487829
    Abstract: 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: Grant
    Filed: July 30, 2015
    Date of Patent: November 8, 2016
    Assignee: The Johns Hopkins University
    Inventors: Bert Vogelstein, Kenneth W. Kinzler, Nickolas Papadopoulos, Isaac Kinde
  • Patent number: 9121046
    Abstract: 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: Grant
    Filed: November 7, 2012
    Date of Patent: September 1, 2015
    Assignee: New England Biolabs, Inc.
    Inventors: Nathan Tanner, Thomas C. Evans, Jr.
  • Publication number: 20150147785
    Abstract: 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 d
    Type: Application
    Filed: July 10, 2013
    Publication date: May 28, 2015
    Inventors: Alexander Seitz, Irmlind Gabler, Lukas Paul
  • Publication number: 20150133317
    Abstract: 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: Application
    Filed: April 27, 2012
    Publication date: May 14, 2015
    Applicants: Department of Veterans Affairs, The Board of Trustees of the Leland Stanford Junior University
    Inventors: William H. Robinson, Yann Chong Tan, Jeremy Sokolove
  • Patent number: 9017973
    Abstract: 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: Grant
    Filed: November 28, 2011
    Date of Patent: April 28, 2015
    Assignee: Intelligent BioSystems, Inc.
    Inventors: Steven Gordon, Jerzy Olejnik
  • Patent number: 9005935
    Abstract: 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: Grant
    Filed: May 11, 2012
    Date of Patent: April 14, 2015
    Assignee: Agilent Technologies, Inc.
    Inventor: Alexander S. Belyaev
  • Patent number: 9005930
    Abstract: 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: Grant
    Filed: August 28, 2014
    Date of Patent: April 14, 2015
    Assignee: Cellscript, LLC
    Inventors: Jerome Jendrisak, Ronald Meis, Gary Dahl
  • Publication number: 20150094211
    Abstract: 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: Application
    Filed: September 30, 2014
    Publication date: April 2, 2015
    Inventors: Peter VANDER HORN, Daniel MAZUR, Theo NIKIFOROV, Mindy LANDES, Eileen TOZER
  • Publication number: 20150087027
    Abstract: 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: Application
    Filed: March 13, 2013
    Publication date: March 26, 2015
    Inventors: Vladimir Makarov, Laurie Kurihara
  • Publication number: 20150087528
    Abstract: 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: Application
    Filed: August 4, 2014
    Publication date: March 26, 2015
    Applicant: RUBICON GENOMICS, INC.
    Inventors: Vladimir L. MAKAROV, Irina SLEPTSOVA, Emmanuel KAMBEROV, Eric BRUENING
  • Publication number: 20150072351
    Abstract: 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: Application
    Filed: April 8, 2013
    Publication date: March 12, 2015
    Inventors: Han Oh Park, Jun Hee Lee, Hyun Seo Kim, Sora Choi, Jong Hoon Kim
  • Patent number: 8962281
    Abstract: 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: Grant
    Filed: February 7, 2011
    Date of Patent: February 24, 2015
    Assignee: Sangamo BioSciences, Inc.
    Inventors: Yannick Doyon, Jeffrey C. Miller
  • Publication number: 20150050696
    Abstract: 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: Application
    Filed: March 27, 2013
    Publication date: February 19, 2015
    Inventors: Johannes Andries Roubos, Herman Jan Pel, Bernard Meijrink
  • Publication number: 20150050658
    Abstract: 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: Application
    Filed: March 12, 2013
    Publication date: February 19, 2015
    Applicant: Codexix, Inc.
    Inventor: Catherine M. Cho
  • Publication number: 20150050697
    Abstract: 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: Application
    Filed: August 19, 2014
    Publication date: February 19, 2015
    Inventor: Dae Hyun Kim
  • Publication number: 20150045546
    Abstract: 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: Application
    Filed: March 15, 2013
    Publication date: February 12, 2015
    Applicant: Vilnius University
    Inventors: Virginijus Siksnys, Giedrius Gasiunas, Tautvydas Karvelis
  • Publication number: 20150037787
    Abstract: 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: Application
    Filed: July 31, 2013
    Publication date: February 5, 2015
    Applicant: INTERNATIONAL BUSINESS MACHINES CORPORATION
    Inventors: Binquan Luan, Ajay K. Royyuru, Gustavo A. Stolovitzky, Chao Wang, Deqiang Wang
  • Patent number: 8940092
    Abstract: 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: Grant
    Filed: September 26, 2012
    Date of Patent: January 27, 2015
    Assignee: University of Washington through its Center for Commercialization
    Inventors: Woon-Hong Yeo, Kieseok Oh, Kyong-Hoon Lee, Fong-Li Chou, Jae-Hyun Chung
  • Publication number: 20150010953
    Abstract: 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: Application
    Filed: July 3, 2013
    Publication date: January 8, 2015
    Inventors: Derek Lee Lindstrom, Jeffrey R. Sampson, Daniel E. Ryan
  • Publication number: 20150004618
    Abstract: 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: Application
    Filed: February 6, 2013
    Publication date: January 1, 2015
    Applicant: MAX-PLANCK GESELLSCHAFT ZUR FOERDERUNG DER WISSENSCHAFTEN E.V.
