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).

  • REAL-TIME ANALYTICAL METHODS AND SYSTEMS
    Publication number: 20150362503
    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: Application
    Filed: June 10, 2015
    Publication date: December 17, 2015
    Inventors: Jonas Korlach, Stephen Turner, Benjamin Flusberg, Mark Chaisson, Eric Schadt, Jeffrey Wegener
  • Real-time sequencing methods and systems
    Patent number: 9200320
    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. 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 either enhance or inhibit such reactions. In certain preferred embodiments, RNA templates are used in single-molecule real-time sequencing reactions.
    Type: Grant
    Filed: December 16, 2014
    Date of Patent: December 1, 2015
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Jonas Korlach, Stephen Turner, Eric Schadt
  • Identification of 5-methyl-C in nucleic acid templates
    Patent number: 9175348
    Abstract: A method for identifying a 5-MeC in a template nucleic is provided. The method comprises providing a template having 5-MeC, converting the 5-MeC into a further modification selected from 5-caC and 5-FC. The converted template is then sequenced, and a change in sequencing is detected that is indicative of the further modification, allowing for identifying the 5-MeC in the template nucleic acid.
    Type: Grant
    Filed: April 23, 2013
    Date of Patent: November 3, 2015
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Jonas Korlach, Chuan He, Tyson A. Clark, Liang Zhang, Xingyu Lu
  • Methods for identifying nucleic acid modifications
    Patent number: 9175338
    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: November 12, 2010
    Date of Patent: November 3, 2015
    Assignee: 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
  • Methods for identifying nucleic acid modifications
    Patent number: 9175341
    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: December 10, 2009
    Date of Patent: November 3, 2015
    Assignee: 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
  • Identifying modified bases using hemi-natural nucleic acids
    Patent number: 9150918
    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: Grant
    Filed: February 10, 2015
    Date of Patent: October 6, 2015
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Stephen Turner, Jonas Korlach
  • Modified base detection with nanopore sequencing
    Patent number: 9116118
    Abstract: Methods, compositions, and systems are provided for characterization of modified nucleic acids. Nanopore sequencing is performed using a processive enzyme to control the rate of translation of a single strand of a nucleic acid through a nanopore. The presence and identity of a modified base can be determined by monitoring the kinetics of translation through the pore even though the events that lead to the kinetic changes are separated in time and space from the translation of the modified base or it's compliment through the nanopore. The invention also comprises the use of hemi-genomic DNA in nanopore sequencing.
    Type: Grant
    Filed: June 10, 2013
    Date of Patent: August 25, 2015
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Stephen Turner, Jonas Korlach
  • Real-time analytical methods and systems
    Patent number: 9063156
    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 11, 2010
    Date of Patent: June 23, 2015
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Jonas Korlach, Stephen Turner, Benjamin Flusberg, Mark Chaisson, Eric Schadt, Jeffrey Wegener
  • NUCLEOTIDE COMPOSITIONS AND USES THEREOF
    Publication number: 20150167074
    Abstract: The present invention relates to preparation of nucleotide compositions and uses thereof for conducting nucleic acid analyses. The compositions and methods embodied in the present invention are particularly useful for nucleic acid analyses that require high-resolution detection of labeled nucleotides or labeled nucleic acid targets.
    Type: Application
    Filed: December 11, 2014
    Publication date: June 18, 2015
    Inventors: Stephen Turner, Jonas Korlach
  • IDENTIFYING MODIFIED BASES USING HEMI-NATURAL NUCLEIC ACIDS
    Publication number: 20150167075
    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: February 10, 2015
    Publication date: June 18, 2015
    Inventors: Stephen Turner, Jonas Korlach
  • DELAYING REAL-TIME SEQUENCING
    Publication number: 20150118685
    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: October 22, 2014
    Publication date: April 30, 2015
    Inventors: Tyson A. Clark, Jonas Korlach, Cheryl Heiner, Kevin Travers, Erik Miller
  • REAL-TIME SEQUENCING METHODS AND SYSTEMS
    Publication number: 20150105273
    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. 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 either enhance or inhibit such reactions. In certain preferred embodiments, RNA templates are used in single-molecule real-time sequencing reactions.
