Patents Examined by Jezia Riley
  • RIG-I ligands and methods for producing them
    Patent number: 11142763
    Abstract: The present invention relates to new triphosphate-modified oligonucleotides which may act as RIG-I ligands as well as a new method allowing the synthesis and purification in high yield and purity suitable for pharmaceutical applications.
    Type: Grant
    Filed: May 2, 2018
    Date of Patent: October 12, 2021
    Assignee: RHEINISCHE FRIEDRICH-WILHELMS-UNIVERSITÄT BONN
    Inventors: Marion Goldeck, Jasper Van Den Boorn, János Ludwig, Christine Schuberth-Wagner
  • Self-assembled structures composed of monomers of peptide nucleic acid and tunable photonic crystals made therefrom
    Patent number: 11124543
    Abstract: Ordered structures composed of a plurality of self-assembled peptide nucleic acid (PNA) monomers, and processes of generating same are provided. The plurality of PNA monomers includes modified PNA monomers which are N-protected PNA monomers and/or which feature at least one aromatic moiety attached to a backbone, a nucleobase and/or a nucleobase linkage unit of the PNA monomer. Tunable photonic crystals formed of the provided ordered structures, uses thereof and articles-of-manufacturing containing same are also provided.
    Type: Grant
    Filed: October 19, 2016
    Date of Patent: September 21, 2021
    Assignee: Ramot at Tel-Aviv University Ltd.
    Inventors: Or Berger, Lihi Adler-Abramovich, Ehud Gazit
  • Methods for synthesizing nucleotide analogues with disulfide linkers
    Patent number: 11117921
    Abstract: The present invention provides methods, compositions, mixtures and kits utilizing deoxynucleoside triphosphates comprising a 3?-O position capped by a group comprising methylenedisulfide as a cleavable protecting group and a detectable label reversibly connected to the nucleobase of said deoxynucleoside. Such compounds provide new possibilities for future sequencing technologies, including but not limited to Sequencing by Synthesis.
    Type: Grant
    Filed: May 28, 2019
    Date of Patent: September 14, 2021
    Assignee: IsoPlexis Corporation
    Inventors: Mong Sano Marma, Jerzy Olejnik, Ilia Korboukh
  • Emulsion compositions and methods of their use
    Patent number: 11118217
    Abstract: Emulsion compositions are provided herein. Also provided herein are kits containing one or more emulsion compositions or components for making such emulsion compositions. Also provided herein are methods of using such emulsion compositions, such as for amplification of target nucleic acids in emulsion droplets.
    Type: Grant
    Filed: January 29, 2018
    Date of Patent: September 14, 2021
    Assignee: Bio-Rad Laboratories, Inc.
    Inventors: Yi Xue, Joshua Ritchey, Robert Meltzer
  • Chemically-enhanced primer compositions, methods and kits
    Patent number: 11104944
    Abstract: A chemically-enhanced primer is provided comprising a negatively charged moiety (NCM), an oligonucleotide sequence having a) non-nuclease resistant inter-nucleotide linkages or b) at least one nuclease resistance inter-nucleotide linkage. The chemically-enhanced primer can be used for sequencing and fragment analysis. Methods for synthesizing the chemically-enhanced primer as well as a method of preparing DNA for sequencing, a method of sequencing DNA, and kits containing the chemically-enhanced primer are also provided. The method of sequencing DNA can comprise contacting amplification reaction products with the composition wherein excess amplification primer is degraded by the nuclease and the chemically-enhanced primer is essentially non-degraded.
    Type: Grant
    Filed: January 14, 2019
    Date of Patent: August 31, 2021
    Assignee: LIFE TECHNOLOGIES CORPORATION
    Inventors: Linda Lee, Sam Woo, Peter Ma
  • Phosphorous protecting groups and methods of preparation and use thereof
    Patent number: 11104699
    Abstract: Aspects of the present disclosure include compositions that make use of phosphorus and/or nucleobase protecting groups which find use in the synthesis of long polynucleotides. Phosphorus protecting groups are provided that help increase the stepwise coupling yield and/or phosphorous protecting groups that can be removed during the oxidation step. Amidine nucleobase protecting groups are provided that find use in the subject compositions and methods which provides for e.g., increased resistance to depurination during polynucleotide synthesis. In some instances, the methods and compositions disclosed herein utilize a combination of the phosphorus and amidine nucleobase protecting groups in the synthesis of polynucleotides having a sequence of 200 or more monomeric units in length. Also provided are methods for synthesizing a polynucleotide (e.g., a DNA) using one or more compounds disclosed herein.
