Patents by Inventor Danith H. Ly

Danith H. Ly 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).

  • Patent number: 11859242
    Abstract: Described herein are genetic recognition reagents comprising terminal aromatic moieties that bind specifically to a template nucleic acid and concatenate. Also provided are methods of using the genetic recognition reagents, e.g., to treat or diagnose a repeat expansion disorder, such as DMI.
    Type: Grant
    Filed: December 21, 2018
    Date of Patent: January 2, 2024
    Assignee: Carnegie Mellon University
    Inventors: Danith H. Ly, Wei-Che Hsieh, Raman Bahal
  • Patent number: 11713340
    Abstract: Described herein are novel divalent nucleobases that each bind two nucleic acid strands, matched or mismatched when incorporated into a nucleic acid or nucleic acid analog backbone (a genetic recognition reagent, or genetic recognition reagent). In one embodiment, the genetic recognition reagent is a peptide nucleic acid (PNA) or gamma PNA (?PNA) oligomer. Uses of the divalent nucleobases and monomers and genetic recognition reagents containing the divalent nucleobases also are provided.
    Type: Grant
    Filed: December 28, 2021
    Date of Patent: August 1, 2023
    Assignee: Carnegie Mellon University
    Inventors: Danith H. Ly, Suresh Kumar Gopalsamy, Arunava Manna
  • Publication number: 20230174985
    Abstract: The present disclosure relates to compounds useful for the detection or modulation of target nucleic acids, including DNA and RNA. The present disclosure further relates to methods for treatment of trinucleotide repeat disorders, which can include administration of oligonucleotide analogues that can bind pathogenic nucleotide repeats in DNA or RNA.
    Type: Application
    Filed: January 27, 2023
    Publication date: June 8, 2023
    Inventors: Danith H. LY, Shivaji A. THADKE, Ramesh U. BATWAL, Dietrich A. STEPHAN
  • Patent number: 11603369
    Abstract: Described herein are divalent nucleobases that each binds two nucleic acid strands, matched or mismatched when incorporated into a nucleic acid or nucleic acid analog backbone, such as in a ?-peptide nucleic acid (?PNA). Also provided are genetic recognition reagents comprising one or more of the divalent nucleobases and a nucleic acid or nucleic acid analog backbone, such as a ?PNA backbone. Uses for the divalent nucleobases and monomers and genetic recognition reagents containing the divalent nucleobases also are provided.
    Type: Grant
    Filed: September 26, 2017
    Date of Patent: March 14, 2023
    Assignee: Carnegie Mellon University
    Inventors: Danith H. Ly, Shivaji A. Thadke, Ali Nakhi, J. Dinithi Rashmini Perera
  • Patent number: 11603530
    Abstract: The present disclosure relates to compounds useful for the detection or modulation of target nucleic acids, including DNA and RNA. The present disclosure further relates to methods for treatment of trinucleotide repeat disorders, which can include administration of oligonucleotide analogues that can bind pathogenic nucleotide repeats in DNA or RNA.
    Type: Grant
    Filed: April 15, 2021
    Date of Patent: March 14, 2023
    Assignee: NEUBASE THERAPEUTICS, INC.
    Inventors: Danith H. Ly, Shivaji A. Thadke, Ramesh U. Batwal, Dietrich A. Stephan
  • Publication number: 20220324914
    Abstract: The present disclosure relates to compounds useful for the detection or modulation of target nucleic acids, including DNA and RNA. The present disclosure further relates to methods for treatment of trinucleotide repeat disorders, which can include administration of oligonucleotide analogues that can bind pathogenic nucleotide repeats in DNA or RNA.
    Type: Application
    Filed: April 15, 2021
    Publication date: October 13, 2022
    Inventors: Danith H. LY, Shivaji A. THADKE, Ramesh U. BATWAL, Valentina DI CARO, Dietrich A. STEPHAN, Letha J. SOOTER, Samuel I. BACKENROTH
  • Publication number: 20220259266
    Abstract: Described herein are novel divalent nucleobases that each bind two nucleic acid strands, matched or mismatched when incorporated into a nucleic acid or nucleic acid analog backbone (a genetic recognition reagent, or genetic recognition reagent). In one embodiment, the genetic recognition reagent is a peptide nucleic acid (PNA) or gamma PNA (?PNA) oligomer. Uses of the divalent nucleobases and monomers and genetic recognition reagents containing the divalent nucleobases also are provided.