    Type: Application
    Filed: December 16, 2014
    Publication date: April 16, 2015
    Applicant: Pacific Biosciences of California, Inc
    Inventors: Jonas KORLACH, Stephen Turner, Eric Schadt
  • Nanopore sequencing devices and methods
    Patent number: 8986928
    Abstract: The invention relates to devices and methods for nanopore sequencing. The invention includes arrays of nanopores having incorporated electronic circuits, for example, in CMOS. In some cases, the arrays of nanopores comprise resistive openings for isolating the electronic signals for improved sequencing. Methods for controlling translocation of through the nanopore are disclosed.
    Type: Grant
    Filed: April 9, 2010
    Date of Patent: March 24, 2015
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Stephen Turner, Benjamin Flusberg, Mathieu Foquet, Hans Callebaut, Robert Sebra, Bidhan Chaudhuri, Jon Sorenson, Keith Bjornson, Adrian Fehr, Jonas Korlach, Robin Emig
  • Articles having localized molecules disposed thereon and methods of producing same
    Patent number: 8975216
    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: March 30, 2006
    Date of Patent: March 10, 2015
    Assignee: Pacific BioSciences of California
    Inventors: David Rank, Jonas Korlach, Yue Xu, Stephen Turner, Jeffrey Wegener, Daniel Roitman, John Lyle
  • Real-time sequencing methods and systems
    Patent number: 8940507
    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. 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 either enhance or inhibit such reactions. In certain preferred embodiments, RNA templates are used in single-molecule real-time sequencing reactions.
    Type: Grant
    Filed: June 21, 2013
    Date of Patent: January 27, 2015
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Jonas Korlach, Stephen Turner, Eric Schadt
  • Active surface coupled polymerases
    Patent number: 8936926
    Abstract: Active surface coupled polymerases, surfaces that include such polymerases, and methods of making and using surface-attached polymerases are provided.
    Type: Grant
    Filed: December 21, 2006
    Date of Patent: January 20, 2015
    Assignee: Pacific Biosciences of California
    Inventors: David Hanzel, Jonas Korlach, Paul Peluso, Geoffrey Otto, Thang Pham, David Rank, Stephen Turner
  • Nucleotide compositions and uses thereof
    Patent number: 8927211
    Abstract: The present invention relates to preparation of nucleotide compositions and uses thereof for conducting nucleic acid analyzes. The compositions and methods embodied in the present invention are particularly useful for nucleic acid analyzes that require high-resolution detection of labeled nucleotides or labeled nucleic acid targets.
    Type: Grant
    Filed: February 4, 2010
    Date of Patent: January 6, 2015
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Stephen Turner, Jonas Korlach
  • Phospholink nucleotides for sequencing applications
    Patent number: 8921532
    Abstract: The present invention provides labeled phospholink, nucleotides that can be used in place of naturally occurring nucleotide triphosphates or other analogs in template directed nucleic acid synthesis reactions and other nucleic acid reactions and various analyses based thereon, including DNA sequencing, single base identification, hybridization assays, and others.
    Type: Grant
    Filed: October 7, 2013
    Date of Patent: December 30, 2014
    Assignee: Pacific Biosciences of California, Inc.
    Inventor: Jonas Korlach
  • Labeled reactants and their uses
    Patent number: 8906614
    Abstract: Labeled reactant compositions, and particularly labeled nucleic acid reaction compositions, that include structural components that 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: November 29, 2012
    Date of Patent: December 9, 2014
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Jeffrey Wegener, Jonas Korlach
  • Single molecule loading methods and compositions
    Patent number: 8906831
    Abstract: 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: Grant
    Filed: March 30, 2009
    Date of Patent: December 9, 2014
    Assignee: 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