    Inventors: Hans-Joerg Warnatz, Joern Gloekler, Hans Lehrach
  • Publication number: 20140377810
    Abstract: 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: Application
    Filed: August 4, 2014
    Publication date: December 25, 2014
    Inventors: Jun LEE, Robert Potter, David Mandelman
  • Publication number: 20140363852
    Abstract: 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: Application
    Filed: August 13, 2014
    Publication date: December 11, 2014
    Inventors: J. William Efcavitch, Suhaib Siddiqi
  • Publication number: 20140363849
    Abstract: 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: Application
    Filed: January 24, 2013
    Publication date: December 11, 2014
    Applicant: Takara Bio Inc.
    Inventors: Kiyoyuki Matsumura, Takashi Uemori, Hiroyuki Mukai
  • Publication number: 20140363851
    Abstract: 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: Application
    Filed: July 28, 2014
    Publication date: December 11, 2014
    Inventors: J. William Efcavitch, Suhaib Siddiqi
  • Publication number: 20140350089
    Abstract: 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: Application
    Filed: March 3, 2014
    Publication date: November 27, 2014
    Applicant: SHIRE HUMAN GENETIC THERAPIES, INC.
    Inventors: Richard F. Selden, Allan M. Miller, Douglas A. Treco
  • Publication number: 20140350074
    Abstract: 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: Application
    Filed: July 10, 2014
    Publication date: November 27, 2014
    Inventor: Bob Dale Brown
  • Publication number: 20140343265
    Abstract: 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: Application
    Filed: June 25, 2014
    Publication date: November 20, 2014
    Inventors: Zhoutao CHEN, Xiaoping DUAN, Kyusung PARK
  • Publication number: 20140342409
    Abstract: 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: Application
    Filed: April 21, 2014
    Publication date: November 20, 2014
    Applicant: Roche Molecular Systems, Inc.
    Inventors: Fred Reichert, Keith Bauer, Thomas W. Myers
  • Publication number: 20140322753
    Abstract: 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: Application
    Filed: June 30, 2014
    Publication date: October 30, 2014
    Inventors: Paul Harris, Elena Vlasenko, Marcus Sakari Kauppinnen, Elizabeth Zaretsky, Sarah Teter, Kimberly Brown
  • Patent number: 8846348
    Abstract: 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: Grant
    Filed: February 20, 2014
    Date of Patent: September 30, 2014
    Assignee: CellScript, LLC
    Inventors: Jerome Jendrisak, Ronald Meis, Gary Dahl
  • Publication number: 20140273100
    Abstract: 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: Application
    Filed: March 11, 2014
    Publication date: September 18, 2014
    Applicant: Seiko Epson Corporation
    Inventors: Yuji Saito, Fumio Takagi
  • Patent number: 8822146
    Abstract: 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: Grant
    Filed: April 1, 2010
    Date of Patent: September 2, 2014
    Assignee: Vilnius University
    Inventors: Saulius Klimasauskas, Zita Liutkeviciute, Edita Kriukiene
  • Publication number: 20140227691
    Abstract: 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: Application
    Filed: May 16, 2011
    Publication date: August 14, 2014
    Applicant: FLUIDIGM, INC.
    Inventors: Andrew May, Alain Mir, Ramesh Ramakrishnan, Bernhard G. Zimmermann
  • Publication number: 20140221454
    Abstract: 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: Application
    Filed: August 20, 2013
    Publication date: August 7, 2014
    Applicant: Dicerna Pharmaceuticals, Inc.
    Inventor: Bob Dale Brown
  • Publication number: 20140220639
    Abstract: 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: Application
    Filed: March 28, 2014
    Publication date: August 7, 2014
    Applicant: ROCHE MOLECULAR SYSTEMS, INC.
    Inventors: FRED REICHERT, KEITH BAUER, THOMAS W. MYERS
  • Publication number: 20140212929
    Abstract: 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: Application
    Filed: March 28, 2014
    Publication date: July 31, 2014
    Applicant: Roche Molecular Systems, Inc.
    Inventors: Fred Reichert, Keith Bauer, Thomas W. Myers
  • Patent number: 8765419
    Abstract: The present technology relates to methods and systems for detection of pyrophosphate. As such, disclosed herein are methods and systems that permit improved pyrophosphate detection. Also disclosed herein are methods and systems which utilize improved pyrophosphate detection for nucleotide sequencing.
    Type: Grant
    Filed: April 29, 2013
    Date of Patent: July 1, 2014
    Assignee: Illumina, Inc.
    Inventors: Bernard Hirschbein, Filiz Gorpe-Yasar
  • Patent number: 8753846
    Abstract: A method of double crossover homologous recombination in a host cell comprising: a first homologous recombination event between a donor DNA molecule comprising a first element of a selectable allele and an acceptor DNA molecule comprising a second element of the selectable allele in the host cell, thereby to form a product of the first homologous recombination event in the host cell; and a second homologous recombination event within the product of the first homologous recombination event, thereby to form a product of the second homologous recombination event in the host cell which confers a selectable phenotype on the host cell, wherein the selectable phenotype arises following and in dependency on the formation of a selectable allele from the first and second elements of the selectable allele.
