Patents by Inventor Jonas Korlach

Jonas Korlach 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).

  • DELAYING REAL-TIME SEQUENCING
    Publication number: 20170009289
    Abstract: Methods, compositions, and systems are provided that allow for reliable sequencing of the initial sequence region of a sequence of interest. The methods of the invention allow for more reliable barcoding of subpopulations of nucleic acids to be sequenced.
    Type: Application
    Filed: July 15, 2016
    Publication date: January 12, 2017
    Inventors: Tyson A. Clark, Jonas Korlach, Cheryl Heiner, Kevin Travers, Erik Miller
  • APPARATUS AND METHOD FOR PERFORMING NUCLEIC ACID ANALYSIS
    Publication number: 20170002409
    Abstract: The present invention relates to optical confinements, methods of preparing and methods of using them for analyzing molecules and/or monitoring chemical reactions. The apparatus and methods embodied in the present invention are particularly useful for high-throughput and low-cost single-molecular analysis.
    Type: Application
    Filed: August 19, 2016
    Publication date: January 5, 2017
    Inventors: Stephen Turner, Jonas Korlach
  • Compositions and methods for selection of nucleic acids
    Patent number: 9528107
    Abstract: Methods are provided for reducing the complexity of a population of nucleic acids prior to performing an analysis of the nucleic acids, e.g., sequence analysis. The methods result in a subset of the initial population enriched for a target region, which is typically located within one or more target fragments. The methods are particularly useful for analyzing populations having a high degree of complexity, e.g., chromosomal-derived DNA, whole genomic DNA, or mRNA populations.
    Type: Grant
    Filed: October 31, 2013
    Date of Patent: December 27, 2016
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Thang Tat Pham, Yu-Chih Tsai, Jonas Korlach, Tyson A. Clark, Stephen Turner
  • REAL-TIME REDOX SEQUENCING METHODS
    Publication number: 20160319343
    Abstract: Real time redox sequencing methods, devices, and systems are described. Arrays of redox devices comprising one or two electrodes are used to provide sequence information about a template nucleic acid in a polymerase-template complex bound proximate to the electrode(s). A sequencing reaction mixture comprising nucleotide analogs comprising redox labels is introduced to the array of redox devices under conditions of polymerase mediated nucleic acid synthesis. The time sequence of incorporation of nucleotide analogs is determined by electrochemically identifying the redox labels of the nucleotide analogs that are incorporated into the growing strand.
    Type: Application
    Filed: March 22, 2016
    Publication date: November 3, 2016
    Inventors: Jonas Korlach, Stephen Turner, Lei Sun
  • Isolation of polymerase-nucleic acid complexes
    Patent number: 9475054
    Abstract: Compositions, methods and systems are provided for the isolation of polymerase-nucleic acid complexes. Complexes can be separated from free enzyme by using hook molecules to target single stranded regions on the nucleic acid. Hook oligonucleotides are used to capture polymerase nucleic acid complexes where the nucleic acids comprise circular nucleic acids having a double stranded central region with hairpin regions on each end. Methods for loading such complexes onto substrates and for single molecule sequencing of such complexes are also provided.
    Type: Grant
    Filed: January 9, 2014
    Date of Patent: October 25, 2016
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Thang Pham, Arunashree Bhamidipati, Kevin Travers, Eric Olivares, Tyson A. Clark, Jonas Korlach
  • Labeled nucleotide analogs
    Patent number: 9464107
    Abstract: Labeled reactant compositions, and particularly labeled nucleic acid reaction compositions that include structural components including double-stranded nucleic acids. In some embodiments, the structural components maintain potentially damaging labeling components sufficiently distal from the reactant portion of the molecule such that damaging effects of the label group on other reaction components, such as enzymes, are reduced, minimized and/or eliminated.
    Type: Grant
    Filed: February 3, 2014
    Date of Patent: October 11, 2016
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Jeffrey Wegener, Jonas Korlach
  • MODULAR NUCLEOTIDE COMPOSITIONS AND USES THEREFOR
    Publication number: 20160244824
    Abstract: Nucleic acid compositions, methods of making and using such compositions that comprise modular functional groups that can be configured to provide desired functionality to different nucleotide types through a swappable and preferably non-covalent linkage component. Such compositions are useful in a variety of applications including nucleic acid analyses.
