Patents by Inventor Jeremiah Hanes
Jeremiah Hanes 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: 20160083789Abstract: Sequencing methods, devices, and systems are described. Arrays of nanoscale electronic elements comprising two electrodes separated by an insulating layer are used to provide sequence information about a template nucleic acid in a polymerase-template complex bound proximate to the insulating region. A sequencing reaction mixture comprising nucleotide analogs having impedance labels is introduced to the array of nanoscale electronic elements under conditions of polymerase mediated nucleic acid synthesis. The time sequence of incorporation of nucleotide analogs is determined by identifying the types of labels of the nucleotide analogs that are incorporated into the growing strand using measured impedance.Type: ApplicationFiled: October 21, 2015Publication date: March 24, 2016Inventors: Stephen Turner, Jeremiah Hanes, Keith Bjornson
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Publication number: 20160010150Abstract: Methods, Compositions, and Systems are provided for nucleic acid sequencing where the sequential incorporation of nucleotides uses two distinct chemical steps. A plurality of nucleotide analogs, each having a labeled leaving group at its 3? hydroxyl can be sequentially added to a growing strand in the presence of a selective cleaving activity that cleaves the 3? hydroxyl leaving group preferentially after it has been incorporated. The selective cleaving agent can comprise an exonuclease activity, and the exonuclease activity can be a polymerase-associated exonuclease activity. Nucleotide analogs having labels on both a cleavable polyphosphate portion and on a 3? hydroxyl leaving group can provide signals characteristic of nucleotide analog incorporation. Systems having illumination optics, collection optics, and substrates observe signals from the labels as they are being incorporated into a growing nucleic acid strand, allowing for the sequencing of template nucleic acids.Type: ApplicationFiled: September 8, 2015Publication date: January 14, 2016Inventors: Robin Emig, Lei Jia, Jeremiah Hanes, Lubomir Sebo
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Publication number: 20150330987Abstract: Compositions, methods, and systems are provided for nucleotide analogs comprising protein shields for improving enzyme photostability in single molecule real time sequencing. Nucleotide analogs of the invention have a protein shield between the dye moieties and nucleotide moieties of the analog. The nucleotide analogs have two avidin proteins connected by a central dye component, and each avidin protein is further connected to a nucleotide component. The protein can prevent the direct interaction of the dye moiety with the enzyme carrying out nucleotide synthesis preventing photodamage to the enzyme. The nucleotide analogs of the invention can have multiple dyes and multiple nucleotide moieties.Type: ApplicationFiled: June 1, 2015Publication date: November 19, 2015Inventors: Keith Bjornson, Jeremiah Hanes, Erik Miller, Satwik Kamtekar, Lubomir Sebo, Louis Brogley
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Patent number: 9175341Abstract: Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid.Type: GrantFiled: December 10, 2009Date of Patent: November 3, 2015Assignee: Pacific Biosciences of California, Inc.Inventors: Benjamin Flusberg, Stephen Turner, Jessica Lee, Lei Jia, Jonas Korlach, Jon Sorenson, Dale Webster, John Lyle, Kevin Travers, Jeremiah Hanes, Joseph Puglisi
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Patent number: 9175338Abstract: Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid.Type: GrantFiled: November 12, 2010Date of Patent: November 3, 2015Assignee: Pacific Biosciences of California, Inc.Inventors: Benjamin Flusberg, Jonas Korlach, Jeffrey Wegener, Tyson A. Clark, Igor Vilfan, Andrey Kislyuk, Stephen Turner, Jon Sorenson, Kevin Travers, Cheryl Heiner, Austin B. Tomaney, Patrick Marks, Jessica Lee, Lei Jia, Dale Webster, John Lyle, Jeremiah Hanes, Joseph Puglisi
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Publication number: 20150240221Abstract: 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: March 9, 2015Publication date: August 27, 2015Inventors: Robin Emig, Insil Park, Lei Jia, Arek Bibillo, Molly He, Jeremiah Hanes, Harold Lee, Fred Christians, Satwik Kamtekar, Erik Miller
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Publication number: 20150203908Abstract: Compositions, kits, methods and systems for single molecule nucleotide sequencing comprising producing polymerase reactions having lithium that control the median pulse width for incorporated nucleotides are disclosed. The levels of lithium are used to control pulse width while allowing other sequencing parameters to remain within a desirable range.Type: ApplicationFiled: March 9, 2015Publication date: July 23, 2015Inventors: Andrei Fedorov, John Lyle, Keith Bjornson, Jeremiah Hanes