    Type: Grant
    Filed: February 13, 2009
    Date of Patent: June 17, 2014
    Assignee: The University of Nottingham
    Inventors: John Timothy Heap, Nigel Peter Minton
  • Patent number: 8753847
    Abstract: Compositions and methods are provided for selection and enrichment of a target gene from a library of polynucleotide sequences such as might be formed from a genome or by random mutagenesis of a genetic sequence. The selection and enrichment occurs in aqueous droplets formed in an emulsion that compartmentalize individual polynucleotides from the library or a plurality of polynucleotides that may include polynucleotides not derived from the library, transcription and translation reagents and optionally additional chemical and enzyme reagents. The selection and enrichment method utilizes a polynucleotide adaptor which when ligated to the polynucleotide fragment enables amplification to occur in the presence of an adaptor specific primer.
    Type: Grant
    Filed: August 13, 2013
    Date of Patent: June 17, 2014
    Assignee: New England Biolabs, Inc.
    Inventors: Yu Zheng, Richard J. Roberts
  • Publication number: 20140154737
    Abstract: The invention provides a cross-linked poly-?-lysine polymer. The poly-?-lysine and cross linker are linked by amide bonds and may the cross linker has at least two functional groups capable of reacting with an alpha carbon amine of poly-?-lysine. The polymer is suitably insoluble in water and other solvents and is provided in particulate form. The invention provides a particulate support comprising the cross-linked poly-?-lysine polymer and the polymer may provide the particle itself or be coated on a particle for example silica. The polymer is useful in a wide range of applications including wound treatment, as a medical diagnostic comprising a particulate support and a functional material bound or retained by the support and solid phase synthesis of peptides, oligonucleotides, oligosaccharides, immobilisation of species, cell culturing and in chromatographic separation.
    Type: Application
    Filed: April 20, 2012
    Publication date: June 5, 2014
    Applicant: SPHERITECH LTD
    Inventor: Donald Wellings
  • Publication number: 20140147840
    Abstract: Methods of labeling and detecting a target nucleic acid by incubating a target nucleic acid with a terminal transferase to extend a terminus of the target nucleic acid and provide an extended region; hybridizing the extended region of the target nucleic acid with a template polynucleotide having a nucleotide sequence complementary to the extended region to obtain a hybridization product; and incubating the hybridization product with a nucleic acid polymerase and either a deoxynucleotide triphosphate (dNTP) having a detectable label or nucleotide triphosphate (NTP) having a detectable label to further extend the extended target nucleic acid.
    Type: Application
    Filed: May 29, 2013
    Publication date: May 29, 2014
    Inventors: Sea-hee KIM, Joo-won RHEE, Ko-bong CHOI
  • Publication number: 20140148589
    Abstract: Aspects herein relate to composition, and related methods, for isolating and assembling DNA molecules without intermediate cloning steps.
    Type: Application
    Filed: September 23, 2011
    Publication date: May 29, 2014
    Inventors: Jonathan William Babb, Shuo Cory Li, Thomas Knight, Ron Weiss
  • Patent number: 8735064
    Abstract: The invention relates to the control of gene expression. Specifically, the invention provides compositions and methods for the production and use of recombinant nucleic acid molecules that have the ability to specifically downregulate an expressed target gene in vivo. In some aspects, the invention provides methods for producing a hairpin DNA molecule where part of the molecule is derived from an mRNA that is a target for a small interfering RNA (siRNA) derived from the hairpin. In other aspects, the invention provides synthetic hairpin adapter oligonucleotides that are used in the construction of siRNA-producing cassettes. In other aspects, the invention provides methods for testing for the presence or absence of specific inhibitory activity of an RNAi trigger molecule, and in still other aspects, the invention provides methods for identifying an active RNAi trigger molecule from a library of RNAi trigger molecules.
    Type: Grant
    Filed: December 23, 2008
    Date of Patent: May 27, 2014
    Assignee: Bergenbio AS
    Inventors: David Micklem, James Lorens
  • Patent number: 8728767
    Abstract: Methods and kits for synthesizing a plurality of oligonucleotides are provided. Methods for providing a plurality of oligonucleotides enriched for full length oligonucleotides are provided. Truncated oligonucleotides are preferentially removed from the sample by digestion. Methods are also provided for amplification of a plurality of oligonucleotides.
    Type: Grant
    Filed: December 21, 2007
    Date of Patent: May 20, 2014
    Assignee: Affymetrix, Inc.
    Inventor: Michael Shapero
  • Publication number: 20140127678
    Abstract: Methods, compositions and kits for selectively altering and detecting modified cytosine residues are provided.
    Type: Application
    Filed: March 14, 2013
    Publication date: May 8, 2014
    Inventors: Shengxi Guan, Nan Dai, Zhenyu Zhu, Ivan R. Correa, Jr., Aine Quimby, Janine Borgaro