    Type: Application
    Filed: August 14, 2014
    Publication date: August 25, 2016
    Inventors: Jonas Korlach, Jeffrey Wegener
  • Delaying real-time sequencing
    Patent number: 9416414
    Abstract: Methods, compositions, and systems are provided that allow for reliable sequencing of the initial sequence region of a sequence of interest. The methods of the invention allow for more reliable barcoding of subpopulations of nucleic acids to be sequenced.
    Type: Grant
    Filed: October 22, 2014
    Date of Patent: August 16, 2016
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Tyson A. Clark, Jonas Korlach, Cheryl Heiner, Kevin Travers, Erik Miller
  • SEQUENCING SYSTEMS WITH TWO SLOW-STEP POLYMERASE ENZYMES
    Publication number: 20160177384
    Abstract: 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: Application
    Filed: January 26, 2016
    Publication date: June 23, 2016
    Inventors: Keith Bjornson, Harold Lee, Jonas Korlach
  • SUBSTRATES AND OPTICAL SYSTEMS AND METHODS OF USE THEREOF
    Publication number: 20160153040
    Abstract: This invention provides substrates for use in various applications, including single-molecule analytical reactions. Methods for propagating optical energy within a substrate are provided. Devices comprising waveguide substrates and dielectric omnidirectional reflectors are provided. Waveguide substrates with improved uniformity of optical energy intensity across one or more waveguides and enhanced waveguide illumination efficiency within an analytic detection region of the arrays are provided.
    Type: Application
    Filed: November 23, 2015
    Publication date: June 2, 2016
    Inventors: Cheng Frank Zhong, Paul Lundquist, Mathieu Foquet, Jonas Korlach, Hovig Bayandorian
  • CLASSIFICATION OF NUCLEIC ACID TEMPLATES
    Publication number: 20160153038
    Abstract: 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: Application
    Filed: September 23, 2015
    Publication date: June 2, 2016
    Inventors: Benjamin Flusberg, Jonas Korlach, Jeffrey Wegener, Tyson A. Clark, Igor Drasko 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
  • Real-time redox sequencing
    Patent number: 9347900
    Abstract: Real time redox sequencing methods, devices, and systems are described. Arrays of redox devices comprising one or two electrodes are used to provide sequence information about a template nucleic acid in a polymerase-template complex bound proximate to the electrode(s). A sequencing reaction mixture comprising nucleotide analogs comprising redox labels is introduced to the array of redox devices under conditions of polymerase mediated nucleic acid synthesis. The time sequence of incorporation of nucleotide analogs is determined by electrochemically identifying the redox labels of the nucleotide analogs that are incorporated into the growing strand.
    Type: Grant
    Filed: October 15, 2012
    Date of Patent: May 24, 2016
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Jonas Korlach, Stephen Turner, Lei Sun
  • METHODS AND COMPOSITIONS FOR SEQUENCING MODIFIED NUCLEIC ACIDS
    Publication number: 20160130646
    Abstract: 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: Application
    Filed: October 2, 2015
    Publication date: May 12, 2016
    Inventors: Jonas Korlach, Stephen Turner, Tyson A. Clark
  • Step-wise nucleic acid sequencing with catalytic and non-catalytic metals
    Patent number: 9279155
    Abstract: The Application relates to methods, and systems for nucleotide sequencing comprising producing polymerase reactions that comprise both catalytic and non-catalytic divalent metal ions. Polymerase/template/primer complexes are immobilized on a substrate. The complexes are exposed to a solution comprising a non-catalytic metal and nucleotides labeled with a detectable label on a portion of the nucleotide that is released upon incorporation. The cognate nucleotide is sequestered in the active site of the polymerase, unable to proceed to incorporation. After observing the sequestered cognate nucleotide, the complex is exposed to a catalytic metal, resulting in the incorporation of the bound cognate nucleotide and consequent release of the label resulting in a single-base extended primer.
