Patents by Inventor Mark Akeson

Mark Akeson 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).

  • Publication number: 20200325535
    Abstract: Devices and methods that can detect and control an individual polymer in a mixture is acted upon by another compound, for example, an enzyme, in a nanopore are provided. The devices and methods also determine (˜>50 Hz) the nucleotide base sequence of a polynucleotide under feedback control or using signals generated by the interactions between the polynucleotide and the nanopore. The invention is of particular use in the fields of molecular biology, structural biology, cell biology, molecular switches, molecular circuits, and molecular computational devices, and the manufacture thereof.
    Type: Application
    Filed: June 9, 2020
    Publication date: October 15, 2020
    Inventors: Mark A. Akeson, David W. Deamer, William B. Dunbar, Kate Lieberman, Noah A. Wilson
  • Patent number: 10760117
    Abstract: Disclosed are methods for polynucleotide sequencing that detect the location of selected nucleobases with greater precision. The methods can be used to determine the location and nature of modified bases in a polynucleotide, that is, non-canonical bases, or to improve accuracy of sequencing of “problem” regions of DNA sequencing such as homopolymers, GC rich areas, etc. The sequencing method exemplified is nanopore sequencing. Nanopore sequencing is used to generate a unique signal at a point in a polynucleotide sequence where an abasic site (AP site, or apurinic or apyrimidinic site) exists. As part of the method, an abasic site is specifically created enzymatically using a DNA glycosylase that recognizes a pre-determined nucleobase species and cleaves the N-glycosidic bond to release only that base, leaving an AP site in its place.
    Type: Grant
    Filed: April 5, 2016
    Date of Patent: September 1, 2020
    Assignee: The Regents of the University of California
    Inventors: Miten Jain, Hugh Edward Olsen, Mark A. Akeson
  • Patent number: 10344327
    Abstract: Devices and methods that can detect and control an individual polymer in a mixture is acted upon by another compound, for example, an enzyme, in a nanopore are provided. The devices and methods also determine (˜>50 Hz) the nucleotide base sequence of a polynucleotide under feedback control or using signals generated by the interactions between the polynucleotide and the nanopore. The invention is of particular use in the fields of molecular biology, structural biology, cell biology, molecular switches, molecular circuits, and molecular computational devices, and the manufacture thereof.
    Type: Grant
    Filed: March 31, 2016
    Date of Patent: July 9, 2019
    Assignee: The Regents of the University of California
    Inventors: Mark A. Akeson, David W. Deamer, William B. Dunbar, Roger Jinteh Arrigo Chen, Noah A. Wilson
  • Patent number: 10208342
    Abstract: Devices and methods that can detect and control an individual polymer in a mixture is acted upon by another compound, for example, an enzyme, in a nanopore are provided. The devices and methods also determine (˜>50 Hz) the nucleotide base sequence of a polynucleotide under feedback control or using signals generated by the interactions between the polynucleotide and the nanopore. The invention is of particular use in the fields of molecular biology, structural biology, cell biology, molecular switches, molecular circuits, and molecular computational devices, and the manufacture thereof.
    Type: Grant
    Filed: September 22, 2017
    Date of Patent: February 19, 2019
    Assignee: The Regents of the University of California
    Inventors: William B. Dunbar, Noah A. Wilson, Mark A. Akeson, David W. Deamer, Kate Lieberman
  • Patent number: 10202645
    Abstract: Devices and methods that can detect and control an individual polymer in a mixture is acted upon by another compound, for example, an enzyme, in a nanopore are provided. The devices and methods also determine (˜>50 Hz) the nucleotide base sequence of a polynucleotide under feedback control or using signals generated by the interactions between the polynucleotide and the nanopore. The invention is of particular use in the fields of molecular biology, structural biology, cell biology, molecular switches, molecular circuits, and molecular computational devices, and the manufacture thereof.