    Type: Application
    Filed: December 28, 2021
    Publication date: August 18, 2022
    Inventors: Danith H. Ly, Suresh Kumar Gopalsamy, Arunava Manna
  • Patent number: 11319349
    Abstract: Described herein are recognition modules that bind specifically to a template nucleic acid and which ligate together in a reducing environment to produce a gamma peptide nucleic acid (?PNA) oligomer. Also provided are methods of synthesizing a ?PNA oligomer on a template using the recognition modules.
    Type: Grant
    Filed: January 17, 2019
    Date of Patent: May 3, 2022
    Assignee: Carnegie Mellon University
    Inventors: Danith H. Ly, Raman Bahal, Dinesh Chandra Bhunia, Yidan Cong, Arunava Manna, Srinivas Rapireddy
  • Publication number: 20220112238
    Abstract: The present disclosure relates to compounds useful for the detection or modulation of target nucleic acids, including DNA and RNA. The present disclosure further relates to methods for treatment of trinucleotide repeat disorders, which can include administration of oligonucleotide analogues that can bind pathogenic nucleotide repeats in DNA or RNA.
    Type: Application
    Filed: April 15, 2021
    Publication date: April 14, 2022
    Inventors: Danith H. LY, Shivaji A. THADKE, Ramesh U. BATWAL, Valentina DI CARO, Dietrich A. STEPHAN, Letha J. SOOTER, Samuel I. BACKENROTH
  • Patent number: 11279736
    Abstract: The present invention relates to ?-PNA monomers according to Formula I where substituent groups R1, R2, R3, R4, R5, R6, B and P are defined as set forth in the specification. The invention also provides methodology for synthesizing compounds according to Formula I and methodology for synthesizing PNA oligomers that incorporate one or more Formula I monomers.
    Type: Grant
    Filed: August 26, 2020
    Date of Patent: March 22, 2022
    Assignee: CARNEGIE MELLON UNIVERSITY
    Inventors: Danith H. Ly, Srinivas Rapireddy, Bichismita Sahu
  • Patent number: 11236130
    Abstract: Described herein are novel divalent nucleobases that each bind two nucleic acid strands, matched or mismatched when incorporated into a nucleic acid or nucleic acid analog backbone (a genetic recognition reagent, or genetic recognition reagent). In one embodiment, the genetic recognition reagent is a peptide nucleic acid (PNA) or gamma PNA (?PNA) oligomer. Uses of the divalent nucleobases and monomers and genetic recognition reagents containing the divalent nucleobases also are provided.
    Type: Grant
    Filed: June 19, 2019
    Date of Patent: February 1, 2022
    Assignee: Carnegie Mellon University
    Inventors: Danith H. Ly, Suresh Kumar Gopalsamy, Arunava Manna
  • Publication number: 20210324012
    Abstract: The present disclosure relates to compounds useful for the detection or modulation of target nucleic acids, including DNA and RNA. The present disclosure further relates to methods for treatment of trinucleotide repeat disorders, which can include administration of oligonucleotide analogues that can bind pathogenic nucleotide repeats in DNA or RNA.
    Type: Application
    Filed: April 15, 2021
    Publication date: October 21, 2021
    Inventors: Danith H. LY, Shivaji A. THADKE, Ramesh U. BATWAL, Valentina DI CARO, Dietrich A. STEPHAN, Letha J. SOOTER, Samuel I. BACKENROTH
  • Publication number: 20210309997
    Abstract: The present disclosure relates to compounds useful for the detection or modulation of target nucleic acids, including DNA and RNA. The present disclosure further relates to methods for treatment of trinucleotide repeat disorders, which can include administration of oligonucleotide analogues that can bind pathogenic nucleotide repeats in DNA or RNA.
    Type: Application
    Filed: March 30, 2021
    Publication date: October 7, 2021
    Inventors: Danith H. LY, Shivaji A. THADKE, Ramesh U. BATWAL, Valentina DI CARO, Dietrich A. STEPHAN, Letha J. SOOTER, Samuel I. BACKENROTH
  • Publication number: 20210309700
    Abstract: The present disclosure relates to compounds useful for the detection or modulation of target nucleic acids, including DNA and RNA. The present disclosure further relates to methods for treatment of trinucleotide repeat disorders, which can include administration of oligonucleotide analogues that can bind pathogenic nucleotide repeats in DNA or RNA.
