Patents by Inventor Aaron Jacobs

Aaron Jacobs 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: 20250236633
    Abstract: The present disclosure relates to a process for the regiochemically and enantiomerically controlled synthesis of phosphoramidite-containing monomers, and to intermediate products of this process. In some embodiments, the phosphoramidite-containing monomers or their precursors are regioisomerically and/or enantiomerically pure and may be polymerized into polymers or copolymers.
    Type: Application
    Filed: September 25, 2024
    Publication date: July 24, 2025
    Applicant: Roche Sequencing Solutions, Inc.
    Inventors: Brent Banasik, Julian Andres Diaz Corral, Aaron Jacobs, Lukas Jud, Hannes Kuchelmeister, Melud Nbavi, Toni Pfaffeneder, Sona Simonyiova, John C. Tabone, Wilma Thuer
  • Publication number: 20250207112
    Abstract: Recombinant DPO4-type DNA polymerase variants with amino acid substitutions that confer modified properties upon the polymerase for improved single molecule sequencing applications are provided. Such properties may include enhanced binding and accurate incorporation of bulky nucleotide analog substrates into daughter strands and the like. Also provided are compositions comprising such DPO4 variants and nucleotide analogs, as well as nucleic acids which encode the polymerases with the aforementioned phenotypes.
    Type: Application
    Filed: March 10, 2025
    Publication date: June 26, 2025
    Inventors: Mark Kokoris, Marc Prindle, Gregory Scott Thiessen, Alexander Isaac Lehmann, Drew Goodman, Aaron Jacobs, John Chase
  • Publication number: 20250075265
    Abstract: The invention relates to compounds, methods and compositions for improving on nucleic acid polymerization, including DNA replication by in vitro primer extension to generate, for example, polymers for nanopore-based single molecule sequencing of a DNA template. A nucleic acid polymerase reaction composition is provided with polymerization enhancement moieties, which allows enhanced DNA polymerase activity with nucleotide analogs, resulting in improved length of primer extension products for sequencing applications.
    Type: Application
    Filed: March 13, 2024
    Publication date: March 6, 2025
    Inventors: Mark Stamatios Kokoris, John Tabone, Melud Nabavi, Aaron Jacobs, Dylan O'Connell, Drew Goodman, Lacey Merrill, Jagadeeswaran Chandrasekar, Kendall Berg, Samantha Vellucci, Jessica Vellucci
  • Publication number: 20240417785
    Abstract: The invention relates to methods and compositions for improving on nucleic acid polymerization, including DNA replication by in vitro primer extension to generate, for example, polymers for nanopore-based single molecule sequencing of a DNA template. A nucleic acid polymerase reaction composition is provided with polymerization enhancement moieties, which allows enhanced DNA polymerase activity with nucleotide analogs, resulting in improved length of primer extension products for sequencing applications.
    Type: Application
    Filed: March 25, 2024
    Publication date: December 19, 2024
    Inventors: Mark Stamatios Kokoris, John Tabone, Melud Nabavi, Aaron Jacobs, Dylan O'Connell, Drew Goodman, Lacey Merrill, Jagadeeswaran Chandrasekar
  • Publication number: 20240383938
    Abstract: Phosphoramidate esters and related nucleotide analogs useful in polynucleotide sequencing techniques, and synthetic methods for preparing those compounds, are disclosed. These compounds include nucleotide phosphoramidates analogs that are modified on the alpha-phosphate to enable attachment of a variety of application-specific substituents such as tether molecules.
    Type: Application
    Filed: July 30, 2024
    Publication date: November 21, 2024
    Inventors: Mark Kokoris, John Tabone, Melud Nabavi, Aaron Jacobs
  • Patent number: 11970731
    Abstract: The invention relates to compounds, methods and compositions for improving on nucleic acid polymerization, including DNA replication by in vitro primer extension to generate, for example, polymers for nanopore-based single molecule sequencing of a DNA template. A nucleic acid polymerase reaction composition is provided with polymerization enhancement moieties, which allows enhanced DNA polymerase activity with nucleotide analogs, resulting in improved length of primer extension products for sequencing applications.
    Type: Grant
    Filed: December 27, 2018
    Date of Patent: April 30, 2024
    Assignee: Roche Sequencing Solutions, Inc.
    Inventors: Mark Stamatios Kokoris, John Tabone, Melud Nabavi, Aaron Jacobs, Dylan O'Connell, Drew Goodman, Lacey Merrill, Jagadeeswaran Chandrasekar, Kendall Berg, Samantha Vellucci, Jessica Vellucci
  • Publication number: 20230313157
    Abstract: Recombinant DPO4-type DNA polymerase variants with amino acid substitutions that confer modified properties upon the polymerase for improved single molecule sequencing applications are provided. Such properties may include enhanced binding and accurate incorporation of bulky nucleotide analog substrates into daughter strands and the like. Also provided are compositions comprising such DPO4 variants and nucleotide analogs, as well as nucleic acids which encode the polymerases with the aforementioned phenotypes.
