Patents Examined by Jezia Riley
  • Patent number: 10689412
    Abstract: This invention provides a process of labeling a polynucleotide analogue to be detected by Raman and/or infrared spectroscopy detection.
    Type: Grant
    Filed: April 18, 2017
    Date of Patent: June 23, 2020
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Jian Wu, Zengmin Li
  • Patent number: 10683539
    Abstract: This disclosure relates to novel compounds for use in various compositions, kits and methods, including, for example, use in polymerase storage buffers and in nucleic acid synthesis or amplification reactions such as a polymerase chain reaction (PCR). Methods for preparing the novel compounds are also described.
    Type: Grant
    Filed: January 29, 2018
    Date of Patent: June 16, 2020
    Assignee: LIFE TECHNOLOGIES CORPORATION
    Inventors: Parul Angrish, Zhiwei Yang
  • Patent number: 10683536
    Abstract: The invention provides improved methods for synthesizing polynucleotides, such as DNA and RNA, using renewable initiators coupled to a solid support. Using the methods of the invention, specific sequences of polynucleotides can be synthesized de novo, base by base, in an aqueous environment, without the use of a nucleic acid template.
    Type: Grant
    Filed: August 18, 2015
    Date of Patent: June 16, 2020
    Assignee: Molecular Assemblies, Inc.
    Inventor: J. William Efcavitch
  • Patent number: 10676780
    Abstract: The present invention provides methods, compositions and devices for stabilizing the extracellular nucleic acid population in a cell-containing biological sample using an apoptosis inhibitor, preferably a caspase inhibitor, a hypertonic agent and/or a compound according to formula (1) as defined in the claims.
    Type: Grant
    Filed: September 25, 2012
    Date of Patent: June 9, 2020
    Assignee: QIAGEN GMbH
    Inventors: Martin Horlitz, Annabelle Schubert, Markus Sprenger-Haussels
  • Patent number: 10676778
    Abstract: Methods, devices, systems and compositions for detecting nucleic acids in polymerase chain reaction assays, such as droplet digital polymerase chain reaction (ddPCR) assays, using intercalating dyes. A dual surfactant system with at least one fluorosurfactant and at least one non-ionic non-fluorosurfactant may be employed for droplet generation and nucleic acid detection.
    Type: Grant
    Filed: November 20, 2017
    Date of Patent: June 9, 2020
    Assignee: Bio-Rad Laboratories, Inc.
    Inventors: Adam Lowe, Geoff McDermott, Christopher M. Hindson, Erin R. Chia, Amy L. Hiddessen, Benjamin J. Hindson, Chunxiao Han, Yaqi Wang
  • Patent number: 10676788
    Abstract: Labeled nucleotide analogs comprising at least one avidin protein, at least one dye-labeled compound, and at least one nucleotide compound are provided. The analogs are useful in various fluorescence-based analytical methods, including the analysis of highly multiplexed optical reactions in large numbers at high densities, such as single molecule real time nucleic acid sequencing reactions. The analogs are detectable with high sensitivity at desirable wavelengths. They contain structural components that modulate the interactions of the analogs with DNA polymerase, thus decreasing photodamage and improving the kinetic and other properties of the analogs in sequencing reactions. Also provided are nucleotide and dye-labeled compounds of the subject analogs, as well as intermediates useful in the preparation of the compounds and analogs. Compositions comprising the compounds, methods of synthesis of the intermediates, compounds, and analogs, and mutant DNA polymerases are also provided.
    Type: Grant
    Filed: May 19, 2017
    Date of Patent: June 9, 2020
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Gene Shen, Stephen Yue, Lubomir Sebo, Louis Brogley
  • Patent number: 10669299
    Abstract: Labeled nucleotide analogs comprising at least one avidin protein, at least one dye-labeled compound, and at least one nucleotide compound are provided. The analogs are useful in various fluorescence-based analytical methods, including the analysis of highly multiplexed optical reactions in large numbers at high densities, such as single molecule real time nucleic acid sequencing reactions. The analogs are detectable with high sensitivity at desirable wavelengths. They contain structural components that modulate the interactions of the analogs with DNA polymerase, thus decreasing photodamage and improving the kinetic and other properties of the analogs in sequencing reactions. Also provided are nucleotide and dye-labeled compounds of the subject analogs, as well as intermediates useful in the preparation of the compounds and analogs. Compositions comprising the compounds, methods of synthesis of the intermediates, compounds, and analogs, and mutant DNA polymerases are also provided.
