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).

  • Patent number: 10294523
    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: September 23, 2015
    Date of Patent: May 21, 2019
    Assignee: Pacific Biosciences of California, Inc.
    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
  • Publication number: 20190136313
    Abstract: Compositions, methods and systems are provided for the loading of extended polymerase-nucleic acid complexes onto substrates. Primed polymerase-template complex comprising a polymerase enzyme and a circular nucleic acid template comprising a double stranded region connected at each end by a single-stranded hairpin region are provides in which the circular nucleic acid template comprises at least one reversible pause point. Nucleic acid synthesis is carried out such that a nascent strand is synthesized up to the reversible stop point producing an extended polymerase-template complex. The extended polymerase-template complex is then attached to a substrate. Such attached complexes can be used for single molecule sequencing in which the nucleic acid synthesis is re-initiated such that nucleic acid synthesis continues past the reversible stop point.
    Type: Application
    Filed: June 13, 2018
    Publication date: May 9, 2019
    Inventors: Thang Pham, Arunashree Bhamidipati, Kevin Travers, Eric Olivares, Tyson A. Clark, Jonas Korlach
  • Publication number: 20190136311
    Abstract: A circuit comprising a substrate with sectors on the substrate is provided, each sector comprising clock and data lines, a controller in electrical communication with the clock and data lines, a counter bias line, an amplifier input line and nano-electronic measurement devices on the substrate. A source of each device is coupled to the counter bias line and a drain of each device is coupled to the amplifier input line to obtain an electrical signal on the drain, the identity of which is determined by electrical interaction between the device and a charge label. Each device drain is gated by a corresponding switch between an on state, in which the drain is connected to the amplifier input line, and an off state, in which the drain is isolated from the amplifier input line. The controller controls switch states responsive to clock signal line pulses and data input line data.
    Type: Application
    Filed: December 17, 2018
    Publication date: May 9, 2019
    Inventors: Stephen Turner, Jonas Korlach, Steven Warren
  • Patent number: 10280457
    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: June 21, 2017
    Date of Patent: May 7, 2019
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Cheng Frank Zhong, Paul Lundquist, Mathieu Foquet, Jonas Korlach, Hovig Bayandorian
  • Patent number: 10273537
    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: March 22, 2016
    Date of Patent: April 30, 2019
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Jonas Korlach, Stephen Turner, Lei Sun
  • Publication number: 20190106741
    Abstract: Real time electronic sequencing devices, chips, and systems are described. Arrays of nanoFET devices are used to provide sequence information about a template nucleic acid in a polymerase-template complex bound to the nanoFET. The nanoFET devices typically have a source, a drain and a gate comprising a nanowire. A single polymerase enzyme complex comprising a polymerase enzyme complexed with the template nucleic acid is bound to the gate. The polymerase is bound to the gate non-covalently through a polymeric binding agent that has two strands, each strand interacting with the nanowire such that the polymerase is in a central location between the strands with the polymeric binding agent extending away from the polymerase complex along the nanowire in both directions.
    Type: Application
    Filed: September 20, 2018
    Publication date: April 11, 2019
    Inventors: Stephen Turner, Jonas Korlach, Satwik Kamtekar, Jeremiah Hanes
  • Publication number: 20190062833
    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: August 21, 2018
    Publication date: February 28, 2019
    Inventors: Tyson A. Clark, Jonas Korlach, Cheryl Heiner, Kevin Travers, Erik Miller
  • Patent number: 10190158
    Abstract: A circuit comprising a substrate with sectors on the substrate is provided, each sector comprising clock and data lines, a controller in electrical communication with the clock and data lines, a counter bias line, an amplifier input line and nano-electronic measurement devices on the substrate. A source of each device is coupled to the counter bias line and a drain of each device is coupled to the amplifier input line to obtain an electrical signal on the drain, the identity of which is determined by electrical interaction between the device and a charge label. Each device drain is gated by a corresponding switch between an on state, in which the drain is connected to the amplifier input line, and an off state, in which the drain is isolated from the amplifier input line. The controller controls switch states responsive to clock signal line pulses and data input line data.
    Type: Grant
    Filed: August 3, 2016
    Date of Patent: January 29, 2019
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Stephen Turner, Jonas Korlach, Steven Warren
  • Publication number: 20190024162
    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: January 19, 2018
    Publication date: January 24, 2019
    Inventors: Jonas Korlach, Stephen Turner, Tyson A. Clark
  • Patent number: 10161002
    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: Grant
    Filed: December 13, 2017
    Date of Patent: December 25, 2018
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Jonas Korlach, Jeffrey Wegener
  • Patent number: 10125391
    Abstract: Real time electronic sequencing methods, devices, and systems are described. Arrays of nanoFET devices are used to provide sequence information about a template nucleic acid in a polymerase-template complex bound to the nanoFET. A sequencing reaction mixture comprising nucleotide analogs having conductivity labels is introduced to the array of nanoscale electronic elements comprising nanoFETs under conditions of polymerase mediated nucleic acid synthesis. The polymerase enzyme template complex is attached to the gate of the nanoFET in an orientation whereby the nucleotide exit region of the polymerase enzyme is directed toward the gate of the nanoFET. Methods for producing nanoFET arrays are provided.