    Type: Grant
    Filed: September 22, 2017
    Date of Patent: February 12, 2019
    Assignee: The Regents of the University of California
    Inventors: Mark A. Akeson, Daniel Branton, David W. Deamer, Seiko L. Endo
  • Patent number: 10196688
    Abstract: Devices and methods that can detect and control an individual polymer in a mixture is acted upon by another compound, for example, an enzyme, in a nanopore are provided. The devices and methods also determine (˜>50 Hz) the nucleotide base sequence of a polynucleotide under feedback control or using signals generated by the interactions between the polynucleotide and the nanopore. The invention is of particular use in the fields of molecular biology, structural biology, cell biology, molecular switches, molecular circuits, and molecular computational devices, and the manufacture thereof.
    Type: Grant
    Filed: October 21, 2015
    Date of Patent: February 5, 2019
    Assignee: THE REGENTS OF THE UNIVERSITY OF CALIFORNIA
    Inventors: Mark A. Akeson, David W. Deamer, William B. Dunbar, Roger Jinteh Arrigo Chen, Noah A. Wilson
  • Publication number: 20180320168
    Abstract: Provided are methods of producing size-selected nucleic acid libraries. The methods include contacting a nucleic acid sample and a nucleic acid binding reagent including an affinity tag, under conditions in which nucleic acids of less than a desired length are substantially bound to the nucleic acid binding reagent and nucleic acids of the desired length are substantially not bound to the nucleic acid binding reagent. The conditions include the duration of the contacting, the concentration of the nucleic acid binding reagent, or both. The methods further include separating, using the affinity tag, the nucleic acids of less than the desired length bound to the nucleic acid binding reagent from the nucleic acids of the desired length not bound to the nucleic acid binding reagent, to produce a size-selected nucleic acid library. Compositions and kits that find use, e.g., in practicing the methods of the present disclosure, are also provided.
    Type: Application
    Filed: May 3, 2018
    Publication date: November 8, 2018
    Inventors: Hugh E. Olsen, Miten Jain, Mark A. Akeson
  • Patent number: 10081835
    Abstract: Devices and methods that can detect and control an individual polymer in a mixture is acted upon by another compound, for example, an enzyme, in a nanopore are provided. The devices and methods also determine (˜>50 Hz) the nucleotide base sequence of a polynucleotide under feedback control or using signals generated by the interactions between the polynucleotide and the nanopore. The invention is of particular use in the fields of molecular biology, structural biology, cell biology, molecular switches, molecular circuits, and molecular computational devices, and the manufacture thereof.
    Type: Grant
    Filed: October 17, 2013
    Date of Patent: September 25, 2018
    Assignee: The Regents of the University of California
    Inventors: Mark A. Akeson, David W. Deamer, William B. Dunbar, Roger Jinteh Arrigo Chen, Noah A. Wilson
  • Publication number: 20180258474
    Abstract: Disclosed are methods for polynucleotide sequencing that detect the location of selected nucleobases with greater precision. The methods can be used to determine the location and nature of modified bases in a polynucleotide, that is, non-canonical bases, or to improve accuracy of sequencing of “problem” regions of DNA sequencing such as homopolymers, GC rich areas, etc. The sequencing method exemplified is nanopore sequencing. Nanopore sequencing is used to generate a unique signal at a point in a polynucleotide sequence where an abasic site (AP site, or apurinic or apyrimidinic site) exists. As part of the method, an abasic site is specifically created enzymatically using a DNA glycosylase that recognizes a pre-determined nucleobase species and cleaves the N-glycosidic bond to release only that base, leaving an AP site in its place.
    Type: Application
    Filed: April 5, 2016
    Publication date: September 13, 2018
    Inventors: Miten Jain, Hugh Edward Olsen, Mark A. Akeson
  • Patent number: 10059988
    Abstract: Devices and methods that can detect and control an individual polymer in a mixture is acted upon by another compound, for example, an enzyme, in a nanopore are provided. The devices and methods also determine (˜>50 Hz) the nucleotide base sequence of a polynucleotide under feedback control or using signals generated by the interactions between the polynucleotide and the nanopore. The invention is of particular use in the fields of molecular biology, structural biology, cell biology, molecular switches, molecular circuits, and molecular computational devices, and the manufacture thereof.
