Patents by Inventor Fred Christians
Fred Christians 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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Patent number: 8906660Abstract: 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 include increased resistance to photodamage, and can also 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: GrantFiled: January 31, 2013Date of Patent: December 9, 2014Assignee: Pacific Biosciences of California, Inc.Inventors: Satwik Kamtekar, Arek Bibillo, Keith Bjornson, Fred Christians, Colleen Cutcliffe, Jeremiah Hanes, Lei Jia, Walter Lee, Erik Miller, Pranav Patel
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Patent number: 8906831Abstract: Methods for non-random loading of single analyte molecules into array structures are provided. The methods allow for distribution of a population of target molecules into a plurality of size confined regions such as wells. Sizing moieties are linked to individual target molecules. The sizing moieties are of sufficient size, relative to the size-confined reaction or observation regions, such that only a selected number of sizing moieties will fit into the size confined regions. The confined regions and the sizing moieties or target molecules comprise a selected charge that allow for controlling the loading of the sizing moities.Type: GrantFiled: March 30, 2009Date of Patent: December 9, 2014Assignee: Pacific Biosciences of California, Inc.Inventors: John Eid, Stephen Turner, Ravi Dalal, Benjamin Flusberg, Jonas Korlach, Steven Lin, Adrian Fehr, Fred Christians, Robin Emig, Jeremy Gray, Robert Sebra, Lei Sun, Stephen Dudek
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Publication number: 20140017690Abstract: Methods, systems and compositions where a target nucleic acid includes a registration sequence disposed therein for identification of the number or relative position of determined sequence from the template sequence. Particularly preferred aspects include a registration sequence in a circular template nucleic acid sequence which is, in turn, used in sequence by incorporation processes that rely upon template dependent, polymerase mediated primer extension in the identification of the sequence of the template.Type: ApplicationFiled: August 14, 2013Publication date: January 16, 2014Applicant: Pacific Biosciences of California, Inc.Inventors: Fred Christians, Stephen Turner
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Patent number: 8628940Abstract: Methods, devices, and systems for performing intermittent detection during analytical reactions are provided. Such methods facilitate collection of reaction data from disparate reaction times. Further, such methods are useful for reducing photo-induced damage of one or more reactants in an illuminated analytical reaction at a given reaction time. In preferred embodiments, the reaction mixture is subjected to at least one illuminated and non-illuminated period and allowed to proceed such that the time in which the reaction mixture is illuminated is less than a photo-induced damage threshold period.Type: GrantFiled: December 30, 2010Date of Patent: January 14, 2014Assignee: Pacific Biosciences of California, Inc.Inventors: Jon Sorenson, Ali Bashir, Fred Christians, Stephen Turner, Eric C. Olivares, Jason Underwood
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Patent number: 8535882Abstract: Methods, systems and compositions where a target nucleic acid includes a registration sequence disposed therein for identification of the number or relative position of determined sequence from the template sequence. Particularly preferred aspects include a registration sequence in a circular template nucleic acid sequence which is, in turn, used in sequence by incorporation processes that rely upon template dependent, polymerase mediated primer extension in the identification of the sequence of the template.Type: GrantFiled: February 3, 2011Date of Patent: September 17, 2013Assignee: Pacific Biosciences of California, Inc.Inventors: Fred Christians, Stephen Turner
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Patent number: 8481264Abstract: 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: GrantFiled: September 18, 2009Date of Patent: July 9, 2013Assignee: Pacific Biosciences of California, Inc.Inventors: Keith Bjornson, Arek Bibillo, Fred Christians, Kevin Travers, Robin Emig
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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: 8389676Abstract: Biotinylation peptides are provided which can be fused with other peptides or proteins of interest using recombinant DNA techniques to provide efficient methods for biotinylating the resulting fusion proteins in vivo or in vitro.Type: GrantFiled: June 14, 2010Date of Patent: March 5, 2013Assignee: Pacific Biosciences of California, Inc.Inventor: Fred Christians
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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: 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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Publication number: 20110306096Abstract: Biotinylation peptides are provided which can be fused with other peptides or proteins of interest using recombinant DNA techniques to provide efficient methods for biotinylating the resulting fusion proteins in vivo or in vitro.Type: ApplicationFiled: June 14, 2010Publication date: December 15, 2011Applicant: Pacific Biosciences of California, Inc.Inventor: Fred Christians
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Publication number: 20110212436Abstract: Methods, systems and compositions where a target nucleic acid includes a registration sequence disposed therein for identification of the number or relative position of determined sequence from the template sequence. Particularly preferred aspects include a registration sequence in a circular template nucleic acid sequence which is, in turn, used in sequence by incorporation processes that rely upon template dependent, polymerase mediated primer extension in the identification of the sequence of the template.Type: ApplicationFiled: February 3, 2011Publication date: September 1, 2011Applicant: Pacific Biosciences of California, Inc.Inventors: Fred Christians, Stephen Turner
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Publication number: 20110195406Abstract: Methods, devices, and systems for performing intermittent detection during analytical reactions are provided. Such methods facilitate collection of reaction data from disparate reaction times. Further, such methods are useful for reducing photo-induced damage of one or more reactants in an illuminated analytical reaction at a given reaction time. In preferred embodiments, the reaction mixture is subjected to at least one illuminated and non-illuminated period and allowed to proceed such that the time in which the reaction mixture is illuminated is less than a photo-induced damage threshold period.Type: ApplicationFiled: December 30, 2010Publication date: August 11, 2011Applicant: Pacific Biosciences of California, Inc.Inventors: Jon Sorenson, Ali Bashir, Fred Christians, Stephen Turner, Eric C. Olivares, Jason Underwood
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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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Patent number: 7901889Abstract: Methods, systems and compositions where a target nucleic acid includes a registration sequence disposed therein for identification of the number or relative position of determined sequence from the template sequence. Particularly preferred aspects include a registration sequence in a circular template nucleic acid sequence which is, in turn, used in sequence by incorporation processes that rely upon template dependent, polymerase mediated primer extension in the identification of the sequence of the template.Type: GrantFiled: July 25, 2008Date of Patent: March 8, 2011Assignee: Pacific Biosciences of California, Inc.Inventors: Fred Christians, Stephen Turner
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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