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Patent number: 9062091Abstract: Compositions and methods are provided for nucleotide analogs comprising protein shields for improving enzyme photostability in single molecule real time sequencing. Nucleotide analogs of the invention have a protein shield between the dye moieties and nucleotide moieties of the analog. The protein prevents the direct interaction of the dye moiety with the enzyme carrying out nucleotide synthesis preventing photodamage to the enzyme. The nucleotide analogs of the invention can have multiple dyes and multiple nucleotide moieties.Type: GrantFiled: February 14, 2013Date of Patent: June 23, 2015Assignee: Pacific Biosciences of California, Inc.Inventors: Keith Bjornson, Jeremiah Hanes, Erik Miller, Satwik Kamtekar, Lubomir Sebo, Louis Brogley
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Patent number: 8986930Abstract: Compositions, kits, methods and systems for single molecule nucleotide sequencing comprising producing polymerase reactions having monovalent cations that control the median pulse width for incorporated nucleotides are disclosed. The levels of alkali metals such as lithium, sodium, potassium, rubidium, and cesium in the polymerization are used to control pulse width while allowing other sequencing parameters to remain within a desirable range.Type: GrantFiled: July 7, 2011Date of Patent: March 24, 2015Assignee: Pacific Biosciences of California, Inc.Inventors: Andrei Fedorov, John Lyle, Keith Bjornson, Jeremiah Hanes
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Publication number: 20150065353Abstract: Real time electronic sequencing methods, devices, and systems are described. Arrays of nanoscale electronic elements comprising capacitive devices with one or two electrodes, or arrays of nanoFET devices are used to provide sequence information about a template nucleic acid in a polymerase-template complex bound proximate to the nanoscale electronic elements or to the substrate proximate to the nanoscale electronic element. A sequencing reaction mixture comprising nucleotide analogs having impedance labels, capacitive labels, or conductivity labels is introduced to the array of nanoscale electronic elements comprising capacitive devices or nanoFETs under conditions of polymerase mediated nucleic acid synthesis. The time sequence of incorporation of nucleotide analogs is determined by identifying the types of labels of the nucleotide analogs that are incorporated into the growing strand using measured impedance, conductivity, or capacitance.Type: ApplicationFiled: May 5, 2014Publication date: March 5, 2015Applicant: Pacific Biosciences of California, Inc.Inventors: Stephen Turner, Jeremiah Hanes, Keith Bjornson
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Publication number: 20150050659Abstract: Protected fluorescent reagent compounds and their methods of synthesis are provided. The compounds are useful in various fluorescence-based analytical methods, including the analysis of highly multiplexed optical reactions in large numbers at high densities, such as single molecule real time nucleic acid sequencing reactions. The compounds contain fluorescent dye elements, that allow the compounds to be detected with high sensitivity at desirable wavelengths, binding elements, that allow the compounds to be recognized specifically by target biomolecules, and protective shield elements, that decrease undesirable contacts between the fluorescent dye elements and the bound target biomolecules and that therefore decrease photodamage of the bound target biomolecules by the fluorescent dye elements.Type: ApplicationFiled: August 5, 2014Publication date: February 19, 2015Inventors: Lubomir SEBO, Jeremiah HANES, Gene SHEN, Louis BROGLEY, Stephen YUE, Frank ZHENG, Yuri LAPIN, John LYLE, Honey OSUNA, Andrei FEDOROV
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Publication number: 20150011433Abstract: Multi-biotinylated reactants are provided which can be used in divalent complexes for various applications such as colocalization, labeling, immobilization, and purification. Methods for constructing, purifying, and using the bis-biotinylated reactants are also provided. In certain embodiments, two bis-biotinylated reactants are bound to a single streptavidin tetramer to provide a complex having a 1:1 stoichiometry with respect to the bis-biotinylated reactants.Type: ApplicationFiled: June 12, 2014Publication date: January 8, 2015Applicant: Pacific Biosciences of California, Inc.Inventors: Erik Miller, Satwik Kamtekar, Keith Bjornson, Jeremiah Hanes
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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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Publication number: 20140274732Abstract: The present invention is directed to methods, devices, compositions and systems for obtaining sequence data from nucleic acid templates by utilizing electronic sensing elements.Type: ApplicationFiled: March 11, 2014Publication date: September 18, 2014Applicant: PACIFIC BIOSCIENCES OF CALIFORNIA, INC.Inventors: Jeremiah HANES, Jonas KORLACH, Stephen TURNER