    Type: Grant
    Filed: September 13, 2012
    Date of Patent: August 28, 2018
    Assignee: THE REGENTS OF THE UNIVERSITY OF CALIFORNIA
    Inventors: Mark A. Akeson, David W. Deamer, Seico Benner, William B. Dunbar, Noah A. Wilson, Kathy Lieberman, Robin Abu-Shumays, Nicholas Hurt
  • Publication number: 20180023136
    Abstract: Devices and methods that can detect and control an individual polymer in a mixture is acted upon by another compound, for example, an enzyme, in a nanopore are provided. The devices and methods also determine (˜>50 Hz) the nucleotide base sequence of a polynucleotide under feedback control or using signals generated by the interactions between the polynucleotide and the nanopore. The invention is of particular use in the fields of molecular biology, structural biology, cell biology, molecular switches, molecular circuits, and molecular computational devices, and the manufacture thereof.
    Type: Application
    Filed: September 22, 2017
    Publication date: January 25, 2018
    Inventors: Mark A. Akeson, Daniel Branton, David W. Deamer, Seico Benner
  • Publication number: 20180023137
    Abstract: Devices and methods that can detect and control an individual polymer in a mixture is acted upon by another compound, for example, an enzyme, in a nanopore are provided. The devices and methods also determine (˜>50 Hz) the nucleotide base sequence of a polynucleotide under feedback control or using signals generated by the interactions between the polynucleotide and the nanopore. The invention is of particular use in the fields of molecular biology, structural biology, cell biology, molecular switches, molecular circuits, and molecular computational devices, and the manufacture thereof.
    Type: Application
    Filed: September 22, 2017
    Publication date: January 25, 2018
    Inventors: William B. Dunbar, Noah A. Wilson, Mark A. Akeson, David W. Deamer, Kate Lieberman
  • Patent number: 9797013
    Abstract: Devices and methods that can detect and control an individual polymer in a mixture is acted upon by another compound, for example, an enzyme, in a nanopore are provided. The devices and methods also determine (˜>50 Hz) the nucleotide base sequence of a polynucleotide under feedback control or using signals generated by the interactions between the polynucleotide and the nanopore. The invention is of particular use in the fields of molecular biology, structural biology, cell biology, molecular switches, molecular circuits, and molecular computational devices, and the manufacture thereof.
    Type: Grant
    Filed: May 23, 2016
    Date of Patent: October 24, 2017
    Assignee: The Regents of the University of California
    Inventors: Mark A. Akeson, David W. Deamer, Roger Jinteh Arrigo Chen
  • Patent number: 9481908
    Abstract: The invention herein disclosed provides for devices and methods that can detect and control an individual polymer in a mixture is acted upon by another compound, for example, an enzyme, in a nanopore in the absence of requiring a terminating nucleotide. The devices and methods are also used to determine rapidly (˜>50 Hz) the nucleotide base sequence of a polynucleotide under feedback control or using signals generated by the interactions between the polynucleotide and the nanopore. The invention is of particular use in the fields of drug discovery, molecular biology, structural biology, cell biology, molecular switches, molecular circuits, and molecular computational devices, and the manufacture thereof.
    Type: Grant
    Filed: February 27, 2014
    Date of Patent: November 1, 2016
    Assignee: The Regents of the University of California
    Inventors: Felix A. Olasagasti, Kathy R. Lieberman, Seico Benner, Mark A. Akeson
  • Publication number: 20160289758
    Abstract: Devices and methods that can detect and control an individual polymer in a mixture is acted upon by another compound, for example, an enzyme, in a nanopore are provided. The devices and methods also determine (˜>50 Hz) the nucleotide base sequence of a polynucleotide under feedback control or using signals generated by the interactions between the polynucleotide and the nanopore. The invention is of particular use in the fields of molecular biology, structural biology, cell biology, molecular switches, molecular circuits, and molecular computational devices, and the manufacture thereof.