    Type: Grant
    Filed: October 29, 2018
    Date of Patent: August 31, 2021
    Assignees: Agilent Technologies, Inc., University of Colorado Boulder
    Inventors: Douglas J. Dellinger, Luca Monfregola, Marvin Caruthers, Mithun Roy
  • Quantitative assessment for cap efficiency of messenger RNA
    Patent number: 11104934
    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: January 16, 2020
    Date of Patent: August 31, 2021
    Assignee: Translate Bio, Inc.
    Inventors: Michael Heartlein, Frank DeRosa, Anusha Dias
  • Methods for generating stabilized lyophilized materials
    Patent number: 11098344
    Abstract: Lyophilized biological reagents, such as enzymes (e.g., PCR reagents) and antibodies, are provided that include a wax component. Thus, in some aspects, a method is provided for storing a biological reagent comprising formulating the reagent into a lyophilized composition including a wax component. Methods for using such lyophilized reagents are likewise provided.
    Type: Grant
    Filed: November 1, 2018
    Date of Patent: August 24, 2021
    Assignee: LUMINEX CORPORATION
    Inventors: Scott Johnson, Jen Dillman
  • Four-color DNA sequencing by synthesis using cleavable fluorescent nucleotide reversible terminators
    Patent number: 11098353
    Abstract: This invention provides a process for sequencing single-stranded DNA employing modified nucleotides.
    Type: Grant
    Filed: December 20, 2019
    Date of Patent: August 24, 2021
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Dae Hyun Kim, Lanrong Bi, Qinglin Meng, Xiaoxu Li
  • Time lapse sequencing: a convertible-nucleoside approach to enrichment-free analysis of RNA dynamics
    Patent number: 11098342
    Abstract: The invention provides methods and compositions for generating mutations in new nucleic acid molecules through incorporation of a transformable nucleoside into the nucleic acid and subsequent transformation of the nucleoside through oxidative-nucleophilic-aromatic-substitution chemistry, referred to as TimeLapse chemistry. The invention further provides methods for detecting the mutations, referred to as TimeLapse-seq.
    Type: Grant
    Filed: March 30, 2018
    Date of Patent: August 24, 2021
    Assignee: Yale University
    Inventors: Matthew Simon, Jeremy Schofield
  • Modified nucleosides, analogs thereof and oligomeric compounds prepared therefrom
    Patent number: 11084844
    Abstract: The present invention provides modified nucleosides, analogs thereof and oligomeric compounds prepared therefrom. More particularly, the present invention provides modified nucleosides and analogs thereof that are useful for incorporation at the terminus of an oligomeric compound. Such oligomeric compounds can also be included in a double stranded composition. In some embodiments, the oligomeric compounds provided herein are expected to hybridize to a portion of a target RNA resulting in loss of normal function of the target RNA.
    Type: Grant
    Filed: August 30, 2018
    Date of Patent: August 10, 2021
    Assignee: Ionis Pharmaceuticals, inc.
    Inventors: Thazha P. Prakash, Punit P. Seth, Eric E. Swayze
  • Synthesis of novel disulfide linker based nucleotides as reversible terminators for DNA sequencing by synthesis
    Patent number: 11085076
    Abstract: Disclosed herein, inter alia, are compounds, compositions, and methods of use thereof in the sequencing of a nucleic acid.
    Type: Grant
    Filed: September 28, 2016
    Date of Patent: August 10, 2021
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Xiaoxu Li, Xin Chen, Zengmin Li, Shiv Kumar, Shundi Shi, Cheng Guo, Jianyi Ren, Min-Kang Hsieh, Minchen Chien, Chuanjuan Tao, Ece Erturk, Sergey Kalachikov, James J. Russo
  • Thiol compounds and the use thereof for the synthesis of modified oligonucleotides
    Patent number: 11078229
    Abstract: The present invention relates to a thiol compound suitable for forming a chain of oligomers that can be grafted to an oligonucleotide. The invention also relates to an oligonucleotide grafted by such a compound, thus having one or more thiol functions, suitable for being immobilized on a gold surface or on a grafted surface.
    Type: Grant
    Filed: January 4, 2018
    Date of Patent: August 3, 2021
    Assignees: CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE, ETABLISSEMENT FRANCAIS DU SANG
    Inventors: François Morvan, Albert Meyer, Jean-Jacques Vasseur, Julie Mayen, Carole Chaix, Carole Farre, Chantal Fournier-Wirth, Jean-François Cantaloube, Myriam Lereau
  • Photocleavable nucleotide reagents with high stability
    Patent number: 11078534
    Abstract: The present invention provides for stable nucleotide reagents used for nucleic acid amplification by PCR and RT-PCR (Reverse Transcriptase-PCR) that comprises modified nucleoside triphosphates. The present invention also provides for methods for using the modified nucleoside triphosphates for detecting the presence or absence of a target nucleic acid sequence in a sample in an amplification reaction.
