Patents Examined by Jezia Riley
  • Patent number: 11453646
    Abstract: The present invention relates to novel nucleic acid molecules, called aptamers, that bind specifically to a small molecule fluorophore and thereby enhance the fluorescence signal of the fluorophore upon exposure to radiation of suitable wavelength. Molecular complexes formed between the novel fluorophores, novel nucleic acid molecules, and their target molecules are described, and the use of multivalent aptamer constructs as fluorescent sensors for target molecules of interest are also described.
    Type: Grant
    Filed: July 27, 2012
    Date of Patent: September 27, 2022
    Assignee: CORNELL UNIVERSITY
    Inventors: Samie R. Jaffrey, Jeremy Paige
  • Patent number: 11453783
    Abstract: Compounds useful as fluorescent or colored dyes are disclosed. The compounds have the following structure (I): or a stereoisomer, tautomer or salt thereof, wherein R1, R2, R3, R4, R5, L1, L2, L3, L4, M1, M2, m and n are as defined herein. Methods associated with preparation and use of such compounds is also provided.
    Type: Grant
    Filed: May 18, 2021
    Date of Patent: September 27, 2022
    Assignee: Sony Corporation
    Inventors: Tracy Matray, Sharat Singh
  • Patent number: 11447519
    Abstract: Herein reported are new tricyclic cytidine compounds, such as 8-diethylamino-tC (8-DEA-tC), that respond to DNA and/or RNA duplex formation with up to a 20-fold increase in fluorescent quantum yield as compared with the free nucleoside, depending on neighboring bases. This turn-on response to duplex formation is by far the greatest of any reported nucleoside analogue that can participate in Watson-Crick base pairing. Measurements of the quantum yield of 8-DEA-tC mispaired with adenosine and, separately, opposite an abasic site show that there is almost no fluorescence increase without the formation of correct Watson-Crick hydrogen bonds. Kinetic isotope effects from the use of deuterated buffer show that the duplex protects 8-DEA-tC against quenching by excited state proton transfer. DFT calculations provide a rationale for the observed photophysical properties that is dependent on duplex integrity and the electronic structure of the analogue.
    Type: Grant
    Filed: November 9, 2017
    Date of Patent: September 20, 2022
    Assignee: San Diego State University Research Foundation
    Inventors: Byron W. Purse, Dillon Burns, Kristine Teppang, Raymond Lee, Melissa Lokensgard
  • Patent number: 11441144
    Abstract: Aspects of the disclosure include methods for the preparation of a polynucleotide. In some embodiments, the method includes contacting a first polynucleotide composition including: a polynucleotide having a sequence of 7 or more nucleoside subunits and at least two of the nucleoside subunits are joined by a N3??P5? thiophosphoramidate inter-subunit linkage; and non-target synthetic products and reagents; with a multivalent cation salt to precipitate a polynucleotide salt including at least one multivalent cation counterion; and separating the polynucleotide salt from the contacted first polynucleotide composition to produce a second polynucleotide composition including the polynucleotide salt. In certain embodiments, the method further includes contacting the polynucleotide salt with a reverse phase chromatography support; and eluting from the chromatography support a third polynucleotide composition including the polynucleotide.
    Type: Grant
    Filed: July 10, 2020
    Date of Patent: September 13, 2022
    Assignee: Geron Corporation
    Inventor: Premchandran H. Ramiya
  • Patent number: 11434520
    Abstract: Aprotic-protic ionic salt (APS) compositions and methods of using aprotic-protic ionic salt compositions to stabilize nucleic acids at ambient temperatures are provided. Certain aspects provide aprotic-protic ionic salt compositions for long term storage of nucleic acids at ambient temperature in the presence of aqueous solvents.
    Type: Grant
    Filed: July 23, 2019
    Date of Patent: September 6, 2022
    Assignee: Florida Gulf Coast University Board of Trustees
    Inventor: Arsalan Mirjafari
  • Patent number: 11427859
    Abstract: Provided for herein is a method for detecting the presence of a nucleic acid target molecule in a biological sample. In certain aspects, the method comprises contacting a test sample that comprises (i) a biological sample comprising a nucleic acid target molecule and (ii) an osmylated single-stranded oligonucleotide probe comprising at least one pyrimidine residue covalently bonded to a substituted or unsubstituted Osmium tetroxide (OsO4)-2,2?-bypyridine group (OsBp group).
    Type: Grant
    Filed: September 3, 2021
    Date of Patent: August 30, 2022
    Inventor: Anastassia Kanavarioti
  • Patent number: 11421271
    Abstract: Embodiments of the present disclosure relate to nucleotides labeled with photoswitchable compounds. Also provided herein are methods and kits of using these labeled nucleotides for sequencing applications.
    Type: Grant
    Filed: March 26, 2020
    Date of Patent: August 23, 2022
    Assignee: Illumina Cambridge Limited
    Inventors: Wayne N. George, Andrew A. Brown
  • Patent number: 11421217
    Abstract: Provided herein are compositions and methods of use thereof for collection, preservation and/or extraction of biologicals from a subject. For example, a solution that enables collection, preservation, and extraction of nucleic acids in a single step, and methods of using such solution are provided. In some embodiments, the compositions, kits, and methods are useful for the collection and analysis of samples from patients that have or are suspected of having SARS-CoV-2 virus that can cause Covid-19.
    Type: Grant
    Filed: April 7, 2021
    Date of Patent: August 23, 2022
    Inventors: Vincent T. Bicocca, Trevor Gilpin Levin
  • Patent number: 11390754
    Abstract: Compositions comprising a polymeric dye and a cyclodextrin are provided. Methods associated with preparation and use of such compounds, for example in methods for detection of any analyte molecule, are also provided.
