Patents by Inventor Arek Bibillo
Arek Bibillo has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).
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Publication number: 20120115736Abstract: Provided are methods for sequencing a nucleic acid with a sequencing enzyme, e.g., a polymerase or exonuclease. The sequencing enzyme can optionally be exchanged with a second sequencing enzyme, which continues the sequencing of the nucleic acid. In certain embodiments, a template is fixed to a surface through a template localizing moiety. The template localizing moiety can optionally anneal with the nucleic acid and/or associate with the sequencing enzyme. Also provided are compositions comprising a nucleic acid and a first sequencing enzyme, which can sequence the nucleic acid and optionally exchange with a second sequencing enzyme present in the composition. Compositions in which a template localizing moiety is immobilized on a surface are provided. Also provided are methods for using data from analytical reactions wherein two different enzymes are employed, e.g., at a same or different reaction regions.Type: ApplicationFiled: October 12, 2011Publication date: May 10, 2012Applicant: Pacific Biosciences of California, Inc.Inventors: Keith Bjornson, Arek Bibillo, Fred Christians, Kevin Travers, Robin Emig, Stephen Turner
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Patent number: 8133672Abstract: Compositions, kits, methods and systems for nucleotide sequencing comprising producing polymerase reactions that exhibit two kinetically observable steps within an observable phase of the polymerase reaction. Two slow step systems can be produced, for example, by selecting the appropriate polymerase enzyme, polymerase reaction conditions including cofactors, and polymerase reaction substrates including the primed template and nucleotides.Type: GrantFiled: March 30, 2009Date of Patent: March 13, 2012Assignee: Pacific Biosciences of California, Inc.Inventors: Keith Bjornson, Harold Lee, Jonas Korlach, Stephen Turner, Arek Bibillo, Fred Christians, Robin Emig, Molly He, Insil Park, Lei Jia, Andrei Fedorov, John Lyle
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Publication number: 20120034602Abstract: 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: ApplicationFiled: July 5, 2011Publication date: February 9, 2012Applicant: Pacific Biosciences of California, Inc.Inventors: Robin Emig, Insil Park, Lei Jia, Arek Bibillo, Keith Bjornson, Molly He, Jeremiah Hanes, Harold Lee, Sonya Clark, Fred Christians, Paul Peluso, John Vieceli, Satwik Kamtekar, Erik Miller, Colleen Cutcliffe, Walter Lee
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Patent number: 8058031Abstract: Labeled nucleotide analogs used in place of naturally occurring nucleoside triphosphates or other analogs in template directed nucleic acid synthesis reactions and other nucleic acid reactions, and various analyses based thereon, including DNA sequencing, single base identification, hybridization assays and others.Type: GrantFiled: July 9, 2010Date of Patent: November 15, 2011Assignee: Pacific Biosciences of California, Inc.Inventors: Yue Xu, Jeffrey Wegener, Arek Bibillo
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Publication number: 20110189659Abstract: Provided are compositions comprising recombinant DNA polymerases that include amino acid substitutions, insertions, deletions and/or heterologous or exogenous features that confer modified properties upon the polymerase for enhanced single molecule sequencing. Such properties can include reduced reaction rates at one or more steps of the polymerase kinetic cycle, increased closed polymerase/DNA complex stability, enhanced metal ion coordination, reduced exonuclease activity, decreased branching fractions, and the like. Polymerases that exhibit branching fractions that are less than the branching fractions of the polymerases from which they were derived, or branching fractions that are less than about 25% for a phosphate-labeled nucleotide analog, are also provided. 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: ApplicationFiled: September 30, 2010Publication date: August 4, 2011Applicant: Pacific Biosciences of California, Inc.Inventors: Sonya Clark, Arek Bibillo, Paul Peluso, Fred Christians, Molly He, Insil Park, Harold Lee, Keith Bjornson, Lei Jia, Robin Emig
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Publication number: 20110059450Abstract: Labeled nucleotide analogs used in place of naturally occurring nucleoside triphosphates or other analogs in template directed nucleic acid synthesis reactions and other nucleic acid reactions, and various analyses based thereon, including DNA sequencing, single base identification, hybridization assays and others.Type: ApplicationFiled: July 9, 2010Publication date: March 10, 2011Applicant: Pacific Biosciences of California, Inc.Inventors: Yue Xu, Jeffrey Wegener, Arek Bibillo
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Publication number: 20110059505Abstract: Compositions that include polymerases with features for improving entry of nucleotide analogues into active site regions and for coordinating with the nucleotide analogues in the active site region are provided. Methods of making the polymerases and of using the polymerases in sequencing and DNA replication and amplification as well as kinetic models of polymerase activity and computer-implemented methods of using the models are also provided.Type: ApplicationFiled: June 8, 2010Publication date: March 10, 2011Inventors: David K. Hanzel, Geoff Otto, Devon Murphy, Paul Peluso, Thang Pham, David R. Rank, Paul Mitsis, Fred Christians, Arek Bibillo, Insil Park, Sonya Clark, John Lyle
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Patent number: 7777013Abstract: Labeled nucleotide analogs used in place of naturally occurring nucleoside triphosphates or other analogs in template directed nucleic acid synthesis reactions and other nucleic acid reactions, and various analyses based thereon, including DNA sequencing, single base identification, hybridization assays and others.Type: GrantFiled: May 15, 2008Date of Patent: August 17, 2010Assignee: Pacific Biosciences of California, Inc.Inventors: Yue Xu, Jeffrey Wegener, Arek Bibillo
