Patents by Inventor Jingyue Ju

Jingyue Ju 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).

  • Chemically cleavable 3?-O-allyl-dNTP-allyl-fluorophore fluorescent nucleotide analogues and related methods
    Patent number: 9297042
    Abstract: This invention provides a nucleotide analog comprising (i) a base selected from the group consisting of adenine, guanine, cytosine, thymine and uracil, (ii) a deoxyribose, (iii) an allyl moiety bound to the 3?-oxygen of the deoxyribose and (iv) a fluorophore bound to the base via an allyl linker, and methods of nucleic acid sequencing employing the nucleotide analog.
    Type: Grant
    Filed: August 4, 2014
    Date of Patent: March 29, 2016
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Lanrong Bi, Dae Hyun Kim, Qinglin Meng
  • METHOD FOR DETECTING MULTIPLE PREDETERMINED COMPOUNDS IN A SAMPLE
    Publication number: 20160041179
    Abstract: This invention provides methods for detecting the presence of a plurality of predetermined compounds in a sample using a plurality of tag moieties and at least one nanopore. This invention also provides methods for determining the quantity of each of a plurality of predetermined compounds in a sample using a plurality of tag moieties and at least one nanopore. This invention further provides methods for detecting interaction of at least two predetermined compounds using at least one tag moiety and at least one nanopore.
    Type: Application
    Filed: March 14, 2014
    Publication date: February 11, 2016
    Applicant: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue JU, Shiv KUMAR, Chuanjuan TAO, Sergey KALACHIKOV, James J. Russo
  • Synthesis of four-color 3?-O-allyl modified photocleavable fluorescent nucleotides and related methods
    Patent number: 9255292
    Abstract: This invention provides a process for making 3?-O-allyl-dGTP-PC-Biodopy-FL-510, 3?-O-allyl-dATP-PC-ROX, 3?-O-allyl-dCTP-PC-Bodipy-650 and 3?-O-allyl-dUTP-PC-R6G, and related methods.
    Type: Grant
    Filed: July 19, 2011
    Date of Patent: February 9, 2016
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Qinglin Meng, Dae H. Kim, Lanrong Bi, Xiaopeng Bai, Nicholas J. Turro
  • Selective capture and release of analytes
    Patent number: 9250169
    Abstract: The described subject matter includes techniques and components for minimally invasive, selective capture and release of analytes. An aptamer is selected for its binding affinity with a particular analyte(s). The aptamer is functionalized on a solid phase, for example, microbeads, polymer monolith, microfabricated solid phase, etc. The analyte is allowed to bind to the aptamer, for example, in a microchamber. Once the analyte has been bound, a temperature control sets the temperature to an appropriate temperature at which the captured analyte is released.
    Type: Grant
    Filed: October 15, 2012
    Date of Patent: February 2, 2016
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Donald W. Landry, Qiao Lin, ThaiHuu Nguyen, Renjun Pei, Chunmei Oiu, Milan N. Stojanovic
  • RAMAN CLUSTER TAGGED MOLECULES FOR BIOLOGICAL IMAGING
    Publication number: 20160024570
    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: Application
    Filed: March 14, 2014
    Publication date: January 28, 2016
    Applicant: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue JU, Shiv KUMAR, Mirko PALLA, James J. RUSSO
  • DNA SEQUENCING WITH NON-FLUORESCENT NUCLEOTIDE REVERSIBLE TERMINATORS AND CLEAVABLE LABEL MODIFIED NUCLEOTIDE TERMINATORS
    Publication number: 20160024574
    Abstract: This invention provides a process for sequencing nucleic acids using 3? modified deoxynucleotide analogues or 3? modified deoxyinosine triphosphate analogues, and 3? modified dideoxynucleotide analogues having a detectable marker attached to a base thereof.