    Type: Grant
    Filed: November 21, 2016
    Date of Patent: June 2, 2020
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Lubomir Sebo, Honey Osuna, Stephen Yue, Yuri Lapin
  • Patent number: 10669538
    Abstract: The present invention relates to a method for synthesising templated molecules. In one aspect of the invention, the templated molecules are linked to the template which templated the synthesis thereof. The invention allows the generation of libraries which can be screened for e.g. therapeutic activity.
    Type: Grant
    Filed: October 13, 2016
    Date of Patent: June 2, 2020
    Assignee: NUEVOLUTION A/S
    Inventors: Henrik Pedersen, Alex Haahr Gouliaev, Thomas Franch, Christian Klarner Sams, Eva Kampmann Olsen, Frank Abilgaard Slok, Gitte Nystrup Husemoen, Jakob Felding, Lene Hyldtoft, Mads Norregaard-Madsen, Michael Anders Godskesen, Sanne Schroder Glad, Thomas Thisted, Per-Ola Freskgard, Anette Holtmann
  • Patent number: 10669535
    Abstract: Compositions and methods for the isolation of protein-nucleic acid complexes and microvesicles (collectively referred to as “bioparticles”) released by mammalian cells into body fluids or cell culture media are provided. Isolated bioparticles of the invention contain biological molecules that are useful as diagnostic/prognostic biomarkers or for identification of therapeutic targets (e.g., disease or disorder-associated miRNAs). The isolation of biological molecules as described herein results in purification and concentration of the molecules. Methods for producing bio fluids that are free of detectable bioparticles, that are largely depleted of bioparticles, or that possess a reduced concentration of bioparticles compared to a bio fluid starting material (collectively termed “bioparticle-depleted”) are also provided. Isolation of bioparticle-depleted biofluid is useful, e.g.
    Type: Grant
    Filed: August 5, 2015
    Date of Patent: June 2, 2020
    Assignee: YMIR GENOMICS, LLC
    Inventors: Patrick Shannon Pendergrast, Robert Scott Pendergrast, John Stephen Pendergrast, Anna Irmina Markowska
  • Patent number: 10669580
    Abstract: The present disclosure relates to compounds comprising a negatively-charged polymer moiety which is capable of entering a nanopore and upon entering a nanopore in the presence of positive ions results in an increased flow of the positive ions through the nanopore. The present disclosure provides methods of preparing the compounds and for their use as nanopore-detectable tags, in particular, for nanopore-based nucleic acid detection and sequencing.
    Type: Grant
    Filed: August 23, 2017
    Date of Patent: June 2, 2020
    Assignee: Roche Sequencing Solutions, Inc.
    Inventors: Dmitriy Gremyachinskiy, Peter Crisalli, Andrew Trans, Ashwini Bhat
  • Patent number: 10669577
    Abstract: This invention provides methods for attaching a nucleic acid to a solid surface and for sequencing nucleic acid by detecting the identity of each nucleotide analogue after the nucleotide analogue is incorporated into a growing strand of DNA in a polymerase reaction. The invention also provides nucleotide analogues which comprise unique labels attached to the nucleotide analogue through a cleavable linker, and a cleavable chemical group to cap the —OH group at the 3?-position of the deoxyribose.
    Type: Grant
    Filed: March 27, 2015
    Date of Patent: June 2, 2020
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Zengmin Li, John Robert Edwards, Yasuhiro Itagaki
  • Patent number: 10669582
    Abstract: This invention provides methods for attaching a nucleic acid to a solid surface and for sequencing nucleic acid by detecting the identity of each nucleotide analogue after the nucleotide analogue is incorporated into a growing strand of DNA in a polymerase reaction. The invention also provides nucleotide analogues which comprise unique labels attached to the nucleotide analogue through a cleavable linker, and a cleavable chemical group to cap the —OH group at the 3?-position of the deoxyribose.
    Type: Grant
    Filed: March 8, 2018
    Date of Patent: June 2, 2020
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Zengmin Li, John Robert Edwards, Yasuhiro Itagaki
  • Patent number: 10669304
    Abstract: Methods and devices are provided herein for surfaces for de novo nucleic acid synthesis which provide for low error rates. In addition, methods and devices are provided herein for increased nucleic acid mass yield resulting from de novo nucleic acid synthesis.