    Type: Grant
    Filed: February 20, 2014
    Date of Patent: March 8, 2016
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Keith Bjornson, Harold Lee, Jonas Korlach
  • APPARATUS AND METHOD FOR PERFORMING NUCLEIC ACID ANALYSIS
    Publication number: 20160061738
    Abstract: The present invention relates to optical confinements, methods of preparing and methods of using them for analyzing molecules and/or monitoring chemical reactions. The apparatus and methods embodied in the present invention are particularly useful for high-throughput and low-cost single-molecular analysis.
    Type: Application
    Filed: September 11, 2015
    Publication date: March 3, 2016
    Inventors: Stephen Turner, Jonas Korlach
  • Nanopores in zero mode waveguides
    Patent number: 9267917
    Abstract: Methods, devices, substrates, and systems are disclosed involving arrays of zero-mode waveguides having nanopores extending through the bases that form the bottoms of the zero-mode-waveguides. Electric fields across the nanopores are used to attach single biomolecules such as polymerase enzymes within each zero-mode-waveguide. Electric fields across the nanopores can also be used for the active loading of nucleic acid templates into enzymes attached within the zero mode waveguides.
    Type: Grant
    Filed: November 5, 2012
    Date of Patent: February 23, 2016
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Meni Wanunu, Jonas Korlach, Mathieu Foquet, Stephen Turner
  • Methods and compositions for sequencing modified nucleic acids
    Patent number: 9238836
    Abstract: 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: Grant
    Filed: March 15, 2013
    Date of Patent: January 19, 2016
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Jonas Korlach, Stephen Turner, Tyson A. Clark
  • IDENTIFYING MODIFIED BASES USING HEMI-NATURAL NUCLEIC ACIDS
    Publication number: 20160010148
    Abstract: Methods, compositions, and systems are provided for characterization of modified nucleic acids. Methods are provided for sequencing hemi-natural nucleic acids such as hemi-genomic DNA, having two complementary strands, one a natural sequence and the other a synthetic sequence. The identification of modified bases can be enhanced by comparing the sequencing information from the natural sequence, which has, for example, natural base modifications, with the synthetic sequence, which typically has no base modifications. The presence and identity of a modified base can be determined by monitoring kinetics, for example the kinetics of polymer meditated nucleic acid synthesis.
    Type: Application
    Filed: August 20, 2015
    Publication date: January 14, 2016
    Inventors: Stephen Turner, Jonas Korlach
  • NANOPORE SEQUENCING METHODS
    Publication number: 20160011169
    Abstract: Methods are provided for sequencing of nucleic acid templates using nanopores. The rate of transport of the template nucleic acids through the nanopore is controlled using a polymerase enzyme having two slow kinetic steps. Methods are provided for sequencing hemi-natural nucleic acids such as hemi-genomic DNA, having two complementary strands, one a natural sequence and the other a synthetic sequence. The identification of modified bases can be enhanced by comparing the sequencing information from the natural sequence, which has, for example, natural base modifications, with the synthetic sequence, which typically has no base modifications. The presence and identity of a modified base can be determined by monitoring kinetics, for example the kinetics of polymer meditated nucleic acid synthesis.
    Type: Application
    Filed: September 10, 2015
    Publication date: January 14, 2016
    Inventors: Stephen Turner, Jonas Korlach
  • Analytic devices comprising optical waveguides and nanometer-scale apertures and methods of uses thereof
    Patent number: 9222123
    Abstract: This invention provides substrates for use in various applications, including single-molecule analytical reactions. Methods for propagating optical energy within a substrate are provided. Devices comprising waveguide substrates and dielectric omnidirectional reflectors are provided. Waveguide substrates with improved uniformity of optical energy intensity across one or more waveguides and enhanced waveguide illumination efficiency within an analytic detection region of the arrays are provided.
    Type: Grant
    Filed: May 24, 2013
    Date of Patent: December 29, 2015
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Cheng Frank Zhong, Paul Lundquist, Mathieu Foguet, Jonas Korlach, Hovig Bayandorian