    Type: Application
    Filed: November 16, 2022
    Publication date: October 5, 2023
    Inventors: Mark Kokoris, Marc Prindle, Gregory Scott Thiessen, Alexander Isaac Lehmann, Drew Goodman, Aaron Jacobs, John Chase
  • Publication number: 20220411458
    Abstract: Phosphoramidate-based monomers are provided for use in the synthesis of expandable polymers for nanopore-based sensing. Such monomers comprising a reporter construct that contain a first reporter code, a symmetrical chemical brancher bearing a translocation control element, and a second reporter code, wherein the ends of the reporter construct are attached to phosphoramidate-nucleoside. Related methods and products are also provided.
    Type: Application
    Filed: November 23, 2021
    Publication date: December 29, 2022
    Inventors: Brent Banasik, Cynthia Cech, Jagadeeswaran Chandrasekar, Drew Goodman, Aaron Jacobs, Mark Stamatios Kokoris, Svetlana Kritzer, Matthew Lopez, Cara Machacek, Lacey Merrill, Melud Nabavi, Dylan O'Connell, John Tabone, Jessica Vellucci
  • Patent number: 11530392
    Abstract: Recombinant DPO4-type DNA polymerase variants with amino acid substitutions that confer modified properties upon the polymerase for improved single molecule sequencing applications are provided. Such properties may include enhanced binding and accurate incorporation of bulky nucleotide analog substrates into daughter strands and the like. Also provided are compositions comprising such DPO4 variants and nucleotide analogs, as well as nucleic acids which encode the polymerases with the aforementioned phenotypes.
    Type: Grant
    Filed: December 10, 2018
    Date of Patent: December 20, 2022
    Assignee: Stratos Genomics, Inc.
    Inventors: Mark Kokoris, Marc Prindle, Gregory Scott Thiessen, Alexander Isaac Lehmann, Drew Goodman, Aaron Jacobs, John Chase
  • Publication number: 20220112548
    Abstract: The invention relates to compounds, methods and compositions for improving on nucleic acid polymerization, including DNA replication by in vitro primer extension to generate, for example, polymers for nanopore-based single molecule sequencing of a DNA template. A nucleic acid polymerase reaction composition is provided with polymerization enhancement moieties, which allows enhanced DNA polymerase activity with nucleotide analogs, resulting in improved length of primer extension products for sequencing applications.
    Type: Application
    Filed: December 21, 2021
    Publication date: April 14, 2022
    Inventors: Jagadeeswaran Chandrasekar, Drew Goodman, Aaron Jacobs, Mark Stamatios Kokoris, Lacey Merrill, Melud Nabavi, Dylan O'Connell, John Tabone
  • Publication number: 20220073556
    Abstract: Phosphoramidate esters and related nucleotide analogs useful in polynucleotide sequencing techniques, and synthetic methods for preparing those compounds, are disclosed. These compounds include nucleotide phosphoramidates analogs that are modified on the alpha-phosphate to enable attachment of a variety of application-specific substituents such as tether molecules.
    Type: Application
    Filed: March 18, 2021
    Publication date: March 10, 2022
    Inventors: Mark Stamatios Kokoris, John Tabone, Melud Nabavi, Aaron Jacobs
  • Publication number: 20220042075
    Abstract: Methods, compositions and devices for single molecule sequencing are provided, particularly for solid-state synthesis and processing of expandable polymers (e.g., Xpandomers), as well as methods and compositions for producing new expandable polymer constructs that provide more accurate sequence information when passed through a nanopore sensor.
    Type: Application
    Filed: August 17, 2021
    Publication date: February 10, 2022
    Inventors: Lacey Merrill, Marc Prindle, Samantha Vellucci, Jagadeeswaran Chandrasekar, Mark Stamatios Kokoris, Gerson Aguirre, John Tabone, Robert N. McRuer, Michael Lee, Matthew Corning, Greg Thiessen, Salka Keller Barrett, Christian Berrios, Aaron Jacobs, Taylor Lehmann
  • Publication number: 20210163903
    Abstract: Recombinant DPO4-type DNA polymerase variants with amino acid substitutions that confer modified properties upon the polymerase for improved single molecule sequencing applications are provided. Such properties may include enhanced binding and accurate incorporation of bulky nucleotide analog substrates into daughter strands and the like. Also provided are compositions comprising such DPO4 variants and nucleotide analogs, as well as nucleic acids which encode the polymerases with the aforementioned phenotypes.
    Type: Application
    Filed: December 10, 2018
    Publication date: June 3, 2021
    Inventors: Mark KOKORIS, Marc PRINDLE, Gregory Scott Thiessen, Alexander Isaac LEHMANN, Drew GOODMAN, Aaron JACOBS, John CHASE
  • Publication number: 20210139966
    Abstract: The invention relates to methods and compositions for improving on nucleic acid polymerization, including DNA replication by in vitro primer extension to generate, for example, polymers for nanopore-based single molecule sequencing of a DNA template. A nucleic acid polymerase reaction composition is provided with polymerization enhancement moieties, which allows enhanced DNA polymerase activity with nucleotide analogs, resulting in improved length of primer extension products for sequencing applications.
