Patents Examined by Richard Hutson
  • DNA polymerases and related methods
    Patent number: 9102924
    Abstract: Disclosed are mutant DNA polymerases having improved extension rates relative to a corresponding, unmodified polymerase. The mutant polymerases are useful in a variety of disclosed primer extension methods. The mutant polymerases overcome the inhibitory effects by an intercalating dye. Therefore, the mutant polymerases are useful in a variety of disclosed methods in combination with an intercalating dye. 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: Grant
    Filed: April 16, 2009
    Date of Patent: August 11, 2015
    Assignee: Roche Molecular Systems, Inc.
    Inventors: Keith A. Bauer, Ellen Fiss, David H. Gelfand, Edward S. Smith, Shawn Suko, Olga Budker, Nancy Schoenbrunner, Susanne Stoffel, Thomas Myers
  • DNA polymerase
    Patent number: 9096835
    Abstract: The present invention relates to DNA polymerases. In particular the invention relates to a method for the generation of DNA polymerases exhibiting a relaxed substrate specificity. Uses of mutant polymerases produced using the methods of the invention are also described.
    Type: Grant
    Filed: June 19, 2012
    Date of Patent: August 4, 2015
    Assignee: Medical Research Council
    Inventors: Philipp Holliger, Farid Ghadessy, Marc d'Abbadie
  • Detection of mutations in a gene associated with resistance to viral infection, OAS1
    Patent number: 9090947
    Abstract: A method for detecting a mutation related to the gene encoding OAS1. This and other disclosed mutations correlate with resistance of humans to viral infection including hepatitis C. Also provided is a therapeutic agent consisting of a protein or polypeptide encoded by the mutated gene, or a polynucleotide encoding the protein or polypeptide. Inhibitors of human OAS1, including antisense oligonucleotides, methods, and compositions specific for human OAS1, are also provided.
    Type: Grant
    Filed: May 28, 2013
    Date of Patent: July 28, 2015
    Assignee: Kineta Two, LLC
    Inventors: Shawn P. Iadonato, Charles L. Magness, Gary Rosenberg, Christina A. Scherer, Thierry Guillaudeux
  • Compositions and methods using split polymerases
    Patent number: 9085762
    Abstract: The invention relates to compositions and methods utilizing split polymerase enzymes composed of at least two discrete polypeptides that stably associate to form a single polymerase. The invention further relates to nucleic acid constructs for expressing the split polymerases of the invention, and methods for using the split polymerases of the invention. The enzymes of the invention are useful in many applications calling for the detectable labeling of nucleic acids and are particularly useful in quantitative PCR (QPCR) and DNA sequencing applications.
    Type: Grant
    Filed: December 31, 2007
    Date of Patent: July 21, 2015
    Assignee: Agilent Technologies, Inc.
    Inventors: Holly Hogrefe, Lydia Wu, Jeffrey D. Fox, Connie Jo Hansen
  • Mutant T7 polymerases
    Patent number: 9062292
    Abstract: Provided are mutant polymerases that comprise a deletion of at least four amino acids among the amino acids at positions corresponding to 167-174 of SEQ ID NO:1. Also provided are mutant polymerases having greater resistance to 30 mM NaCl, 7.5 mM phosphate, or 20 ?g/ml single stranded DNA than a wild-type T7 RNA polymerase having SEQ ID NO:1 or a wild-type T3 RNA polymerase having SEQ ID NO:3. Nucleic acids comprising a nucleotide sequence encoding any of the above mutant polymerases are also provided, as are vectors comprising those nucleic acids and host cells transformed with the vectors Additionally, methods of amplifying mRNA using the mutant polymerases described herein are also provided. Further, compositions comprising any of the mutant polymerases described herein, and a reagent at a concentration that is inhibitory to wild-type T7 RNA polymerase is provided.
    Type: Grant
    Filed: September 13, 2010
    Date of Patent: June 23, 2015
    Assignee: Enzo Life Sciences Inc.
