Patents Assigned to Epoch Biosciences, Inc.
  • Patent number: 8067177
    Abstract: Methods are provided for amplification and monitoring of oligonucleotide amplification in which a primer has an overlap with one or more bases of a detection probe.
    Type: Grant
    Filed: March 17, 2010
    Date of Patent: November 29, 2011
    Assignee: Epoch Biosciences, Inc.
    Inventors: Walt Mahoney, Nicolaas M. J. Vermeulen, Irina Afonina
  • Publication number: 20100137614
    Abstract: The present invention provides a negatively charged minor groove binding compound, oligonucleotide conjugates comprising the same, and methods for using the same. The negatively charged minor groove binding compounds of the present invention comprises an acidic moiety that is capable of being ionized under physiological conditions. In particular, the negatively charged minor groove binding compound of the present invention comprises a binding moiety that binds preferentially into a minor groove of a double, triple or higher stranded DNA, RNA, PNA or hybrids thereof. The binding moiety comprises at least one aryl moiety and an acidic moiety which is covalently attached to a phenyl portion of the aryl moiety or to a heteroatom of a heteroaryl portion of the aryl moiety.
    Type: Application
    Filed: August 14, 2009
    Publication date: June 3, 2010
    Applicant: Epoch Biosciences, Inc.
    Inventors: Eugeny A. Lukhtanov, Nicolaas M.J. Vermeulen, Alexander A. Gall
  • Patent number: 7601851
    Abstract: Dye reagents useful in labeling biological materials are provided along with methods for their use.
    Type: Grant
    Filed: May 10, 2005
    Date of Patent: October 13, 2009
    Assignee: Epoch Biosciences, Inc.
    Inventors: Eugeny A. Lukhtanov, Alexei V. Vorobiev, Michael W. Reed, Nicolaas M. J. Vermeulen
  • Patent number: 7582739
    Abstract: The present invention provides a negatively charged minor groove binding compound, oligonucleotide conjugates comprising the same, and methods for using the same. The negatively charged minor groove binding compounds of the present invention comprises an acidic moiety that is capable of being ionized under physiological conditions. In particular, the negatively charged minor groove binding compound of the present invention comprises a binding moiety that binds preferentially into a minor groove of a double, triple or higher stranded DNA, RNA, PNA or hybrids thereof. The binding moiety comprises at least one aryl moiety and an acidic moiety which is covalently attached to a phenyl portion of the aryl moiety or to a heteroatom of a heteroaryl portion of the aryl moiety.
    Type: Grant
    Filed: March 11, 2003
    Date of Patent: September 1, 2009
    Assignee: Epoch Biosciences, Inc.
    Inventors: Eugeny A. Lukhtanov, Nicolaas M. J. Vermeulen, Alexander A. Gall
  • Patent number: 7556923
    Abstract: Conjugates between a minor groove binding molecule, such as the trimer of 1,2-dihydro-(3H)-pyrrolo[3,2-e]indole-7-carboxylate (CDPI3), and an oligonucleotide form unusually stable hybrids with complementary target sequences, in which the tethered CDPI3 group resides in the minor groove of the duplex. These conjugates can be used as probes and primers. Due to their unusually high binding affinity, conjugates as short as 8-mers can be used as amplification primers with high specificity and efficiency. MGB conjugation also increases the discriminatory power of short oligonucleotides, providing enhanced detection of nucleotide sequence mismatches by short oligonucleotides.
    Type: Grant
    Filed: April 6, 2007
    Date of Patent: July 7, 2009
    Assignee: Epoch Biosciences, Inc.
    Inventors: Joel Hedgpeth, Irina A. Afonina, Igor V. Kutyavin, Eugeny A. Lukhtanov, Evgeniy S. Belousov, Rich B. Meyer, Jr.
  • Patent number: 7553643
    Abstract: The present invention provides a novel method for nucleic acid amplification. The method includes contacting the sample with at least one forward primer and at least one reverse primer, an AP endonuclease, and a nucleic acid polymerase. under conditions sufficient to allow the forward and reverse primers to hybridize to the target nucleic acid and form a reaction mixture, wherein at least one of the forward and reverse primer includes an AP endonuclease-cleavable linker L, and incubating the reaction mixture under reaction conditions that simultaneously allow the AP endonuclease to cleave at a linker site L and the extension of the primers in a template-specific manner to amplify the target nucleic acid sequence.
    Type: Grant
    Filed: May 10, 2006
    Date of Patent: June 30, 2009
    Assignee: EPoch Biosciences, Inc.