    Type: Application
    Filed: December 20, 2018
    Publication date: May 13, 2021
    Inventors: Mark Stamatios Kokoris, John Tabone, Melud Nabavi, Aaron Jacobs, Dylan O'Connell, Drew Goodman, Lacey Merrill, Jagadeeswaran Chandrasekar
  • Publication number: 20210062251
    Abstract: The invention relates to compounds, methods and compositions for improving on nucleic acid polymerization, including DNA replication by in vitro primer extension to generate, for example, polymers for nanopore-based single molecule sequencing of a DNA template. A nucleic acid polymerase reaction composition is provided with polymerization enhancement moieties, which allows enhanced DNA polymerase activity with nucleotide analogs, resulting in improved length of primer extension products for sequencing applications.
    Type: Application
    Filed: December 27, 2018
    Publication date: March 4, 2021
    Inventors: Mark Stamatios Kokoris, John Tabone, Melud Nabavi, Aaron Jacobs, Dylan O'Connell, Drew Goodman, Lacey Merrill, Jagadeeswaran Chandrasekar, Kendall Berg, Samantha Vellucci, Jessica Vellucci
  • Patent number: 10774105
    Abstract: Phosphoramidate esters and related nucleotide analogs useful in polynucleotide sequencing techniques, and synthetic methods for preparing those compounds, are disclosed, including compounds having the following structure: wherein R1, R2, R3 and R4 are as defined herein. These compounds include nucleotide phosphoramidates analogs that are modified on the alpha-phosphate to enable attachment of a variety of application-specific substituents such as tether molecules.
    Type: Grant
    Filed: April 10, 2019
    Date of Patent: September 15, 2020
    Assignee: STRATOS GENOMICS, INC.
    Inventors: Mark Stamatios Kokoris, John Tabone, Melud Nabavi, Aaron Jacobs
  • Patent number: 10657987
    Abstract: This disclosure is related to systems, devices, processes, and methods to optimize a laser power boost amplitude, a laser power boost duration, or both in a heat-assisted data recording device, such as in heat-assisted magnetic recording (HAMR). The amplitude and duration for the laser power boost may be determined for a specific portion of a write operation, such as a first sector of the write operation. During operation of a data storage device, the laser power boost may provide additional power to the laser for the specific portion. Once the laser power boost duration has elapsed, the data storage device may continue providing power to the laser at the normal power input range of the laser. The laser power boost settings may be determined on a per head per zone basis, per track basis, or another configuration.
    Type: Grant
    Filed: December 3, 2018
    Date of Patent: May 19, 2020
    Assignee: Seagate Technology LLC
    Inventors: Alfredo Sam Chu, Franklin P. Martens, Aaron Jacobs
  • Publication number: 20190330254
    Abstract: Phosphoramidate esters and related nucleotide analogs useful in polynucleotide sequencing techniques, and synthetic methods for preparing those compounds, are disclosed. These compounds include nucleotide phosphoramidates analogs that are modified on the alpha-phosphate to enable attachment of a variety of application-specific substituents such as tether molecules.
    Type: Application
    Filed: April 10, 2019
    Publication date: October 31, 2019
    Inventors: Mark Stamatios Kokoris, John Tabone, Melud Nabavi, Aaron Jacobs
  • Patent number: 10301345
    Abstract: Phosphoramidate esters and related nucleotide analogs useful in polynucleotide sequencing techniques, and synthetic methods for preparing those compounds, are disclosed, including compounds having the following structure: wherein R1, R2, R3 and R4 are as defined herein.
    Type: Grant
    Filed: November 20, 2015
    Date of Patent: May 28, 2019
    Assignee: STRATOS GENOMICS, INC.
    Inventors: Mark Stamatios Kokoris, John Tabone, Melud Nabavi, Aaron Jacobs
  • Patent number: 10147453
    Abstract: This disclosure is related to systems, devices, processes, and methods to optimize a laser power boost amplitude, a laser power boost duration, or both in a heat-assisted data recording device, such as in heat-assisted magnetic recording (HAMR). The amplitude and duration for the laser power boost may be determined for a specific portion of a write operation, such as a first sector of the write operation. During operation of a data storage device, the laser power boost may provide additional power to the laser for the specific portion. Once the laser power boost duration has elapsed, the data storage device may continue providing power to the laser at the normal power input range of the laser. The laser power boost settings may be determined on a per head per zone basis, per track basis, or another configuration.
    Type: Grant
    Filed: October 13, 2015
    Date of Patent: December 4, 2018
    Assignee: Seagate Technology LLC
    Inventors: Alfredo Sam Chu, Franklin P Martens, Aaron Jacobs