    Type: Application
    Filed: May 23, 2016
    Publication date: October 6, 2016
    Inventors: Mark A. Akeson, David W. Deamer, Roger Jinteh Arrigo Chen
  • Publication number: 20160209350
    Abstract: Devices and methods that can detect and control an individual polymer in a mixture is acted upon by another compound, for example, an enzyme, in a nanopore are provided. The devices and methods also determine (˜>50 Hz) the nucleotide base sequence of a polynucleotide under feedback control or using signals generated by the interactions between the polynucleotide and the nanopore. The invention is of particular use in the fields of molecular biology, structural biology, cell biology, molecular switches, molecular circuits, and molecular computational devices, and the manufacture thereof.
    Type: Application
    Filed: March 31, 2016
    Publication date: July 21, 2016
    Inventors: Mark A. Akeson, David W. Deamer, William B. Dunbar, Roger Jinteh Arrigo Chen, Noah A. Wilson
  • Publication number: 20160040230
    Abstract: Devices and methods that can detect and control an individual polymer in a mixture is acted upon by another compound, for example, an enzyme, in a nanopore are provided. The devices and methods also determine (˜>50 Hz) the nucleotide base sequence of a polynucleotide under feedback control or using signals generated by the interactions between the polynucleotide and the nanopore. The invention is of particular use in the fields of molecular biology, structural biology, cell biology, molecular switches, molecular circuits, and molecular computational devices, and the manufacture thereof.
    Type: Application
    Filed: October 21, 2015
    Publication date: February 11, 2016
    Inventors: Mark A. Akeson, David W. Deamer, William B. Dunbar, Roger Jinteh Arrigo Chen, Noah A. Wilson
  • Publication number: 20160032236
    Abstract: Described herein is a device and method for translocating a protein through a nanopore and monitoring electronic changes caused by different amino acids in the protein. The device comprises a nanopore in a membrane, an amplifier for providing a voltage between the cis side and trans side of the membrane, and an NTP driven unfoldase which processed the protein to be translocated. The exemplified unfoldase is the ClpX unfoldase from E. coli.
    Type: Application
    Filed: February 15, 2013
    Publication date: February 4, 2016
    Applicant: THE REGENTS OF THE UNIVERSITY OF CALIFORNIA
    Inventors: Jeffrey M Nivala, Douglas B Marks, Mark A Akeson
  • Publication number: 20150307931
    Abstract: The invention relates to a method for detecting a double-stranded region in a nucleic acid by (1) providing two separate, adjacent pools of a medium and a interface between the two pools, the interface having a channel so dimensioned as to allow sequential monomer-by-monomer passage of a single-stranded nucleic acid, but not of a double-stranded nucleic acid, from one pool to the other pool; (2) placing a nucleic acid polymer in one of the two pools; and (3) taking measurements as each of the nucleotide monomers of the single-stranded nucleic acid polymer passes through the channel so as to differentiate between nucleotide monomers that are hybridized to another nucleotide monomer before entering the channel and nucleotide monomers that are not hybridized to another nucleotide monomer before entering the channel.
    Type: Application
    Filed: January 9, 2014
    Publication date: October 29, 2015
    Inventors: Mark AKESON, Daniel BRANTON, George CHURCH, David W. DEAMER
  • Publication number: 20150031024
    Abstract: The invention herein disclosed provides for devices, reagents, and methods that can detect and control an individual polymer in a mixture is acted upon by another compound, for example, an enzyme, in a nanopore. Of particular note is the use of reagents to rapidly sequence a polynucleotide. The invention is of particular use in the fields of forensic biology, molecular biology, structural biology, cell biology, molecular switches, molecular circuits, and molecular computational devices, and the manufacture thereof.
    Type: Application
    Filed: July 30, 2012
    Publication date: January 29, 2015
    Applicant: THE REGENTS OF THE UNIVERSITY OF CALIFORNIA
    Inventors: Hugh E. Olsen, Mark A. Akeson