Involving The Making Of Multiple Rna Copies Patents (Class 435/91.21)
  • Patent number: 11639517
    Abstract: Disclosed herein include systems, methods, compositions, and kits for labeling nucleic acid targets in a sample. In some embodiments, nucleic acid targets (e.g., mRNAs) are initially barcoded on the 3? end and are subsequently barcoded on the 5? end following a template switching reaction and intermolecular and/or intramolecular hybridization and extension. There are provided, in some embodiments, methods of 5?-based and 3?-based gene expression profiling. Immune repertoire profiling methods are also provided in some embodiments.
    Type: Grant
    Filed: September 30, 2019
    Date of Patent: May 2, 2023
    Assignee: Becton, Dickinson and Company
    Inventors: Christina Chang, Eleen Shum
  • Patent number: 11441175
    Abstract: Methods and kits for depleting amplicons that correspond to undesired RNA species present in a sample are provided. The disclosed methods and kits employ a blocker that anneals with at least a portion of the undesired RNA, resulting in a duplex that is not a suitable substrate for ligating an adapter to the end of the undesired RNA.
    Type: Grant
    Filed: February 27, 2018
    Date of Patent: September 13, 2022
    Assignee: BIOO Scientific Corporation
    Inventors: Suk Ho Eun, Adam Morris
  • Patent number: 11352622
    Abstract: Described herein are methods and compositions that provide highly efficient nucleic acid amplification. In some embodiments, this allows a 3-fold or greater increase of amplification product for each amplification cycle and therefore increased sensitivity and speed over conventional PCR. Modified bases can be employed in primers to provide this base-3 or greater amplification with satisfactory PCR cycle times, which are improved, as compared to those observed in the absence of modified bases.
    Type: Grant
    Filed: October 29, 2019
    Date of Patent: June 7, 2022
    Assignee: CEPHEID
    Inventor: Russell Higuchi
  • Patent number: 11028434
    Abstract: Described herein are methods and compositions that provide highly efficient nucleic acid amplification. In some embodiments, this allows a greater than 2-fold increase of amplification product for each amplification cycle and therefore increased sensitivity and speed over conventional PCR.
    Type: Grant
    Filed: March 20, 2019
    Date of Patent: June 8, 2021
    Assignee: CEPHEID
    Inventor: Russell Higuchi
  • Patent number: 11015213
    Abstract: Methods for in situ amplification (ISA) of cfNA, such as cfDNA, in a sample are provided wherein the cfNA in the sample is not subject to a nucleic acid purification step. The methods disclosed may be used to generate an analyzable pool of cfNA present in the sample. The analyzable pool may be used with a variety of analytical techniques to characterize the nucleic acid in the sample. Methods of diagnosis, determining a therapeutic intervention and monitoring of a subject are also provided.
    Type: Grant
    Filed: August 12, 2016
    Date of Patent: May 25, 2021
    Assignee: CIRCULOGENE THERANOSTICS, LLC
    Inventor: Chen-Hsiung Yeh
  • Patent number: 10190143
    Abstract: The invention relates to a method for synthesizing a selectively labeled RNA, and an apparatus for performing the method. Specific segments or discrete residues within the RNA may be selectively labeled, and different segments may include different labels.
    Type: Grant
    Filed: July 8, 2014
    Date of Patent: January 29, 2019
    Assignees: THE BOARD OF REGENTS OF THE UNIVERSITY OF TEXAS SYSTEM, THE UNITED STATES OF AMERICA, AS REPRESENTED BY THE SECRETARY, DEPARTMENT OF HEALTH AND HUMAN SERVICES OFFICE OF TECHNOLOGY TRANSFER, NATIONAL INSTITUTES OF HEALTH
    Inventors: Yun-Xing Wang, Yu Liu, Rui Sousa
  • Patent number: 9556466
    Abstract: The present invention is directed to compositions and methods useful for the amplification of nucleic acid molecules by reverse transcriptase-polymerase chain reaction (RT-PCR). Specifically, the invention provides compositions and methods for the amplification of nucleic acid molecules in a simplified one- or two-step RT-PCR procedure using combinations of reverse transcriptase and thermostable DNA polymerase enzymes in conjunction with sulfur-containing molecules or acetate-containing molecules (or combinations of such sulfur-containing molecules and acetate-containing molecules), and optionally bovine serum albumin. The invention thus facilitates the rapid and efficient amplification of nucleic acid molecules and the detection and quantitation of RNA molecules. The invention also is useful in the rapid production and amplification of cDNAs which may be used for a variety of industrial, medical and forensic purposes.