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Publication number: 20100112645Abstract: Provided are compositions comprising modified recombinant polymerases that exhibit branching fractions that are less than the branching fractions of the polymerases from which they were derived, or branching fractions that are less than about 25% for a phosphate-labeled nucleotide analog. Also provided are compositions comprising modified recombinant polymerases that exhibit closed polymerase/DNA complexes with increased stability relative to the parental polymerases. Also provided are compositions comprising modified recombinant polymerases that exhibit decreased rate constants relative to the parental polymerases. Provided are methods for generating polymerases with the aforementioned phenotypes. Provided are methods of using such polymerases to make a DNA or to sequence a DNA template.Type: ApplicationFiled: March 30, 2009Publication date: May 6, 2010Applicant: Pacific Biosciences of California, Inc.Inventors: Sonya Clark, Arek Bibillo, Paul Peluso, Fred Christians, Molly He, Insil Park, Harold Lee, Keith Bjornson, Lei Jia, Robin Emig
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Publication number: 20100075328Abstract: Provided are methods for sequencing a nucleic acid that include fixing a template to a surface through a template localizing moiety and sequencing the nucleic acid with a sequencing enzyme, e.g. a polymerase or exonuclease. The sequencing enzyme can optionally be exchanged with a second sequencing enzyme, which continues the sequencing of the nucleic acid. The template localizing moiety can optionally anneal with the nucleic acid and/or associate with the sequencing enzyme. Also provided are compositions comprising a nucleic acid fixed to a surface via a template localizing moiety, and a first sequencing enzyme, which can sequence the nucleic acid and optionally exchange with a second sequencing enzyme present in the composition. Compositions in which a template localizing moiety is immobilized on a surface are provided. Compositions for sequencing reactions are provided. Also provided are sequencing systems comprising reaction regions in which or near which template localizing moieties are immobilized.Type: ApplicationFiled: September 18, 2009Publication date: March 25, 2010Applicant: Pacific Biosciences of California, Inc.Inventors: KEITH BJORNSON, Arek Bibillo, Fred Christians, Kevin Travers, Robin Emig
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Publication number: 20090286245Abstract: Compositions, kits, methods and systems for nucleotide sequencing comprising producing polymerase reactions that exhibit two kinetically observable steps within an observable phase of the polymerase reaction. Two slow step systems can be produced, for example, by selecting the appropriate polymerase enzyme, polymerase reaction conditions including cofactors, and polymerase reaction substrates including the primed template and nucleotides.Type: ApplicationFiled: March 30, 2009Publication date: November 19, 2009Applicant: Pacific Biosciences of California, Inc.Inventors: Keith Bjornson, Harold Lee, Jonas Korlach, Stephen Turner, Arek Bibillo, Fred Christians, Robin Emig, Molly He, Insil Park, Lei Jia, Andrei Fedorov, John Lyle
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Publication number: 20090208961Abstract: Compositions, methods, substrates and systems for use in analysis of single molecule reactions and particularly single molecule nucleic acid sequence analysis. Compositions that include non-reactive, distinguishable or undetectable competitive substrates for the reaction system of interest are provided, as well as their use in systems and substrates for such applications, such compounds typically preferably polyphosphate chains or analogous structures.Type: ApplicationFiled: February 12, 2009Publication date: August 20, 2009Applicant: Pacific Biosciences of California, Inc.Inventors: Keith Bjornson, Arek Bibillo, Lubomir Sebo
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Publication number: 20090018324Abstract: Labeled nucleotide analogs used in place of naturally occurring nucleoside triphosphates or other analogs in template directed nucleic acid synthesis reactions and other nucleic acid reactions, and various analyses based thereon, including DNA sequencing, single base identification, hybridization assays and others.Type: ApplicationFiled: May 15, 2008Publication date: January 15, 2009Applicant: Pacific Biosciences of California, Inc.Inventors: Yue Xu, Jeffrey Wegener, Arek Bibillo
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Patent number: 7405281Abstract: Labeled nucleotide analogs used in place of naturally occurring nucleoside triphosphates or other analogs in template directed nucleic acid synthesis reactions and other nucleic acid reactions, and various analyses based thereon, including DNA sequencing, single base identification, hybridization assays and others.Type: GrantFiled: September 29, 2005Date of Patent: July 29, 2008Assignee: Pacific Biosciences of California, Inc.Inventors: Yue Xu, Jeffrey Wegener, Arek Bibillo
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Publication number: 20080108082Abstract: Compositions that include DNA polymerases having increased residence times for nucleotide analogues, particularly modified recombinant ?29-type DNA polymerases with such increased residence times, are provided. Methods of making the polymerases and of using the polymerases in sequencing and DNA amplification are also provided. Compositions including ?-thiophosphate nucleotide analogues with four or more phosphate groups are described, as are methods for determining the sequence of nucleic acid molecules using such analogues.Type: ApplicationFiled: October 22, 2007Publication date: May 8, 2008Applicant: Pacific Biosciences of California, Inc.Inventors: David Rank, Arek Bibillo, David Hanzel, Paul Peluso, Jeff Wegener
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Publication number: 20070072196Abstract: Labeled nucleotide analogs used in place of naturally occurring nucleoside triphosphates or other analogs in template directed nucleic acid synthesis reactions and other nucleic acid reactions, and various analyses based thereon, including DNA sequencing, single base identification, hybridization assays and others.Type: ApplicationFiled: September 29, 2005Publication date: March 29, 2007Applicant: Pacific Biosciences of California, Inc.Inventors: Yue Xu, Jeffrey Wegener, Arek Bibillo