Patents by Inventor Insil Park
Insil Park 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: 20150167072Abstract: Methods, Compositions, and Systems are provided for obtaining polymerase-template complex mixtures with improved levels of active polymerase. In some aspects active polymerase-template complex is separated by affinity for nucleoside phosphate moieties attached to a resin. In some aspects, a polymerase-template complex is exposed to reaction conditions in which a complementary strand to the template is produced. The extended reaction mixture is purified by reaction with a resin comprising nucleoside phosphate moieties. This purified mixture can be loaded onto substrates and can be used for further analyses including single molecule sequencing.Type: ApplicationFiled: December 12, 2014Publication date: June 18, 2015Inventors: Lei Sun, Insil Park
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Patent number: 8936911Abstract: Methods, Compositions, and Systems are provided for obtaining polymerase-template complex mixtures with improved levels of active polymerase. In some aspects, methods are described in which a polymerase-template complex is exposed to reaction conditions in which a complementary strand to the template is produced. The extended reaction mixture is purified, for example by gel filtration chromatography to produce a mixture of polymerase-template complex having a higher active fraction. This purified mixture can be used for further analyses including single molecule sequencing.Type: GrantFiled: September 15, 2011Date of Patent: January 20, 2015Assignee: Pacific Biosciences of California, Inc.Inventors: Lei Sun, Insil Park
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Patent number: 8921086Abstract: 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: GrantFiled: December 21, 2006Date of Patent: December 30, 2014Assignee: Pacific Biosciences of California, Inc.Inventors: David K. Hanzel, Geoff Otto, 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: 8420366Abstract: 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: GrantFiled: September 30, 2010Date of Patent: April 16, 2013Assignee: 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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Patent number: 8257954Abstract: 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: GrantFiled: March 30, 2009Date of Patent: September 4, 2012Assignee: 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: 20120071359Abstract: Methods, Compositions, and Systems are provided for obtaining polymerase-template complex mixtures with improved levels of active polymerase. In some aspects, methods are described in which a polymerase-template complex is exposed to reaction conditions in which a complementary strand to the template is produced. The extended reaction mixture is purified, for example by gel filtration chromatography to produce a mixture of polymerase-template complex having a higher active fraction. This purified mixture can be used for further analyses including single molecule sequencing.Type: ApplicationFiled: September 15, 2011Publication date: March 22, 2012Applicant: Pacific Biosciences of California, Inc.Inventors: Lei Sun, Insil Park
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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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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: 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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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: 20100093555Abstract: Provided are compositions comprising modified DNA polymerases that exhibit improved photostability compared to the parental polymerases from which they were derived. Provided are methods for generating enzymes, such as DNA polymerases, with the aforementioned phenotype. Provided are methods of using polymerases with increased resistance to photodamage to make a DNA or to sequence a DNA template.Type: ApplicationFiled: March 30, 2009Publication date: April 15, 2010Applicant: Pacific Biosciences of California, Inc.Inventors: Keith Bjornson, Sonya Clark, Insil Park, Fred Christians
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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