    Type: Grant
    Filed: February 11, 2013
    Date of Patent: January 31, 2017
    Assignee: LIFE TECHNOLOGIES CORPORATION
    Inventors: Jun Lee, Ayoub Rashtchian
  • Patent number: 9388465
    Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing. Such polynucleotide processing may be useful for a variety of applications, including polynucleotide sequencing. In some cases, this disclosure provides methods for the generation of polynucleotide barcode libraries, and for the attachment of such polynucleotides to target polynucleotides.
    Type: Grant
    Filed: February 7, 2014
    Date of Patent: July 12, 2016
    Assignee: 10X GENOMICS, INC.
    Inventors: Benjamin Hindson, Mirna Jarosz, Paul Hardenbol, Michael Schnall-Levin, Kevin Ness, Serge Saxonov
  • Patent number: 9334328
    Abstract: The present disclosure provides modified nucleosides, nucleotides, and nucleic acids, and methods of using thereof.
    Type: Grant
    Filed: January 11, 2013
    Date of Patent: May 10, 2016
    Assignee: Moderna Therapeutics, Inc.
    Inventors: Jason P. Schrum, Suhaib Siddiqi, Kenechi Ejebe
  • Patent number: 9109262
    Abstract: Compositions are disclosed as nucleic acid sequences that may be used as amplification oligomers, including primers, capture probes for sample preparation, and detection probes specific for Candida albicans 26S rRNA sequences or DNA encoding 26S rRNA. Methods are disclosed for detecting the presence of C. albicans in samples by using the disclosed compositions in methods that include in vitro nucleic acid amplification of a 26S rRNA sequence or DNA encoding the 26S rRNA sequence to produce a detectable amplification product.
    Type: Grant
    Filed: March 1, 2010
    Date of Patent: August 18, 2015
    Assignee: Gen-Probe Incorporated
    Inventors: James J. Hogan, Irene Andruszkiewicz, Jennifer J. Bungo, Shannon K. Kaplan
  • Publication number: 20150119291
    Abstract: The present invention provides methods for the amplification of nucleic acid molecules. Methods for amplifying target polynucleotides, including mRNA, using oligonucleotides, DNA and RNA polymerases are provided. The invention further provides compositions and kits for practicing the methods, as well as methods which use the amplification products.
    Type: Application
    Filed: October 29, 2014
    Publication date: April 30, 2015
    Inventors: Mark G. ERLANDER, Ranelle C. SALUNGA
  • Publication number: 20150111789
    Abstract: Provided are methods of adding adapters to nucleic acids. The methods include combining in a reaction mixture a template ribonucleic acid (RNA), a template switch oligonucleotide including a 3? hybridization domain and a sequencing platform adapter construct, a polymerase, and dNTPs. The reaction mixture components are combined under conditions sufficient to produce a product nucleic acid that includes the template RNA and the template switch oligonucleotide each hybridized to adjacent regions of a single product nucleic acid that includes a region polymerized from the dNTPs by the polymerase. Aspects of the invention further include compositions and kits.
    Type: Application
    Filed: September 5, 2014
    Publication date: April 23, 2015
    Inventors: Craig Betts, Steve Oh, George Jokhadze
  • 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: 20150079637
    Abstract: 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: Application
    Filed: April 11, 2014
    Publication date: March 19, 2015
    Applicant: RUBICON GENOMICS, INC.
    Inventors: Vladimir L. MAKAROV, Emmanuel KAMBEROV, Brendan J. TARRIER
  • Publication number: 20150024434
    Abstract: Herein is reported a method for a multiplex one tube real-time reverse-transcriptase gene-specific polymerase chain reaction for the amplification and quantification of cognate IgG heavy and light chains encoding nucleic acids (human IgG isotype) from a single cell.
    Type: Application
    Filed: September 20, 2012
    Publication date: January 22, 2015
    Inventors: Hans-Willi Krell, Alexander Lifke, Valeria Lifke, Kairat Madin, Christian Weilke
  • Publication number: 20150024959
    Abstract: The problem to be solved by the present invention is to provide a method for preparing a sample for comprehensively and accurately analyzing gene expression in a single cell or a few cells, for example, by a large-scale DNA sequencer.