    Type: Application
    Filed: August 6, 2015
    Publication date: January 28, 2016
    Applicant: The Trustees of Columbia University in the City of New York
    Inventors: Jingyue Ju, Dae Hyun Kim, Jia Guo, Qinglin Meng, Zengmin Li, Huanyan Cao
  • CHEMICAL METHODS FOR PRODUCING TAGGED NUCLEOTIDES
    Publication number: 20150368710
    Abstract: This disclosure provides systems and methods for attaching nanopore-detectable tags to nucleotides. The disclosure also provides methods for sequencing nucleic acids using the disclosed tagged nucleotides.
    Type: Application
    Filed: March 23, 2015
    Publication date: December 24, 2015
    Applicants: The Trustees of Columbia University in the City of New York, Genia Technologies, Inc.
    Inventors: Carl W. Fuller, Shiv Kumar, Jingyue Ju, Randall Davis, Roger Chen
  • Synthesis of cleavable fluorescent nucleotides as reversible terminators for DNA sequencing by synthesis
    Patent number: 9175342
    Abstract: This invention provides novel azido linkers for deoxynucleotide analogues having a detectable marker attached thereto.
    Type: Grant
    Filed: July 25, 2013
    Date of Patent: November 3, 2015
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Huanyan Cao, Zengmin Li, Qinglin Meng, Jia Guo, Shenglong Zhang
  • Pyrosequencing methods and related compositions
    Patent number: 9169510
    Abstract: This invention provides methods for pyrosequencing and compositions comprising 3?-O— modified deoxynucleoside triphosphates.
    Type: Grant
    Filed: June 20, 2006
    Date of Patent: October 27, 2015
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Jian Wu, Dae H. Kim
  • Massive parallel method for decoding DNA and RNA
    Patent number: 9133511
    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: August 5, 2013
    Date of Patent: September 15, 2015
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Zengmin Li, John Robert Edwards, Yasuhiro Itagaki
  • DNA sequence with non-fluorescent nucleotide reversible terminators and cleavable label modified nucleotide terminators
    Patent number: 9115163
    Abstract: This invention provides a process for sequencing nucleic acids using 3? modified deoxynucleotide analogues or 3? modified deoxyinosine triphosphate analogues, and 3? modified dideoxynucleotide analogues having a detectable marker attached to a base thereof.
    Type: Grant
    Filed: October 17, 2008
    Date of Patent: August 25, 2015
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Dae H. Kim, Jia Guo, Qinglin Meng, Zengmin Li, Huanyan Cao
  • MASSIVE PARALLEL METHOD FOR DECODING DNA AND RNA
    Publication number: 20150197800
    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: Application
    Filed: March 27, 2015
    Publication date: July 16, 2015
    Inventors: Jingyue Ju, Zengmin Li, John Robert Edwards, Yasuhiro Itagaki
  • UNIVERSAL METHYLATION PROFILING METHODS
    Publication number: 20150148240
    Abstract: This invention provides methods of derivatizing a double-stranded DNA comprising contacting double-stranded DNA with a CpG methyltransferase and an s-adenosylmethionine analog. This invention also provides methods of sequencing DNA to determine methylation patterns.
    Type: Application
    Filed: December 19, 2014
    Publication date: May 28, 2015
    Applicant: The Trustees of Columbia University in the City of New York
    Inventors: Timothy H. Bestor, John R. Edwards, Jingyue Ju, Xiaoxu Li
  • NUCLEIC ACID SEQUENCING BY NANOPORE DETECTION OF TAG MOLECULES
    Publication number: 20150119259
    Abstract: This disclosure provides systems and methods for sequencing nucleic acids using nucleotide analogues and translocation of tags from incorporated nucleotide analogues through a nanopore. In aspects, this disclosure is related to composition, method, and system for sequencing a nucleic acid using tag molecules and detection of translocation through a nanopore of tags released from incorporation of the molecule.