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Publication number: 20140127680Abstract: Methods, Compositions, and Systems are provided for nucleic acid sequencing where the sequential incorporation of nucleotides uses two distinct chemical steps. A plurality of nucleotide analogs, each having a labeled leaving group at its 3? hydroxyl can be sequentially added to a growing strand in the presence of a selective cleaving activity that cleaves the 3? hydroxyl leaving group preferentially after it has been incorporated. The selective cleaving agent can comprise an exonuclease activity, and the exonuclease activity can be a polymerase-associated exonuclease activity. Nucleotide analogs having labels on both a cleavable polyphosphate portion and on a 3? hydroxyl leaving group can provide signals characteristic of nucleotide analog incorporation. Systems having illumination optics, collection optics, and substrates observe signals from the labels as they are being incorporated into a growing nucleic acid strand, allowing for the sequencing of template nucleic acids.Type: ApplicationFiled: November 5, 2013Publication date: May 8, 2014Applicant: PACIFIC BIOSCIENCES OF CALIFORNIA, INC.Inventors: Robin Emig, LEI JIA, JEREMIAH HANES, LUBOMIR SEBO
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Patent number: 8603741Abstract: Methods, Compositions, and Systems are provided for nucleic acid sequencing where the sequential incorporation of nucleotides uses two distinct chemical steps. A plurality of nucleotide analogs, each having a labeled leaving group at its 3? hydroxyl can be sequentially added to a growing strand in the presence of a selective cleaving activity that cleaves the 3? hydroxyl leaving group preferentially after it has been incorporated. The selective cleaving agent can comprise an exonuclease activity, and the exonuclease activity can be a polymerase-associated exonuclease activity. Nucleotide analogs having labels on both a cleavable polyphosphate portion and on a 3? hydroxyl leaving group can provide signals characteristic of nucleotide analog incorporation. Systems having illumination optics, collection optics, and substrates observe signals from the labels as they are being incorporated into a growing nucleic acid strand, allowing for the sequencing of template nucleic acids.Type: GrantFiled: February 8, 2011Date of Patent: December 10, 2013Assignee: Pacific Biosciences of California, Inc.Inventors: Robin Emig, Lei Jia, Jeremiah Hanes, Lubomir Sebo
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Publication number: 20130316916Abstract: Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid.Type: ApplicationFiled: June 28, 2013Publication date: November 28, 2013Inventors: Benjamin Flusberg, Stephen Turner, Jessica Lee, Lei Jia, Jonas Korlach, Jon Sorenson, Dale Webster, John Lyle, Kevin Travers, Jeremiah Hanes, Joseph Puglisi
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Publication number: 20130316912Abstract: Compositions and methods are provided for nucleotide analogs comprising protein shields for improving enzyme photostability in single molecule real time sequencing. Nucleotide analogs of the invention have a protein shield between the dye moieties and nucleotide moieties of the analog. The protein prevents the direct interaction of the dye moiety with the enzyme carrying out nucleotide synthesis preventing photodamage to the enzyme. The nucleotide analogs of the invention can have multiple dyes and multiple nucleotide moieties.Type: ApplicationFiled: February 14, 2013Publication date: November 28, 2013Applicant: Pacific Biosciences of California, Inc.Inventors: Keith Bjornson, Jeremiah Hanes, Erik Miller, Satwik Kamtekar, Lubomir Sebo, Louis Brogley
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Patent number: 8530164Abstract: Provided are methods for enhanced sequencing of nucleic acid templates. Also provided are reaction conditions that increase branching fractions during polymerization reactions. Also provided are compositions comprising modified recombinant polymerases that exhibit branching fractions that are higher than the branching fractions of the polymerases from which they were derived. Provided are compositions comprising modified recombinant polymerases that exhibit delayed translocation relative to the polymerases from which they were derived. Also provided are compositions comprising modified recombinant polymerases that exhibit increased nucleotide or nucleotide analog residence time at an active site of the polymerase. Provided are methods for generating polymerases with the aforementioned phenotypes and methods of using such polymerases to sequence a DNA template or make a DNA.Type: GrantFiled: September 4, 2009Date of Patent: September 10, 2013Assignee: Pacific Biosciences of California, Inc.Inventors: Pranav Patel, Jonas Korlach, Arkadiusz Bibillo, Keith Bjornson, Jeremiah Hanes
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Publication number: 20130029853Abstract: Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid.Type: ApplicationFiled: October 2, 2012Publication date: January 31, 2013Applicant: Pacific Biosciences of California, Inc.Inventors: Benjamin Flusberg, Stephen Turner, Jessica Lee, Lei Jia, Jonas Korlach, Jon Sorenson, Dale Webster, John Lyle, Kevin Travers, Jeremiah Hanes, Joseph Puglisi