    Type: Application
    Filed: November 21, 2012
    Publication date: January 22, 2015
    Inventors: Hiroyuki Tsunoda, Huan Huang, Mari Ohta, Hideki Kambara
  • Publication number: 20150010951
    Abstract: The present invention relates to a method of enriching for membranous microvesicles relative to the cellular population in a biological sample. More particularly, there is provided a method for enriching for exosomes from plasma. In a related aspect, there is provided a method of reducing the concentration of cellular and cellular derived molecules in a biological sample. Still further, the present invention provides methods for selectively isolating mRNA subpopulations from exosomes. Yet further, there are provided methods of amplifying exosome derived RNA. The method of the present invention is useful in a range of applications including, but not limited to, diagnostic, prognostic, therapeutic, research and development applications, to the extent that the enrichment of exosomes is required.
    Type: Application
    Filed: October 26, 2011
    Publication date: January 8, 2015
    Applicant: Clinical Genomics Pty. Ltd.
    Inventors: Lawrence Charles LaPointe, Susanne Kartin Pedersen, Aidan McEvoy
  • Patent number: 8900814
    Abstract: The present invention provides a versatile mutant reverse transcriptase with high thermal stability, a nucleic acid thereof and a method for producing a mutant reverse transcriptase, a versatile kits for reverse transcription and detection, a method for improving thermal stability of a nucleic acid-related enzyme, which significantly improves thermal stability of a nucleic acid-related enzyme, and a reverse transcription method, which efficiently performs a reverse transcription. An amino acid residue in a nucleic acid interaction region of a wild-type enzyme is substituted with a positively-charged amino acid residue or a nonpolar amino acid residue, to form a nucleic acid interaction region having a positive effective charge larger than the nucleic acid interaction region of a wild-type enzyme.
    Type: Grant
    Filed: August 9, 2011
    Date of Patent: December 2, 2014
    Assignee: Kyoto University
    Inventors: Kiyoshi Yasukawa, Kuniyo Inouye
  • Publication number: 20140349858
    Abstract: The present invention relates to methods and compositions for tagging, amplifying, purifying, and or characterizing of ribonucleic acid (RNA) in a sample. In particular, methods are provided for preparing RNA from a sample for subsequent analysis.
    Type: Application
    Filed: December 21, 2012
    Publication date: November 27, 2014
    Applicant: IBIS BIOSCIENCE, INC.
    Inventors: Stanley T. Motley, Mark W. Eshoo
  • Publication number: 20140349890
    Abstract: Compositions and methods for amplifying selected polynucleotides, including DNA and RNA, particularly in multiplex amplification reactions using common primers amplification. Generally, methods of the invention employ multiple steps such as template-specific hybridization, a linear amplification, partial degradation of nucleic acid, and ligation. At the end of the process the sequences of selected polynucleotides are flanked by the common sequences which can be used for exponential amplification using common primers. In some aspects the polynucleotides are associated with a barcode and the presence of the barcode is detected to measure the amount of the polynucleotide.
    Type: Application
    Filed: August 11, 2014
    Publication date: November 27, 2014
    Inventor: Eugeni A. NAMSARAEV
  • Patent number: 8895269
    Abstract: Methods and compositions relating to the generation and use of gene expression data from tissue samples that have been fixed and embedded are provided. The data can be electronically stored and implemented as well as used to augment diagnosis and treatment of diseases.
    Type: Grant
    Filed: August 8, 2011
    Date of Patent: November 25, 2014
    Inventors: Mark G. Erlander, Ranelle C. Salunga
  • Publication number: 20140336079
    Abstract: Provided in certain embodiments are new methods for forming azido modified nucleic acid conjugates of reporter molecules, carrier molecules or solid support. In other embodiments are provided methods for enzymatically labeling nucleic acids with an azide group.
    Type: Application
    Filed: July 30, 2014
    Publication date: November 13, 2014
    Inventors: Brian AGNEW, Maura Ford, Kyle Gee, Kapil Kumar
  • Publication number: 20140322761
    Abstract: Provided is a method of preparing a sample for nucleic acid amplification reaction, including: a procedure of dissolving a solid phase reagent at least containing DNA polymerase, cyclodextrin, and a binder, in a liquid containing a nucleic acid.