    Inventor: Jack Coleman
  • Poly(ADP-ribose) polymerase genes
    Patent number: 9051553
    Abstract: The invention relates to poly(ADP-ribose)polymerase (PARP) homologs which have an amino acid sequence which has a) a functional NAD binding domain and b) no zinc finger sequence motif of the general formula CX2CXmHX2C in which m is an integral value from 28 or 30, and the X radicals are, independently of one another, any amino acid; and the functional equivalents thereof; nucleic acids coding therefor; antibodies with specificity for the novel protein; pharmaceutical and gene therapy compositions which comprise products according to the invention; methods for the analytical determination of the proteins and nucleic acids according to the invention; methods for identifying effectors or binding partners of the proteins according to the invention; novel PARP effectors; and methods for determining the activity of such effectors.
    Type: Grant
    Filed: May 12, 2010
    Date of Patent: June 9, 2015
    Assignee: AbbVie Deutschland GmbH & Co. KG
    Inventors: Michael Kock, Thomas Höger, Burkhard Kröger, Bernd Otterbach, Wilfried Lubisch, Hans-Georg Lemaire
  • DNA binding protein-polymerase chimeras
    Patent number: 9040276
    Abstract: The invention relates to compositions and methods directed to chimeric DNA polymerases, which comprise a mutated DNA binding polypeptide domain and a mutated or wild-type DNA polymerase polypeptide domain.
    Type: Grant
    Filed: July 17, 2006
    Date of Patent: May 26, 2015
    Assignee: Agilent Technologies, Inc.
    Inventor: Michael Borns
  • Altering the interface of hydrocarbon-coated surfaces
    Patent number: 9029123
    Abstract: Methods and compositions are provided wherein microorganisms are used to alter the interface of hydrocarbons and hydrocarbon-coated surfaces to increase oil recovery, for improved bioremediation and/or to benefit pipeline maintenance.
    Type: Grant
    Filed: September 7, 2011
    Date of Patent: May 12, 2015
    Assignee: E I du Pont de Nemours and Company
    Inventors: Edwin R. Hendrickson, Abigail K. Luckring, Michael P. Perry
  • Chimeric DNA polymerases
    Patent number: 9023633
    Abstract: The present invention provides, among other things, chimeric DNA polymerases containing heterologous domains having sequences derived from at least two DNA polymerases that have at least one distinct functional characteristics (e.g., elongation rate, processivity, error rate or fidelity, salt tolerance or resistance) and methods of making and using the same. In some embodiments, the present invention can combine desired functional characteristics (e.g., high processivity; high elongation rate; thermostability; resistance to salt, PCR additives (e.g., PCR enhancers) and other impurities; and high fidelity) of different DNA polymerases in a chimeric polymerase.
    Type: Grant
    Filed: November 3, 2009
    Date of Patent: May 5, 2015
    Assignee: Kapa Biosystems
    Inventors: Bjarne Faurholm, Paul McEwan, William Bourn, Gavin Rush
  • Sensor chip for screening topoisomerase inhibitor and screening method thereof
    Patent number: 9005922
    Abstract: The present invention discloses a sensor chip for screening a topoisomerase inhibitor and a screening method thereof. The sensor chip comprises topoisomerase I and a biochip. The topoisomerase I is immobilized on the biochip, and the topoisomerase I has DNA catalytic activity. This provides a rapid screening method for topoisomerase I inhibitors.
    Type: Grant
    Filed: September 21, 2010
    Date of Patent: April 14, 2015
    Assignee: Taipei Medical University
    Inventors: Chun-Mao Lin, Hsiang-Ping Tsai, Chwen-Ming Shih, Jau-Lang Hwang, Chi-Ming Lee
  • Methods and apparatus for single molecule sequencing using energy transfer detection
    Patent number: 8999674
    Abstract: Provided herein are systems and methods for nucleotide incorporation reactions. The systems comprise polymerases having altered nucleotide incorporation kinetics and are linked to an energy transfer donor moiety, and nucleotide molecules linked with at least one energy transfer acceptor moiety. The donor and acceptor moieties undergo energy transfer when the polymerase and nucleotide are proximal to each other during nucleotide binding and/or nucleotide incorporation. As the donor and acceptor moieties undergo energy transfer, they generate an energy transfer signal which can be associated with nucleotide binding or incorporation. Detecting a time sequence of the generated signals, or the change in the signals, can be used to determine the order of the incorporated nucleotides, and can therefore be used to deduce the sequence of the target molecule.