    Type: Application
    Filed: April 8, 2013
    Publication date: April 30, 2015
    Inventors: Jingyue Ju, Randall Davis, Roger Chen
  • METHOD OF PREPARATION OF NANOPORE AND USES THEREOF
    Publication number: 20150111759
    Abstract: This disclosure provides systems and methods for sequencing nucleic acids using nucleotide analogues and translocation of tags from incorporated nucleotide analogues through a nanopore. In aspects, this disclosure is related to composition, method, and system for sequencing a nucleic acid using tag molecules and detection of translocation through a nanopore of tags released from incorporation of the molecule.
    Type: Application
    Filed: April 8, 2013
    Publication date: April 23, 2015
    Applicants: The Trustees of Columbia University in the City of New York, Government of the United States of America, as Represented by the Secretary of Commerce
    Inventors: Jingyue Ju, Shiv Kumar, Chuanjuan Tao, Minchen Chien, James J. Russo, John J. Kasianowicz, Joseph W.F. Robertson
  • DNA SEQUENCING BY SYNTHESIS USING RAMAN AND INFRARED SPECTROSCOPY DETECTION
    Publication number: 20150080232
    Abstract: This invention provides nucleoside triphosphate analogues having the structure: wherein B is a base and is adenine, guanine, cytosine, uracil or thymine, wherein R? is an OH or an H, and wherein R? is azidomethyl, a hydrocarbyl, or a substituted hydrocarbyl, and which has a Raman spectroscopy peak with wavenumber from 2000 cm?1 to 2300 cm?1 or a Fourier transform-infrared spectroscopy spectroscopy peak with wavenumber from 2000 cm?1 to 2300 cm?1, and also to methods of DNA sequencing and SNP detection.
    Type: Application
    Filed: May 23, 2012
    Publication date: March 19, 2015
    Applicant: The Trustees of Columbia University in the City of New York
    Inventors: Jingyue Ju, Jian Wu, Zengmin Li
  • DNA SEQUENCING BY NANOPORE USING MODIFIED NUCLEOTIDES
    Publication number: 20150037788
    Abstract: This invention provides a process for sequencing single-stranded DNA by employing a nanopore and modified nucleotides.
    Type: Application
    Filed: October 17, 2014
    Publication date: February 5, 2015
    Applicant: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventor: Jingyue Ju
  • CHEMICALLY CLEAVABLE 3'-O-ALLYL-DNTP-ALLYL-FLUOROPHORE FLUORESCENT NUCLEOTIDE ANALOGUES AND RELATED METHODS
    Publication number: 20140377743
    Abstract: This invention provides a nucleotide analogue comprising (i) a base selected from the group consisting of adenine, guanine, cytosine, thymine and uracil, (ii) a deoxyribose, (iii) an allyl moiety bound to the 3?-oxygen of the deoxyribose and (iv) a fluorophore bound to the base via an allyl linker, and methods of nucleic acid sequencing employing the nucleotide analogue.
    Type: Application
    Filed: August 4, 2014
    Publication date: December 25, 2014
    Applicant: The Trustees of Columbia University in the City of New York
    Inventors: Jingyue Ju, Lanrong Bi, Dae Hyun Kim, Qinglin Meng
  • DNA sequencing by nanopore using modified nucleotides
    Patent number: 8889348
    Abstract: This invention provides a process for sequencing single-stranded DNA by employing a nanopore and modified nucleotides.
    Type: Grant
    Filed: June 7, 2007
    Date of Patent: November 18, 2014
    Assignee: The Trustees of Columbia University in the City of New York
    Inventor: Jingyue Ju
  • FOUR-COLOR DNA SEQUENCING BY SYNTHESIS USING CLEAVABLE FLUORESCENT NUCLEOTIDE REVERSIBLE TERMINATORS
    Publication number: 20140315191
    Abstract: This invention provides a process for sequencing single-stranded DNA employing modified nucleotides.
    Type: Application
    Filed: April 1, 2014
    Publication date: October 23, 2014
    Applicant: The Trustees of Columbia University in the City of New York
    Inventors: Jingyue Ju, Dae Hyun Kim, Lanrong Bi, Qinglin Meng, Xiaoxu Li