    Type: Application
    Filed: February 26, 2014
    Publication date: October 30, 2014
    Applicant: SONY CORPORATION
    Inventors: Tomohiko Nakamura, Kenzo Machida
  • 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
  • Patent number: 8841120
    Abstract: The present invention provides polypeptides having a composite amino acid sequence derived from a consensus sequence representing the capsid proteins of two or more circulating strains of a non-enveloped virus. In particular, the invention provides virus-like particles comprising at least one composite polypeptide. Such virus-like particles have antigenic epitopes of two or more circulating strains of a non-enveloped virus and produce an increase in antisera cross-reactivity to one or more circulating strains of the non-enveloped virus. Methods of making composite virus-like particles and vaccine formulations comprising composite virus-like particles are also disclosed.
    Type: Grant
    Filed: February 8, 2011
    Date of Patent: September 23, 2014
    Assignee: Takeda Vaccines, Inc.
    Inventors: Charles Richardson, Robert F. Bargatze, Joel Haynes, Bryan Steadman
  • Patent number: 8829174
    Abstract: Improved anti-HCV immunogens and nucleic acid molecules that encode them are disclosed. Immunogens disclosed include those having consensus HCV genotype 1 a/1 b NS3 and NS4A. Pharmaceutical composition, recombinant vaccines comprising and live attenuated vaccines are disclosed as well methods of inducing an immune response in an individual against HCV are disclosed.
    Type: Grant
    Filed: October 29, 2008
    Date of Patent: September 9, 2014
    Assignees: The Trustees of the University of Pennsylvania, Inovio Pharmaceuticals, Inc.
    Inventors: David B Weiner, Krystle A. Lang Kuhs, Jian Yan, Ruxandra Draghia-Akli, Amir Khan
  • Patent number: 8822152
    Abstract: The present invention is in the field of nucleic acid amplification, and in particular in transcription-based amplification, providing improvements thereof. Specifically, the present invention provides primers, and methods for using them, that improve transcription-based amplification reactions, in particular multiplex reactions.
    Type: Grant
    Filed: November 7, 2007
    Date of Patent: September 2, 2014
    Assignee: bioMerieux B.V.
    Inventors: Paul van de Wiel, Birgit Deiman, Dianne van Strijp
  • Patent number: 8822168
    Abstract: The present invention includes assays and kits for detecting the assembly of an RNA binding protein-RNA complex and for detecting the activity of an RNA binding protein.
    Type: Grant
    Filed: March 10, 2006
    Date of Patent: September 2, 2014
    Assignee: The Trustees of the University of Pennsylvania
    Inventors: Gideon Dreyfuss, Lili Wan, Elizabeth Ottinger
  • Publication number: 20140242639
    Abstract: A method for designing a bi-shRNA expression cassette encoding a bi-shRNA comprising: selecting one or more target site sequences; providing a backbone sequence comprising a first and a second stem-loop structure, inserting a first passenger strand and a second passenger strand and providing for synthesis of the bi-shRNA expression cassette.
    Type: Application
    Filed: May 6, 2014
    Publication date: August 28, 2014
    Applicant: Gradalis, Inc.
    Inventor: Donald Rao
  • Publication number: 20140206562
    Abstract: Fabrication of a microfluidic multi-temperature reaction device (MMR) and the design and fabrication of the equipment to drive various molecular biological methods on the device are provided. The device can be applicable, for example, to nucleic acid (DNA, RNA, cDNA, etc) amplification, cell lysis, reverse transcription and other enzymatic temperature sensitive and also temperature cycling reactions.
    Type: Application
    Filed: January 20, 2014
    Publication date: July 24, 2014
    Applicant: QUANTUMDX GROUP LIMITED
    Inventors: JOHN EDWARD MCCORMACK, ELAINE HARRINGTON WARBURTON, JONATHAN JAMES O'HALLORAN, MATTHEW DANIEL SOLOMON, DAVID JAMES BRIGGS, MINDY LEE ANDRE, MATTHIAS SCHUENEMANN
  • 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: 8697352
    Abstract: The present invention is related to nucleic acid sequences that can be used in the field of virus diagnostics, more specifically the diagnosis of infections with the AIDS causing Human Immuno-deficiency Virus (HIV). With the present invention nucleotide sequences are provided that can be used as primers and probes in the amplification and detection of HIV-1 nucleic acid. The oligonucleotide sequences provided with the present invention are located in the LTR part of the HIV viral genome. It has been found that, by using the sequences of the present invention in methods for the amplification and detection of nucleic acid a sensitive and specific detection of HIV-1 can be obtained. The benefit of the sequences of the present invention primarily resides in the fact that, with the aid of primers and probes comprising the sequences according to the invention the nucleic acid of all presently known subtypes of HIV-1 can be detected with high accuracy and sensitivity.
