Patents by Inventor Jan F. Simons

Jan F. Simons 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: 20220112550
    Abstract: The invention is directed to methods for analyzing polymers comprising linear chains of at least two types of monomers, such as polynucleotides, including DNA, RNA, and the like, using nanopores and optical detection. In some embodiments, as few as two different kinds of nucleotide are labeled with different optical labels that generate distinguishable optical signals for the selected kinds of nucleotide in both sense strands and antisense strands of target polynucleotides. Labeled strands are translocated through nanopores where nucleotides of the strands are constrained to pass sequentially through an optical detection region where their labels generate a sequence of optical signals making up an optical signature. In some embodiments, information from optical signatures from both sense and antisense strands are combined to determine complete nucleotide sequences of target polynucleotides.
    Type: Application
    Filed: August 3, 2021
    Publication date: April 14, 2022
    Applicant: Quantapore, Inc.
    Inventors: Karl GUEGLER, Jan F. SIMONS, Stephen C. MACEVICZ
  • Publication number: 20220106629
    Abstract: The invention provides methods for analyzing polynucleotides using nanopores that allow passage of single stranded polynucleotides but not double stranded polynucleotides. In accordance with some embodiments, a double-stranded product is produced that comprises a labeled strand with a single stranded tail or overhang. The double stranded product is exposed to one or more nanopores in the presence of an electric field across the one or more nanopores such that the single stranded tail may be captured and the labeled strand translocated by unzipping from the double stranded product. The ionic composition of the reaction mixture and electric field strength are selected so that nucleotides translocate a nanopore at a rate of less than 1000 nucleotides per second.
    Type: Application
    Filed: July 2, 2021
    Publication date: April 7, 2022
    Applicant: Quantapore, Inc.
    Inventors: Tao HONG, Karl GUEGLER, Jan F. SIMONS
  • Publication number: 20190277829
    Abstract: The invention is directed to articles of manufacture for constraining movement of molecules, such as polynucleotides, and methods of using the same. In some embodiments, article of manufacture of the invention comprise (i) a solid state membrane having at least one aperture extending therethrough from a first side to a second side; (ii) an annular DNA sheet having a central opening disposed on the first side of the solid state membrane such that the annular DNA sheet spans an aperture and the central opening is aligned with the aperture to provide fluid communication between the first side and the second side of the solid state membrane through the aperture; and (iii) a protein nanopore immobilized in the central opening of the annular DNA sheet spanning the aperture. Uses of such articles of manufacture include determining sequences of nucleic acids.
    Type: Application
    Filed: November 7, 2017
    Publication date: September 12, 2019
    Applicant: Quantapore, Inc.
    Inventors: Jan F. SIMONS, Martin HUBER
  • Publication number: 20190112649
    Abstract: The invention is directed to methods for analyzing polymers comprising linear chains of at least two types of monomers, such as polynucleotides, including DNA, RNA, and the like, using nanopores and optical detection. In some embodiments, as few as two different kinds of nucleotide are labeled with different optical labels that generate distinguishable optical signals for the selected kinds of nucleotide in both sense strands and antisense strands of target polynucleotides. Labeled strands are translocated through nanopores where nucleotides of the strands are constrained to pass sequentially through an optical detection region where their labels generate a sequence of optical signals making up an optical signature. In some embodiments, information from optical signatures from both sense and antisense strands are combined to determine complete nucleotide sequences of target polynucleotides.
    Type: Application
    Filed: May 4, 2017
    Publication date: April 18, 2019
    Applicant: Quantapore, Inc.
    Inventors: Karl GUEGLER, Jan F. SIMONS, Stephen C. MACEVICZ
  • Publication number: 20190078145
    Abstract: The invention provides methods for analyzing polynucleotides using nanopores that allow passage of single stranded polynucleotides but not double stranded polynucleotides. In accordance with some embodiments, a double-stranded product is produced that comprises a labeled strand with a single stranded tail or overhang. The double stranded product is exposed to one or more nanopores in the presence of an electric field across the one or more nanopores such that the single stranded tail may be captured and the labeled strand translocated by unzipping from the double stranded product. The ionic composition of the reaction mixture and electric field strength are selected so that nucleotides translocate a nanopore at a rate of less than 1000 nucleotides per second.
    Type: Application
    Filed: November 28, 2016
    Publication date: March 14, 2019
    Applicant: QUANTAPORE, INC.
    Inventors: Tao HONG, Karl GUEGLER, Jan F. SIMONS
  • Publication number: 20180364169
    Abstract: The invention is directed to devices and methods for optically based nanopore analysis which employ FRET signaling wherein at least one member of a FRET pair is mobile within a lipid bilayer containing one or more nanopores. In some embodiments, mobile FRET donors are constrained to a lipid bilayer so that they may continuously diffuse into and within a FRET distance of acceptor-labeled analytes entering or exiting a nanopore so that bleached or degraded FRET donors are continuously replaced.
    Type: Application
    Filed: June 6, 2016
    Publication date: December 20, 2018
    Applicant: Quantapore, Inc.
    Inventors: Brett N. ANDERSON, Martin HUBER, Daniel KOSLOVER, Jan F. SIMONS
  • Publication number: 20110003701
    Abstract: An embodiment of an adaptor element for efficient target processing is described that comprises a semi-complementary double stranded nucleic acid adaptor comprising a non-complementary region and a complementary region, where the non-complementary region comprises a first amplification primer site and a second amplification primer site and the complementary region comprises a sequencing primer site and one or more inosine species.
    Type: Application
    Filed: February 23, 2009
    Publication date: January 6, 2011
    Inventors: Gianni Calogero Ferreri, Jan F. Simons, Michael Todd Ronan, Michael Egholm, Brian C. Godwin, David Roderick Riches, Stephen Kyle Hutchison, Michael S. Braverman, Melinda D. Palmer, Jeffrey Jeddeloh, Jacob Kitzman, Thomas J. Albert