Patents Examined by Jezia Riley
  • Massive parallel method for decoding DNA and RNA
    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
  • Tagged multi-nucleotides useful for nucleic acid sequencing
    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
  • Modular flow cells and methods of sequencing
    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
  • Multisignal labeling reagents and processes and uses therefor
    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
  • Massive parallel method for decoding DNA and RNA
    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
  • Raman cluster tagged molecules for biological imaging
    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
  • Multisignal labeling reagents and processes and uses therefor
    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
  • Post-transcriptionally chemically modified double strand RNAs
    Patent number: 10640769
    Abstract: Described are post transcriptionally chemically modified double strand RNAs (MdsRNAs) having more than 30 base pairs. The MdsRNAs inhibit gene expression in target organisms. Also described are methods of making and using MdsRNAs.
    Type: Grant
    Filed: October 22, 2018
    Date of Patent: May 5, 2020
    Assignee: nanoSUR LLC
    Inventors: Juan P. Arhancet, Sreevishnu Cheerla, Graciela B. Arhancet, David B. Rozema
  • Massive parallel method for decoding DNA and RNA
    Patent number: 10633700
    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: April 28, 2020
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Zengmin Li, John Robert Edwards, Yasuhiro Itagaki
  • Pharmaceutical targeting of a mammalian cyclic di-nucleotide signaling pathway
    Patent number: 10633411
    Abstract: Cyclic-GMP-AMP synthase (cGAS) and cyclic-GMP-AMP (cGAMP), including 2?3-cGAMP, 2?2-cGAMP, 3?2?-cGAMP and 3?3?-GAMP, are used in pharmaceutical formulations (including vaccine adjuvants), drug screens, therapies, and diagnostics.
    Type: Grant
    Filed: November 18, 2019
    Date of Patent: April 28, 2020
    Assignee: THE BOARD OF REGENTS OF THE UNIVERSITY OF TEXAS SYSTEM
    Inventors: Zhijian Chen, Lijun Sun, Jiaxi Wu, Heping Shi, Chuo Chen
  • Methods and compositions of non-enzymatic amplification and direct detection of nucleic acids
    Patent number: 10626447
    Abstract: The detection and quantification of nucleic acid sequences can be done using template catalyzed TARA transfer reactions without enzyme and PCR. It comes with the novel chemistry platform technology using Template Assisted Rapid Assay (TARA), an enzyme-free, PCR-less and rapid transfer reaction assay directly from samples from nasopharyngeal swab, nasal aspirate, oropharyngeal swab or blood. The procedures of the detection and quantification of nucleic acid sequences include utilizing two or more oligonucleotide probes that reversibly bind a target nucleic acid in close proximity to each other and possess complementary reactive TARA reaction moieties. In addition, various methods, reagents, and kits for detecting and quantifying nucleic acid sequences and for determining the sequence of nucleic acids are provided.
    Type: Grant
    Filed: March 11, 2016
    Date of Patent: April 21, 2020
    Assignee: CROSSLIFE TECHNOLOGIES INC.
    Inventors: HyunDae Cho, Chang Hee Kim
  • Method for the site-specific enzymatic labelling of nucleic acids in vitro by incorporation of unnatural nucleotides
    Patent number: 10626138
    Abstract: Provided herein are analogs of unnatural nucleotides bearing predominantly hydrophobic nucleobase analogs that form unnatural base pairs during DNA polymerase-mediated replication of DNA or RNA polymerase-mediated transcription of RNA. In this manner, the unnatural nucleobases can be introduced in a site-specific way into oligonucleotides (single or double stranded DNA or RNA), where they can provide for site-specific cleavage, or can provide a reactive linker than can undergo functionalization with a cargo-bearing reagent by means of reaction with a primary amino group or by means of click chemistry with an alkyne group of the unnatural nucleobase linker.
    Type: Grant
    Filed: August 8, 2014
    Date of Patent: April 21, 2020
    Assignees: THE SCRIPPS RESEARCH INSTITUTE NATIONAL INSTITUTES OF HEALTH (NIH), U.S. DEPT OF HEALTH AND HUMAN SERVICES (DHHS), U.S. GOVERNMENT NIH DIVISION OF EXTRAMURAL INVENTIONS AND TECHNOLOGY RESOURCES (DEITR)
    Inventors: Floyd E. Romesberg, Denis A. Malyshev, Lingjun Li, Thomas Lavergne, Zhengtao Li
  • Quantitative assessment for cap efficiency of messenger RNA
    Patent number: 10626439
    Abstract: The present invention provides, among other things, methods of quantitating mRNA capping efficiency, particularly mRNA synthesized in vitro. In some embodiments, methods according to the present invention comprise providing an mRNA sample containing capped and uncapped mRNA, providing a cap specific binding substance under conditions that permit the formation of a complex between the cap specific binding substance and the capped mRNA, and quantitatively determining the amount of the complex as compared to a control, thereby quantifying mRNA capping efficiency.
    Type: Grant
    Filed: March 14, 2014
    Date of Patent: April 21, 2020
    Assignee: Translate Bio, Inc.