    Type: Grant
    Filed: April 18, 2005
    Date of Patent: April 15, 2014
    Assignee: bioMerieux, B.V.
    Inventors: Jaap Goudsmit, Pieter Oudshoorn, Suzanne Jurriaans, Vladimir Vladimirovich Lukashov
  • Publication number: 20140093883
    Abstract: The invention is in general directed to the rapid exponential amplification of short DNA or RNA sequences at a constant temperature.
    Type: Application
    Filed: October 30, 2013
    Publication date: April 3, 2014
    Applicant: Ionian Technologies, Inc.
    Inventors: Brian K. Maples, Rebecca C. Holmberg, Andrew P. Miller, Jarrod Provins, Richard Roth, Jeffrey Mandell
  • Patent number: 8673595
    Abstract: One embodiment is related to a method of analyzing plural samples. The method includes amplifying a plurality of samples using a first primer and second primer, wherein the first primer includes a tag sequence having a sequence different from a sample to one another and wherein a second primer used in pair with the first primer in independent reaction systems for the respective samples to obtain an amplified product in which the tag sequence is introduced, mixing amplified products obtained in the plurality of reaction systems, making the mixed amplified product react with a nucleic acid probe immobilized on a substrate, and detecting the amount of hybridization that has occurred.
    Type: Grant
    Filed: December 29, 2011
    Date of Patent: March 18, 2014
    Assignee: Kabushiki Kaisha Toshiba
    Inventors: Naoko Nakamura, Koji Hashimoto, Nobuhiro Gemma
  • Publication number: 20140051126
    Abstract: Disclosed are DNA polymerases having increased reverse transcriptase efficiency relative to a corresponding, unmodified polymerase. The 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 DNA polymerases.
    Type: Application
    Filed: December 5, 2012
    Publication date: February 20, 2014
    Applicant: Roche Molecular Systems, Inc.
    Inventors: Keith Bauer, Thomas W. Myers, Shawn Suko
  • Publication number: 20140004508
    Abstract: A method of amplifying RNA template is provided. The method comprises reverse-transcribing a ribonucleic acid (RNA) template to form a cDNA using a first reaction mixture comprising RNA template, at least one primer capable of hybridizing to the RNA template, a reverse transcriptase and deoxynucleoside triphosphates (dNTPs); and amplifying the cDNA to form an amplified product using a second reaction mixture comprising at least one strand displacement DNA polymerase, at least one inosine-containing primer and a nuclease that is capable of nicking DNA 3? to an inosine residue of the primer. The method is accomplished under an isothermal condition without denaturing the cDNA template. A method of quantifying RNA template in a sample and a method of detecting RNA template in a sample are also provided.
    Type: Application
    Filed: June 29, 2012
    Publication date: January 2, 2014
    Applicant: GENERAL ELECTRIC COMPANY
    Inventors: John Richard Nelson, Robert Scott Duthie, Gregory Andrew Grossmann, Ryan Charles Heller
  • Publication number: 20140004569
    Abstract: A method of preparing a DNA copy of a target polynucleotide using template switching is described. The method includes mixing a double stranded template/primer substrate made up of a DNA primer oligonucleotide associated with a complementary oligonucleotide template strand with a target polynucleotide in a reaction medium and adding a suitable amount of a non-retroviral reverse transcriptase to the reaction medium to extend the DNA primer oligonucleotide from its 3? end to provide a DNA copy polynucleotide. The DNA copy polynucleotide includes a complementary target DNA polynucleotide that is synthesized using the target polynucleotide as a template. Methods of adding nucleotides to the double stranded template/primer substrate are also described. The method can be used to facilitate detection, PCR amplification, cloning, and determination of RNA and DNA sequences.