    Type: Grant
    Filed: August 3, 2016
    Date of Patent: November 13, 2018
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Stephen Turner, Jonas Korlach, Satwik Kamtekar, Jeremiah Hanes
  • Patent number: 10081836
    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: July 15, 2016
    Date of Patent: September 25, 2018
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Tyson A. Clark, Jonas Korlach, Cheryl Heiner, Kevin Travers, Erik Miller
  • Publication number: 20180201993
    Abstract: Methods are provided for sequencing of nucleic acid templates using nanopores. A polymerase-nucleic acid complex having a strand displacing polymerase is provided. The nucleic acid in the polymerase-nucleic acid complex is a circular nucleic acid template. Components required for nucleic acid synthesis are provided whereby the polymerase produces a nascent strand that passes through the nanopore while the nascent strand is produced. Current through the nanopore over time is measured allowing for the determination of the sequence of the nascent strand as it translates through the pore using the measured current over time. Because the polymerase can proceed around the circular template multiple times, multiple reads corresponding to the same sequence in the circular template can be obtained in one sequencing process. Where modified bases are present in the template, the method can be used to determine the presence and position of the modified bases using the kinetics of the polymerase.
    Type: Application
    Filed: January 12, 2018
    Publication date: July 19, 2018
    Inventors: Stephen Turner, Jonas Korlach
  • Patent number: 10000805
    Abstract: Compositions, methods and systems are provided for isolating DNA having a modified or unnatural base. Circular DNA fragments, each comprising a double stranded DNA central region and single stranded regions on the ends of the double stranded regions, are obtained. Some of the fragments have one or more modified or unnatural base. The DNA fragments are treated with a primer and a polymerase such that the polymerase extends the primer to copy at least one of the strand of the double stranded region. This results in rendering the other strand single stranded. A binding protein or antibody that is specific to the modified or unnatural base is then used to isolate strands containing the modified or unnatural bases. Methods for loading such complexes onto substrates and for single molecule sequencing of such complexes are also provided.
    Type: Grant
    Filed: September 20, 2016
    Date of Patent: June 19, 2018
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Thang Pham, Arunashree Bhamidipati, Kevin Travers, Eric Olivares, Tyson A. Clark, Jonas Korlach
  • Publication number: 20180163267
    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: December 13, 2017
    Publication date: June 14, 2018
    Inventors: Jonas Korlach, Jeffrey Wegener
  • Patent number: 9944980
    Abstract: Methods of producing substrates having selected active chemical regions by employing elements of the substrates in assisting the localization of active chemical groups in desired regions of the substrate. The methods may include optical, chemical and/or mechanical processes for the deposition, removal, activation and/or deactivation of chemical groups in selected regions of the substrate to provide selective active regions of the substrate.
    Type: Grant
    Filed: October 31, 2007
    Date of Patent: April 17, 2018
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: David R. Rank, Jonas Korlach, Yue Xu, Stephen Turner, Jeffery Wegener, Daniel Roitman, John Lyle
  • Patent number: 9879319
    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: Grant
    Filed: December 14, 2016
    Date of Patent: January 30, 2018
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Jonas Korlach, Jeffrey Wegener
  • Publication number: 20170362652
    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: June 21, 2017
    Publication date: December 21, 2017
    Inventors: Cheng Frank Zhong, Paul Lundquist, Mathieu Foquet, Jonas Korlach, Hovig Bayandorian
  • Publication number: 20170343479
    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: June 8, 2017
    Publication date: November 30, 2017
    Inventors: Stephen Turner, Jonas Korlach
  • Patent number: 9746476
    Abstract: The present invention is generally directed to compositions, methods, and systems for performing single-molecule, real-time analysis of a variety of different biological reactions, and for determining various characteristics of the different biological reactions. The ability to analyze such reactions provides an opportunity to study those reactions as well as to potentially identify factors and/or approaches for impacting such reactions, e.g., to stimulate, enhance, or inhibit such reactions.
    Type: Grant
    Filed: June 10, 2015
    Date of Patent: August 29, 2017
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Jonas Korlach, Stephen Turner, Benjamin Flusberg, Mark Chaisson, Eric Schadt, Jeffrey Wegener