    Type: Grant
    Filed: November 26, 2018
    Date of Patent: August 3, 2021
    Assignee: Roche Molecular Systems, Inc.
    Inventors: Alexander Nierth, Hannes Kuchelmeister, Concordio Anacleto, Amar Gupta, Dieter Heindl, Igor Kozlov, Christian Wellner, Stephen Gordon Will
  • Multisignal reagents for labeling analytes
    Patent number: 11073512
    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. Additionally provided is a multisignal labeling reagent comprising a first polymer covalently bound to (a) a reactive group or a first member of a first binding pair, and (b) more than one digoxigenin molecule.
    Type: Grant
    Filed: November 28, 2018
    Date of Patent: July 27, 2021
    Assignee: Enzo Life Sciences, Inc.
    Inventors: Jack Coleman, Maciej Szczepanik, Richard Jin
  • High performance fluorescence imaging module for genomic testing assay
    Patent number: 11053540
    Abstract: Fluorescence imaging system designs are described that provide larger fields-of-view, increased spatial resolution, improved modulation transfer and image quality, higher spatial sampling frequency, faster transitions between image capture when repositioning the sample plane to capture a series of images (e.g., of different fields-of-view), and improved imaging system duty cycle, and thus enable higher throughput image acquisition and analysis for genomics and other imaging applications.
    Type: Grant
    Filed: September 9, 2020
    Date of Patent: July 6, 2021
    Assignee: ELEMENT BIOSCIENCES, INC.
    Inventors: Steve Xiangling Chen, Minghao Guo, Michael Previte, Chunhong Zhou, Derek Fuller
  • Ruthenium-based photolinkers and methods of use
    Patent number: 11046721
    Abstract: The present invention provides ruthenium-based photolinker compounds, caged molecules comprising the ruthenium-based photolinker compounds, and methods of use. In certain aspects, the compositions disclosed herein comprise an active domain conjugated to a ruthenium-based photolinker, such that irradiation of the photolinker exposes the active domain.
    Type: Grant
    Filed: August 4, 2015
    Date of Patent: June 29, 2021
    Assignee: The Trustees of the University of Pennsylvania
    Inventors: Ivan J. Dmochowski, Julianne C. Griepenburg, Teresa L. Rapp
  • Methods and compositions for genomic target enrichment and selective DNA sequencing
    Patent number: 11046999
    Abstract: It has been established that one or more large double stranded DNA fragments (each 2,000 to 40,000 base pairs in size) can be captured and isolated from genomic DNA fragments using sequence specific PNA hybridization probes. Compositions and methods for enrichment of a multiplicity of long DNA sequences selected from the genome of any eukaryote are provided. Capture is performed using multiple PNA molecules with gamma-modified chiral backbones, comprising a mixture of neutral and positive chemical groups. Two or more PNA probes with covalently bound haptens, preferably biotin, target each DNA domain of interest for capture, isolation, and subsequent sequencing analysis of the multiplicity of enriched targets, including DNA methylation sequencing. The methods include enhancement of probe-DNA binding specificity through single strand binding proteins (SSB).
    Type: Grant
    Filed: September 16, 2016
    Date of Patent: June 29, 2021
    Assignee: PetaOmics, Inc.
    Inventors: Paul M. Lizardi, Brent W. Ferguson
  • Method for assessing juice/cider quality and/or safety
    Patent number: 11046994
    Abstract: A novel method for isolating DNA from juices and ciders is described. This method is low cost and yield large quantities of highly purified DNA even though one uses a small quantity of juice or cider. A method for determining if a juice or cider is safe to consume and/or the quality of the juice or cider are also described. For these methods, one can perform qPCR on the DNA which can be obtained using the disclosed method or any other prior art method, and comparing the amount of DNA from microorganisms is present in the juice and/or cider to determine the safety and/or quality of the juice and/or cider. These methods work even if the liquid was pasteurized.
    Type: Grant
    Filed: July 5, 2018
    Date of Patent: June 29, 2021
    Assignee: The United States of America, as represented by the Secretary of Agriculture
    Inventors: Wei Zhao, Elizabeth A Baldwin, Jinhe Bai, Anne Plotto
  • Nucleotide analogues
    Patent number: 11046726
    Abstract: The present invention provides methods, compositions, mixtures and kits utilizing deoxynucleoside triphosphates comprising a 3?-O position capped by a group comprising methylenedisulfide as a cleavable protecting group and a detectable label reversibly connected to the nucleobase of said deoxynucleoside. Such compounds provide new possibilities for future sequencing technologies, including but not limited to Sequencing by Synthesis.
    Type: Grant
    Filed: March 22, 2018
    Date of Patent: June 29, 2021
    Assignee: QIAGEN SCIENCES, LLC
    Inventors: Mong Sano Marma, Jerzy Olejnik, Ilia Korboukh