    Inventors: Michael Heartlein, Frank DeRosa, Anusha Dias
  • Multisignal reagents for labeling analytes
    Patent number: 10627397
    Abstract: Provided is a composition comprising an analyte bound covalently or through a first binding pair to a polymer. In this composition, the analyte is less than about 2000 MW; the polymer further comprises more than one signal or first member of a second binding pair; and the analyte is not a member of the first binding pair or the second binding pair. Also provided is an assay for an analyte. The assay comprises: combining a sample suspected of containing the analyte with the above-described composition and a binding agent that binds to the analyte; and detecting the signal or the first member of the second binding pair that is bound to the binding agent. In this assay, the amount of the signal or the first member of the second binding pair bound to the binding agent is inversely proportional to the analyte in the sample.
    Type: Grant
    Filed: April 9, 2019
    Date of Patent: April 21, 2020
    Assignee: Enzo Life Sciences, Inc.
    Inventors: Jack Coleman, Maciej Szczepanik, Richard Jin
  • Nucleic acid amplification and library preparation
    Patent number: 10619199
    Abstract: Processes and kits for preparing a plurality of amplification products with reduced non-specific amplification artifacts.
    Type: Grant
    Filed: March 4, 2016
    Date of Patent: April 14, 2020
    Assignee: Sigma-Aldrich Co. LLC
    Inventors: Timothy Seebeck, Fuqiang Chen, Brian W Ward
  • Isolation of cell-free nucleic acids from bodily fluid samples using solid chaotropic agents
    Patent number: 10619152
    Abstract: Disclosed is a process for isolating cell-free nucleic acid (including both DNA and RNA) or an analog thereof from a bodily fluid, and which entails: a) mixing in a container the bodily fluid, a chaotropic agent in solid form, a detergent and a buffer, and a solid phase which includes magnetic particles, thus forming a reaction mixture containing the cell-free nucleic acid; b) magnetically separating the solid phase having the cell-free nucleic acid bound thereto from the reaction mixture; and optionally c) dissociating the nucleic acid from the solid phase. Compositions and kits are also disclosed.
    Type: Grant
    Filed: February 10, 2015
    Date of Patent: April 14, 2020
    Inventor: Nancy Quan
  • Composition for reducing inhibition of nucleic acid amplification
    Patent number: 10619189
    Abstract: A composition for reducing the inhibitory effects of contaminants on nucleic acid amplification is provided. The composition includes a plurality of zirconium oxide particles, a non-ionic surfactant, and an organic iron-chelating reagent. The organic iron-chelating reagent has a first affinity constant greater than or equal to 104.2 with respect to ferric iron and a second affinity constant less than 103.8 with respect to magnesium, wherein the first affinity constant and the second affinity constant are determined in deionized water at pH 8.45 and 20° C. Optionally, the composition includes polyvinylpyrrolidone. Optionally, the composition comprises water. The composition has a pH of about 8.45 to 8.85. Methods of using the composition to prepare a sample for nucleic acid amplification are also provided.
    Type: Grant
    Filed: May 9, 2016
    Date of Patent: April 14, 2020
    Assignee: 3M Innovative Properties Company
    Inventors: Gregory W. Sitton, Wensheng Xia, Tonya D. Bonilla
  • Molecule detection using boronic acid substituted probes
    Patent number: 10597702
    Abstract: Provided are polymeric scaffold compositions and methods for detecting or quantitating diols such as carbohydrates or carbohydrate containing molecules (e.g., glycosylated protein). Provided herein are capture probes configured to bind to a scaffold. Also provided herein are capture probes linked to one or more reactive organoboronic moiety for binding diol-containing compounds in a solution. Methods of detecting complexes comprising diol-containing compounds for detecting or quantifying the presence of diol-containing compounds in solution using a nanopore device are also provided herein.
    Type: Grant
    Filed: August 26, 2014
    Date of Patent: March 24, 2020
    Assignee: Ontera Inc.
    Inventor: Trevor J. Morin
  • Reversible metal ion chelators
    Patent number: 10590162
    Abstract: Provided herein are chelator constructs (e.g., nucleic acid, peptide, peptide nucleic acid, etc.) that sequester metal ions (e.g., Mg2+) under a first set of conditions and fail to sequester or release sequestered metal ions under a second set of conditions. In particular, nucleic acid constructs are provided that sequester metal ions (e.g., Mg2+) under conditions that favor secondary and tertiary structure formation and release or fail to sequester metal ions under conditions that disfavor the formation of such structures.
    Type: Grant
    Filed: July 2, 2015
    Date of Patent: March 17, 2020
    Assignee: PROMEGA CORPORATION
    Inventors: Thomas Kirkland, Mark McDougall, Poncho Meisenheimer, Min Zhou
  • Method and composition for biomolecule stabilization
    Patent number: 10590408
    Abstract: The present invention relates to biomolecule stabilization to provide biomolecules, such as sensitive polymerases, in a convenient ready-to-go format. The invention provides a method and composition in which non-ionic surfactant or detergents of the polyoxyethylene cetyl ether family are used, preferably a Brij reagent or a combination of Brij reagents.
    Type: Grant
    Filed: February 10, 2017
    Date of Patent: March 17, 2020
    Assignee: GE Healthcare UK Limited
    Inventors: Peter James Tatnell, Elizabeth Mary Ashman