    Type: Grant
    Filed: May 10, 2017
    Date of Patent: July 19, 2022
    Assignee: Sony Corporation
    Inventors: Sharat Singh, Tracy Matray
  • Patent number: 11390619
    Abstract: The present application relates to secondary amine-substituted coumarin compounds and their uses as fluorescent labels. The compounds may be used as fluorescent labels for nucleotides in nucleic acid sequencing applications.
    Type: Grant
    Filed: October 16, 2018
    Date of Patent: July 19, 2022
    Assignee: Illumina Cambridge Limited
    Inventors: Nikolai Nikolaevich Romanov, Patrick McCauley, Carole Anastasi, Xiaolin Wu, Niall Hynes
  • Patent number: 11390753
    Abstract: The present application relates to exocyclic amine-substituted coumarin derivatives and their uses as fluorescent labels. These compounds may be used as fluorescent labels for nucleotides in nucleic acid sequencing applications.
    Type: Grant
    Filed: February 28, 2020
    Date of Patent: July 19, 2022
    Assignee: Illumina Cambridge Limited
    Inventors: Nikolai Nikolaevich Romanov, Carole Anastasi, Patrick McCauley
  • Patent number: 11390643
    Abstract: The present invention relates to a modified oligonucleotide having two or more thiol functions, which can be immobilized on a gold surface or on a grafted surface, in particular a surface comprising at least one carbon-carbon double bond or carbon-carbon triple bond or haloacetamide functions, preferably maleimide or acrylamide functions. The invention also relates to a method for detecting a nucleic acid in a biological sample comprising a step of detecting hybridization between a modified oligonucleotide and a target nucleic acid amplified from the biological sample. The invention relates more particularly to a method for detecting, genotyping or sequencing a pathogenic organism, preferably a virus.
    Type: Grant
    Filed: February 8, 2019
    Date of Patent: July 19, 2022
    Assignees: ETABLISSEMENT FRANÇAIS DU SANG, CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE (CNRS), UNIVERSITE DE MONTPELLIER, UNIVERSITE CLAUDE BERNARD LYON 1
    Inventors: Chantal Fournier-Wirth, Myriam Lereau, Jean-François Cantaloube, Jean-Jacques Vasseur, François Morvan, Albert Meyer, Julie Mayen, Carole Chaix, Carole Farre
  • Patent number: 11384377
    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: April 6, 2020
    Date of Patent: July 12, 2022
    Assignee: Molecular Assemblies, Inc.
    Inventors: J. William Efcavitch, Kim Albizati, Natasha Paul, Sanjay Agarwalla
  • Patent number: 11384391
    Abstract: This invention provides nucleotide analogues each of which comprises a tag comprising one or more Forster resonance energy transfer (FRET) acceptor fluorophores, a nucleotide polymerase having one or more FRET donor fluorophores, and methods for sequencing single-stranded.
    Type: Grant
    Filed: April 4, 2017
    Date of Patent: July 12, 2022
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Shiv Kumar, James J. Russo, Steffen Jockusch, Zengmin Li, Xiaoxu Li, Sergey M. Kalachikov, Irina Morozova
  • Patent number: 11377680
    Abstract: The present disclosure provides labeling reagents for labeling substrates such as nucleotides, proteins, antibodies, lipids, and cells. The labeling reagents provided herein may comprise fluorescent labels and semi-rigid linkers. Methods for nucleic acid sequencing using materials comprising such labeling reagents are also provided here.
    Type: Grant
    Filed: August 5, 2021
    Date of Patent: July 5, 2022
    Assignee: Ultima Genomics, Inc.
    Inventors: Linda G. Lee, Gilad Almogy, Steven Menchen
  • Patent number: 11365443
    Abstract: This disclosure relates to the use of one or more proteins (e.g., globular proteins) having a low isoelectric point and/or a limited number (e.g., zero) of modifying groups in nucleic acid polymerization and/or amplification reactions such as polymerase chain reaction (PCR).
    Type: Grant
    Filed: December 6, 2018
    Date of Patent: June 21, 2022
    Assignee: Life Technologies Corporation
    Inventors: Jonathan Wang, David Dupont
  • Patent number: 11365445
    Abstract: Provided herein are methods for sequencing both strands of a double stranded nucleic acid fragment that improves fidelity and accuracy of a sequence determination compared to traditional next generation sequencing methods. Compositions and kits for use in the methods are also provided.
    Type: Grant
    Filed: October 13, 2021
    Date of Patent: June 21, 2022
    Assignee: Singular Genomics Systems, Inc.
    Inventors: Eli N. Glezer, Martin Maria Fabani, Sabrina Shore, Daan Witters
  • Patent number: 11359235
    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: June 13, 2019
    Date of Patent: June 14, 2022
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Gene Shen, Stephen Yue, Lubomir Sebo, Louis Brogley
  • Patent number: 11359238
    Abstract: Provided herein are methods for sequencing both strands of a double stranded nucleic acid fragment that improves fidelity and accuracy of a sequence determination compared to traditional next generation sequencing methods. Compositions and kits for use in the methods are also provided.
    Type: Grant
    Filed: March 5, 2021
    Date of Patent: June 14, 2022
    Inventors: Eli N. Glezer, Martin Maria Fabani, Sabrina Shore, Daan Witters
  • Patent number: 11359229
    Abstract: Provided herein are molecular verification (authentication) systems, methods and compositions that use molecular (DNA/RNA) circuitry to enable specific molecularly encrypted solutions.
    Type: Grant
    Filed: September 19, 2017
    Date of Patent: June 14, 2022
    Assignee: President and Fellows of Harvard College
    Inventors: Jongmin Kim, Jocelyn Yoshiko Kishi, Peng Yin, Steven Henry Strassmann, Thomas E. Schaus