    Type: Grant
    Filed: July 30, 2012
    Date of Patent: April 7, 2015
    Assignee: Life Technologies Corporation
    Inventors: Joseph Beechem, Theo Nikiforov, Vi-En Choong, Xinzhan Peng, Guobin Luo, Cheng-Yao Chen, Michael Previte
  • Recombinant polymerases for improved single molecule sequencing
    Patent number: 8999676
    Abstract: Provided are compositions comprising recombinant DNA polymerases that include amino acid substitutions, insertions, deletions, and/or exogenous features that confer modified properties upon the polymerase for enhanced single molecule sequencing. Such properties can include enhanced metal ion coordination, reduced exonuclease activity, reduced reaction rates at one or more steps of the polymerase kinetic cycle, decreased branching fraction, altered cofactor selectivity, increased yield, increased thermostability, increased accuracy, increased speed, increased readlength, and the like. Also provided are nucleic acids which encode the polymerases with the aforementioned phenotypes, as well as methods of using such polymerases to make a DNA or to sequence a DNA template.
    Type: Grant
    Filed: July 5, 2011
    Date of Patent: April 7, 2015
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Robin Emig, Lei Jia, Satwik Kamtekar, Erik Miller, Colleen Cutcliffe, Walter Lee
  • Compositions and methods for enhancing the degradation or conversion of cellulose-containing material
    Patent number: 8999696
    Abstract: The present invention relates to methods for degrading or converting a cellulose-containing material, comprising: treating the cellulose-containing material with an effective amount of a cellulolytic enzyme composition comprising a polypeptide having cellulolytic enhancing activity, and one or more (several) components selected from the group consisting of a CEL7 polypeptide having endoglucanase activity, a CEL12 polypeptide having endoglucanase activity, a CEL45 polypeptide having endoglucanase activity, a CEL7 polypeptide having cellobiohydrolase activity with a cellulose binding domain, and a CEL7 polypeptide having cellobiohydrolase activity without a cellulose binding domain. The present invention also relates to such cellulolytic enzyme compositions.
    Type: Grant
    Filed: May 9, 2008
    Date of Patent: April 7, 2015
    Assignee: Novozymes, Inc.
    Inventor: Keith McFarland
  • Method for producing alkaloids
    Patent number: 8993280
    Abstract: The present invention provides a method for producing an alkaloid, for example, reticuline, comprising providing dopamine as a substrate for a series of actions of monoamine oxidase, norcoclaurine-6-O-methyltransferase, coclaurine-N-methyltransferase and 3?-hydroxy-N-methylcoclaurine-4?-O-methyltransferase.
    Type: Grant
    Filed: June 12, 2008
    Date of Patent: March 31, 2015
    Assignee: Kyoto University
    Inventors: Fumihiko Sato, Hiromichi Minami
  • Thermostable DNA polymerase
    Patent number: 8986968
    Abstract: There is provided a polypeptide having thermostable DNA polymerase activity and comprising or consisting of an amino acid sequence with at least 55% identity to Thermodesulfatator indicus DNA polymerase I Large fragment shown in SEQ ID NO: 1 or in SEQ ID NO:32.
    Type: Grant
    Filed: February 13, 2009
    Date of Patent: March 24, 2015
    Assignee: Genesys Biotech Ltd.
    Inventors: Duncan Clark, Nicholas Morant
  • Fermentative production of acetone from renewable resources by means of novel metabolic pathway
    Patent number: 8986961
    Abstract: The invention describes a process for preparing acetone starting from acetyl-coenzyme A comprising process steps A. enzymatic conversion of acetyl-CoA into acetoacetyl-CoA B. enzymatic conversion of acetoacetyl-CoA into acetoacetate and CoA and C. decarboxylation of acetoacetate to acetone and CO2, which is characterized in that the coenzyme A is not transferred in process step B to an acceptor molecule. In addition, process step B is surprisingly catalyzed by enzymes of the classes of acyl-CoA thioesterase, acyl-CoA synthetase or acyl-CoA thiokinase. A completely novel metabolic pathway is concerned, because the enzymatic hydrolysis of acetoacetyl-CoA without simultaneous transfer of CoA to a receptor molecule has never previously been described for any microbial enzyme.