    Type: Application
    Filed: April 15, 2021
    Publication date: October 7, 2021
    Inventors: Danith H. LY, Shivaji A. THADKE, Ramesh U. BATWAL, Valentina DI CARO, Dietrich A. STEPHAN, Letha J. SOOTER, Samuel I. BACKENROTH
  • Patent number: 11136597
    Abstract: Compositions and methods for enhancing targeted gene editing and methods of use thereof are disclosed. In the most preferred embodiments, gene editing is carried out utilizing a gene editing composition such as triplex-forming oligonucleotides, CRISPR, zinc finger nucleases, TALENS, or others, in combination with a gene modification potentiating agent such as stem cell factor (SCF), a CHK1 or ATR inhibitor, or a combination thereof. A particular preferred gene editing composition is triplex-forming peptide nucleic acids (PNAs) substituted at the ? position for increased DNA binding affinity. Nanoparticle compositions for intracellular delivery of the gene editing composition are also provided and particular advantageous for use with in vivo applications.
    Type: Grant
    Filed: February 16, 2017
    Date of Patent: October 5, 2021
    Assignees: Yale University, Carnegie Mellon University
    Inventors: W. Mark Saltzman, Peter Glazer, Raman Bahal, Nicole Ali McNeer, Danith H. Ly, Elias Quijano
  • Publication number: 20210230680
    Abstract: Described herein are divalent nucleobases that each binds two nucleic acid strands, matched or mismatched when incorporated into a nucleic acid or nucleic acid analog backbone, such as in a ?-peptide nucleic acid (?PNA). Also provided are genetic recognition reagents comprising one or more of the divalent nucleobases and a nucleic acid or nucleic acid analog backbone, such as a ?PNA backbone. Uses for the divalent nucleobases and monomers and genetic recognition reagents containing the divalent nucleobases also are provided.
    Type: Application
    Filed: June 7, 2019
    Publication date: July 29, 2021
    Inventors: Danith H. Ly, Shivaji A. Thadke, Ashif Y. Shaikh, Wei-Che Hsieh, Ali Nakhi, J. Dinithi Perera
  • Publication number: 20210214397
    Abstract: The present invention relates to ?-PNA monomers according to Formula I where substituent groups R1, R2, R3, R4, R5, R6, B and P are defined as set forth in the specification. The invention also provides methodology for synthesizing compounds according to Formula I and methodology for synthesizing PNA oligomers that incorporate one or more Formula I monomers.
    Type: Application
    Filed: August 26, 2020
    Publication date: July 15, 2021
    Applicant: CARNEGIE MELLON UNIVERSITY
    Inventors: Danith H. LY, Srinivas RAPIREDDY, Bichismita SAHU
  • Patent number: 10851407
    Abstract: A method of making optically pure preparations of chiral ?PNA (gamma peptide nucleic acid) monomers is provided. Nano structures comprising chiral ?PNA structures also are provided. Methods of amplifying and detecting specific nucleic acids, including in situ methods are provided as well as compositions and kits useful in those methods. Lastly, methods of converting nucleobase sequences from right-handed helical PNA, nucleic acid and nucleic acid analog structures to left-handed ?PNA, and vice-versa, are provided.
    Type: Grant
    Filed: May 8, 2015
    Date of Patent: December 1, 2020
    Assignee: Carnegie Mellon University
    Inventors: Danith H. Ly, Wei-Che Hsieh, Iulia Sacui, Arunava Manna
  • Publication number: 20200340044
    Abstract: Described herein are genetic recognition reagents comprising terminal aromatic moieties that bind specifically to a template nucleic acid and concatenate. Also provided are methods of using the genetic recognition reagents, e.g., to treat or diagnose a repeat expansion disorder, such as DMI.
    Type: Application
    Filed: December 21, 2018
    Publication date: October 29, 2020
    Inventors: Danith H. Ly, Wei-Che Hsieh, Raman Bahal
  • Publication number: 20200318195
    Abstract: Genetic recognition reagents comprising bivalent nucleobases are provided that bind two strands of nucleic acid, such as an expanded repeat sequence associated with an expanded repeat disease. In one example the expanded repeat disease is a polyQ disease, such as Huntington's disease. Methods of use of the reagents are provided, including a method of binding nucleic acid, such as an expanded repeat sequence associated with an expanded repeat disease, a method of identifying the presence of a nucleic acid comprising an expanded repeat, and a method of treating an expanded repeat disease are provided.
    Type: Application
    Filed: December 21, 2018
    Publication date: October 8, 2020
    Inventors: Danith H. Ly, Shivaji A. Thadke, J. Dinithi Rashmini Perera