    Type: Grant
    Filed: February 3, 2016
    Date of Patent: June 2, 2020
    Assignee: TWIST BIOSCIENCE CORPORATION
    Inventors: Pierre F. Indermuhle, Eugene P. Marsh, Andres Fernandez, William Banyai, Bill J. Peck
  • Patent number: 10662472
    Abstract: This invention provides methods for attaching a nucleic acid to a solid surface and for sequencing nucleic acid by detecting the identity of each nucleotide analogue after the nucleotide analogue is incorporated into a growing strand of DNA in a polymerase reaction. The invention also provides nucleotide analogues which comprise unique labels attached to the nucleotide analogue through a cleavable linker, and a cleavable chemical group to cap the —OH group at the 3?-position of the deoxyribose.
    Type: Grant
    Filed: November 26, 2018
    Date of Patent: May 26, 2020
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Zengmin Li, John Robert Edwards, Yasuhiro Itagaki
  • Patent number: 10655174
    Abstract: The present disclosure relates to tagged multi-nucleotide compounds, which comprise a single tag moiety covalently linked to a plurality of nucleoside-5?-oligophosphate moieties. As disclosed herein, these tagged multi-nucleotide compounds have improved characteristics as polymerase substrates and can be used in a range of nucleic acid detection and sequencing methods, including nanopore sequencing-by-synthesis.
    Type: Grant
    Filed: May 24, 2017
    Date of Patent: May 19, 2020
    Assignee: Roche Sequencing Solutions, Inc.
    Inventors: Dmitriy Gremyachinskiy, Meng Taing, Aruna Ayer, Peter J. Crisalli
  • Patent number: 10655171
    Abstract: Modular flow cells, devices with modular flow cells, and methods of sequencing using modular flow cells, as well as systems and kits including modular flow cells, are described, permitting sequencing wherein less than the full capacity for sequencing is desired.
    Type: Grant
    Filed: November 6, 2018
    Date of Patent: May 19, 2020
    Assignees: QIAGEN SCIENCES, LLC, QIAGEN GmbH
    Inventors: Jerzy Olejnik, Dirk Zimmermann
  • Patent number: 10647740
    Abstract: Provided are compounds comprising two DNA supramolecular binding molecules covalently joined by a linker group. Also provided are multisignal labeling reagents comprising (i) an oligomer of nucleotides or nucleotide analogs; (ii) a DNA supramolecular binding molecule noncovalently bound to the oligomer; and (iii) a first reactive group or a first partner of a first binding pair covalently bound to the oligomer. Additionally provided are methods of producing multisignal labeling reagents.
    Type: Grant
    Filed: December 21, 2017
    Date of Patent: May 12, 2020
    Assignee: Enzo Life Science, Inc.
    Inventors: Jack Coleman, Elazar Rabbani, Jannis Stavrianopoulos, Praveen Pande
  • Patent number: 10648026
    Abstract: This invention provides nucleoside polyphosphate analogs each of which comprises a tag comprising a plurality of Raman-scattering moieties; compounds comprising said nucleoside polyphosphate analogs; and methods for determining the sequence of a single-stranded DNA or RNA using said nucleoside polyphosphate analogs. This invention also provides methods for detecting the interaction of a plurality of predetermined compounds, at least one of which having attached thereto a tag comprising a plurality of Raman-scattering moieties.
    Type: Grant
    Filed: March 14, 2014
    Date of Patent: May 12, 2020
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Shiv Kumar, Mirkó Palla, James J. Russo
  • Patent number: 10648028
    Abstract: This invention provides methods for attaching a nucleic acid to a solid surface and for sequencing nucleic acid by detecting the identity of each nucleotide analogue after the nucleotide analogue is incorporated into a growing strand of DNA in a polymerase reaction. The invention also provides nucleotide analogues which comprise unique labels attached to the nucleotide analogue through a cleavable linker, and a cleavable chemical group to cap the —OH group at the 3?-position of the deoxyribose.
    Type: Grant
    Filed: November 26, 2018
    Date of Patent: May 12, 2020
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Zengmin Li, John Robert Edwards, Yasuhiro Itagaki
  • Patent number: 10640529
    Abstract: Provided are compounds comprising two DNA supramolecular binding molecules covalently joined by a linker group. Also provided are multisignal labeling reagents comprising (i) an oligomer of nucleotides or nucleotide analogs; (ii) a DNA supramolecular binding molecule noncovalently bound to the oligomer; and (iii) a first reactive group or a first partner of a first binding pair covalently bound to the oligomer. Additionally provided are methods of producing multisignal labeling reagents.
    Type: Grant
    Filed: December 21, 2017
    Date of Patent: May 5, 2020
    Assignee: Enzo Life Sciences, Inc.
    Inventors: Jack Coleman, Elazar Rabbani, Jannis Stavrianopoulos, Praveen Pande