    Type: Application
    Filed: February 23, 2012
    Publication date: January 2, 2014
    Applicant: Board of Regents, The University of Texas System
    Inventors: Alan M. Lambowitz, Sabine Mohr, Travis B. White, Scott Kuersten
  • Publication number: 20130344491
    Abstract: A random-primed reverse transcriptase-in vitro transcription method of linearly amplifying RNA is provided. According to the methods of the invention, source RNA (or other single-stranded nucleic acid), preferably, mRNA, is converted to double-stranded cDNA using two random primers, one of which comprises a RNA polymerase promoter sequence (“promoter-primer”), to yield a double-stranded cDNA that comprises a RNA polymerase promoter that is recognized by a RNA polymerase. Preferably, the primer for first-strand cDNA synthesis is a promoter-primer and the primer for second-strand cDNA synthesis is not a promoter-primer. The double-stranded cDNA is then transcribed into RNA by the RNA polymerase, optimally in the presence of a reverse transcriptase that is rendered incapable of RNA-dependent DNA polymerase activity during this transcription step. The subject methods produce linearly amplified RNA with little or no 3? bias in the sequences of the nucleic acid population amplified.
    Type: Application
    Filed: May 17, 2013
    Publication date: December 26, 2013
    Applicant: LIFE TECHNOLOGIES CORPORATION
    Inventors: MICHAEL ZIMAN, COLLEEN DAVIS
  • Publication number: 20130330778
    Abstract: A method of processing a target RNA is provided. In certain embodiments, this method comprises: contacting the products of an RNA ligase-mediated ligation reaction with an CAS6 protein, wherein: (i) the RNA ligase-mediated ligation reaction comprises: a target RNA, an RNA ligase, and first and second adaptors that can ligate together to produce an adaptor dimer that contains a CRISPR stem loop; and (ii) the CAS6 protein recognizes the CRISPR stem loop; thereby preventing the adaptor dimer from being reverse transcribed.
    Type: Application
    Filed: May 15, 2013
    Publication date: December 12, 2013
    Inventors: Gusti Zeiner, Laurakay Bruhn
  • Publication number: 20130303407
    Abstract: 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: Application
    Filed: February 13, 2013
    Publication date: November 14, 2013
    Inventors: Vladimir L. MAKAROV, Emmanuel KAMBEROV, Brendan J. TARRIER
  • Patent number: 8575427
    Abstract: The nucleotide sequence of a 992 bp region of cDNA and the nucleotide sequence of a 1973 bp (or a 1913 bp) of genomic DNA of the Gr-cm-1 gene were determined for G. rostochiensis. PCR primers and probes specific for G. rostochiensis and G. pallida were generated. PCR assays, including a real-time TaqMan PCR were used to identify G. rostochiensis and G. pallida and to differentiate G. rostochiensis from G. pallida. Transgenic hairy roots expressing Gr-cm-1 dsRNA were generated. There was a 52% reduction in the average number of females per root in the Gr-cm-1 dsRNA transgenic lines when compared with the infected control lines.
    Type: Grant
    Filed: July 24, 2009
    Date of Patent: November 5, 2013
    Assignee: The United States of America as represented by the Secretary of Agriculture
    Inventors: Xiaohong Wang, Shunwen Lu
  • Publication number: 20130280713
    Abstract: A first polynucleotide including at least two complementary regions that are complementary to a target nucleic acid and have a reverse configuration, a second polynucleotide complementary to the first polynucleotide, and uses thereof, are provided.
    Type: Application
    Filed: April 19, 2013
    Publication date: October 24, 2013
    Applicant: SAMSUNG ELECTRONICS CO., LTD.
    Inventors: DONG-HYUN PARK, SUNG-WOO HONG, MYO-YONG LEE
  • Patent number: 8557518
    Abstract: The present invention discloses the integration of programmable microfluidic circuits to achieve practical applications to process biochemical and chemical reactions and to integrate these reactions. In some embodiments workflows for biochemical reactions or chemical workflows are combined. Microvalves such as programmable microfluidic circuit with Y valves and flow through valves are disclosed. In some embodiments microvalves of the present invention are used for mixing fluids, which may be part of an integrated process. These processes include mixing samples and moving reactions to an edge or reservoir for modular microfluidics, use of capture regions, and injection into analytical devices on separate devices. In some embodiments star and nested star designs, or bead capture by change of cross sectional area of a channel in a microvalve are used. Movement of samples between temperature zones are further disclosed using fixed temperature and movement of the samples by micropumps.
    Type: Grant
    Filed: July 28, 2010
    Date of Patent: October 15, 2013
    Assignee: IntegenX Inc.