    Type: Grant
    Filed: October 1, 2008
    Date of Patent: March 24, 2015
    Assignee: Evonik Degussa GmbH
    Inventors: Stefan Verseck, Steffen Schaffer, Werner Freitag, Friedrich-Georg Schmidt, Matthias Orschel, Gerda Grund, Wilfried Schmidt, Hubert Johannes Bahl, Ralf-Joerg Fischer, Antje May, Peter Duerre, Simone Lederle
  • Mutant delta-9 elongases and their use in making polyunsaturated fatty acids
    Patent number: 8980589
    Abstract: Mutant delta-9 elongases having the ability to convert linoleic acid [18:2, LA] to eicosadienoic acid [20:2, EDA] and/or ?-linolenic [18:3, ALA] to eicosatrienoic acid [20:3, ETrA] are disclosed herein. Isolated nucleic acid fragments and recombinant constructs comprising such fragments encoding mutant delta-9 elongases, along with a method of making long chain polyunsaturated fatty acids [“PUFAs”] using these mutant delta-9 elongases in oleaginous yeast are also disclosed.
    Type: Grant
    Filed: August 26, 2011
    Date of Patent: March 17, 2015
    Assignee: E I du Pont de Nemours and Company
    Inventors: Michael W. Bostick, Hongxian He, Yougen Li, Quinn Qun Zhu
  • DNA polymerases and related methods
    Patent number: 8962293
    Abstract: Disclosed are mutant DNA polymerases having improved extension rates 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: Grant
    Filed: October 17, 2007
    Date of Patent: February 24, 2015
    Assignee: Roche Molecular Systems, Inc.
    Inventors: Keith A. Bauer, Ellen Fiss, David H. Gelfand, Edward S. Smith, Shawn Suko, Thomas Myers
  • Recombinant reverse transcriptases
    Patent number: 8956841
    Abstract: The present invention relates to a gene that encodes a hyperactive reverse transcriptase having DNA polymerase activity and substantially reduced RNase H activity, vectors containing the gene and host cells transformed with the invention. The present invention also includes a method of producing the hyperactive reverse transcriptase, producing cDNA from mRNA using the reverse transcriptase of the invention, kits and assay templates made using the hyperactive reverse transcriptase.
    Type: Grant
    Filed: December 28, 2012
    Date of Patent: February 17, 2015
    Assignee: Applied Biosystems, LLC
    Inventors: Liangjing Chen, Robert Setterquist, Gary Latham
  • Targeted disruption of T cell receptor genes using engineered zinc finger protein nucleases
    Patent number: 8956828
    Abstract: Disclosed herein are methods and compositions for inactivating TCR genes, using zinc finger nucleases (ZFNs) comprising a zinc finger protein and a cleavage domain or cleavage half-domain in conditions able to preserve cell viability. Polynucleotides encoding ZFNs, vectors comprising polynucleotides encoding ZFNs and cells comprising polynucleotides encoding ZFNs and/or cells comprising ZFNs are also provided. Disclosed herein are also methods and compositions for expressing a functional exogenous TCR in the absence of endogenous TCR expression in T lymphocytes, including lymphocytes with a central memory phenotype. Polynucleotides encoding exogenous TCR, vectors comprising polynucleotides encoding exogenous TCR and cells comprising polynucleotides encoding exogenous TCR and/or cells comprising exogenous TCR are also provided.
    Type: Grant
    Filed: November 10, 2010
    Date of Patent: February 17, 2015
    Assignees: Sangamo BioSciences, Inc., Ospedale San Raffaele S.R.L.
    Inventors: Maria Chiara Bonini, Pietro Genovese, Philip D. Gregory, Michael C. Holmes, Luigi Naldini, David Paschon, Elena Provasi, Lei Zhang