    Inventors: Stevan Bogdan Jovanovich, Iuliu I. Blaga, Michael Nguyen, William D. Nielsen, Mattias Vangbo
  • Publication number: 20130203122
    Abstract: The present invention provides a method for amplifying a nucleic acid molecule. The method involves mixing an RNA template with a composition having a reverse transcriptase, a DNA polymerase and a RT inhibition reducer. The RT inhibition reducer can be Sso7d, Sac7d, Sac7e, Sso7e, AluI methylase, suramin, a phosphorothioate oligodeoxycytosine, a phosphorothioate oligodeoxyadenine, a phosphorothioate oligodeoxythymine or poly(rA)(dT). The mixing forms a mixture that is incubated under conditions sufficient to synthesize a DNA molecule complementary to all or a portion of the RNA template, thereby amplifying the nucleic acid molecule.
    Type: Application
    Filed: November 19, 2012
    Publication date: August 8, 2013
    Applicant: Bio Rad Laboratories, Inc.
    Inventor: Bio Rad Laboratories, Inc.
  • Publication number: 20130157259
    Abstract: Provided are methods of efficiently amplifying DNA from RNA in sample, methods of efficiently estimating an amount of RNA in a sample, and compositions for efficiently amplifying DNA from RNA in a sample.
    Type: Application
    Filed: December 14, 2012
    Publication date: June 20, 2013
    Applicant: SAMSUNG ELECTRONICS CO., LTD.
    Inventor: SAMSUNG ELECTRONICS CO., LTD.
  • Publication number: 20130143225
    Abstract: The present invention provides a versatile mutant reverse transcriptase with high thermal stability, a nucleic acid thereof and a method for producing a mutant reverse transcriptase, a versatile kits for reverse transcription and detection, a method for improving thermal stability of a nucleic acid-related enzyme, which significantly improves thermal stability of a nucleic acid-related enzyme, and a reverse transcription method, which efficiently performs a reverse transcription. An amino acid residue in a nucleic acid interaction region of a wild-type enzyme is substituted with a positively-charged amino acid residue or a nonpolar amino acid residue, to form a nucleic acid interaction region having a positive effective charge larger than the nucleic acid interaction region of a wild-type enzyme.
    Type: Application
    Filed: August 9, 2011
    Publication date: June 6, 2013
    Applicant: Kyoto University
    Inventors: Kiyoshi Yasukawa, Kuniyo Inouye
  • Publication number: 20130122507
    Abstract: The present invention provides a method for amplification of a target nucleic acid sequence or signal, wherein an amplification reaction mixture is used which contains at least one reversibly modified oligonucleotide having a non-hydroxyl group 3? end which can be converted into a hydroxyl 3? end upon exposure to a chemical and/or irradiation and/or a range of temperature. The present invention also provides a reversibly modified oligonucleotide as described above, and a nucleic acid amplification reaction mixture and kit comprising such an oligonucleotide.
    Type: Application
    Filed: November 20, 2012
    Publication date: May 16, 2013
    Inventor: Wanli Bi
  • Patent number: 8404446
    Abstract: A method is provided for nucleic acid amplification with enhanced sensitivity. The method for enhanced sensitivity involves carrying out the amplification reaction in the presence of gellan. For instance, the method allows for the production of detectable amounts of PCR amplified DNA from at least 10 fold fewer target molecules than a comparable PCR reaction in absence of gellan.
    Type: Grant
    Filed: October 23, 2009
    Date of Patent: March 26, 2013
    Assignee: Shin-Etsu Chemical Co. Ltd.
    Inventor: Richard W. Armentrout
  • Patent number: 8389244
    Abstract: Amplification-based methods and kits for rapidly producing siRNA expression cassettes are provided. Also provided are methods for expressing amplified siRNA expression cassettes in cells.
    Type: Grant
    Filed: July 31, 2003
    Date of Patent: March 5, 2013
    Assignee: City of Hope
    Inventors: John J. Rossi, Daniela Castanotto
  • Patent number: RE44596
    Abstract: The present invention relates to a method for the diagnosis and/or the follow up of the evolution of cancer, which includes the analysis and quantification of over expressed and amplified genes in the plasma/serum of cancer patients or persons suspected to harbor cancer. This is achieved by analyzing together the amount of DNA and RNA of certain genes in the plasma/serum of cancer patients that are the reflection of a gene amplification and/or a gene over expression in comparison to healthy controls.
    Type: Grant
    Filed: April 13, 2012
    Date of Patent: November 12, 2013
    Assignee: Guardant Health, Inc.
    Inventors: Maurice Stroun, Philippe Anker