    Inventors: Igor V. Kutyavin, David Milesi, Merl F. Hoekstra
  • Patent number: 7541454
    Abstract: Compounds useful in the fluorescent labeling of biological materials are provided along with methods for their use and preparation.
    Type: Grant
    Filed: October 25, 2004
    Date of Patent: June 2, 2009
    Assignee: Epoch Biosciences, Inc.
    Inventor: Eugeny A. Lukhtanov
  • Publication number: 20090093612
    Abstract: The present invention provides amide-substituted xanthene fluorescent dyes and reagent for the introduction of phosphonate or sulfo groups into the fluorescent dyes.
    Type: Application
    Filed: October 2, 2008
    Publication date: April 9, 2009
    Applicant: Epoch Biosciences, Inc.
    Inventor: Eugene Lukhtanov
  • Publication number: 20090092967
    Abstract: The present invention provides methods of generating target nucleic acids for amplification using nicking enzymes and methods for amplifying the generated target nucleic acids.
    Type: Application
    Filed: June 26, 2007
    Publication date: April 9, 2009
    Applicant: Epoch Biosciences, Inc.
    Inventors: Zuxu Yao, Graham Lidgard, Yevgeniy Belousov
  • Publication number: 20090087922
    Abstract: Methods and probes are provided for the analysis of target sequences having two or more polymorphisms wherein one of the polymorphisms is to be distinguished and another polymorphism is to be masked.
    Type: Application
    Filed: January 28, 2008
    Publication date: April 2, 2009
    Applicant: Epoch Biosciences, Inc.
    Inventors: Yevgeniy Belousov, Robert O. Dempcy, Sergey G. Lokhov, Alexei Vorobiev
  • Publication number: 20090048427
    Abstract: Conjugates between a minor groove binding molecule, such as the trimer of 1,2-dihydro-(3H)-pyrrolo[3,2-e]indole-7-carboxylate (CDPI3), and an oligonucleotide form unusually stable hybrids with complementary target sequences, in which the tethered CDPI3 group resides in the minor groove of the duplex. These conjugates can be used as probes and primers. Due to their unusually high binding affinity, conjugates as short as 8-mers can be used as amplification primers with high specificity and efficiency. MGB conjugation also increases the discriminatory power of short oligonucleotides, providing enhanced detection of nucleotide sequence mismatches by short oligonucleotides.
    Type: Application
    Filed: July 14, 2008
    Publication date: February 19, 2009
    Applicant: EPOCH BIOSCIENCES, INC.
    Inventors: JOEL HEDGPETH, IRINA A. AFONINA, IGOR V. KUTYAVIN, EUGENY A. LUKHTANOV, EVGENIY S. BELOUSOV, RICH B. MEYER, JR.
  • Patent number: 7485442
    Abstract: Oligonucleotide probes/conjugates are provided along with method for their use in assays to monitor amplification wherein the signal produced does not rely on 5? nuclease digestion.
    Type: Grant
    Filed: June 19, 2006
    Date of Patent: February 3, 2009
    Assignee: Epoch Biosciences, Inc.
    Inventors: Irina A. Afonina, Yevgeniy S. Belousov, Robert O. Dempcy, Igor V. Kutyavin, Sergey G. Lokhov, Eugeny A. Lukhtanov
  • Publication number: 20080293586
    Abstract: Minor groove binder-oligonucleotide probes are provided along with methods for their use wherein the probes have an attached fluorophore which, in an unhybridized form exhibits very low background signal.
    Type: Application
    Filed: March 12, 2008
    Publication date: November 27, 2008
    Applicant: Epoch Biosciences, Inc.
    Inventors: Sergey Lokhov, Eugene Lukhtanov
  • Publication number: 20080248474
    Abstract: Methods are provided for amplification and monitoring of oligonucleotide amplification in which a primer has an overlap with one or more bases of a detection probe.
    Type: Application
    Filed: December 18, 2007
    Publication date: October 9, 2008
    Applicant: EPOCH BIOSCIENCES, INC
    Inventors: WALT MAHONEY, Nicolaas M.J. Vermeulen, Irina Afonina
  • Publication number: 20080207887
    Abstract: Reagents are provided for the introduction of phosphonate groups into fluorescent dyes. Methods are also provided for preparing dye conjugates.
    Type: Application
    Filed: November 8, 2007
    Publication date: August 28, 2008
    Applicant: EPOCH BIOSCIENCES, INC.
    Inventors: Eugeny Lukhtanov, Alexei Vorobiev
  • Publication number: 20080166782
    Abstract: The present invention provides a novel method for detection and/or genotyping of nucleic acids that utilizes the specificity of an AP endonuclease. In addition, the present invention provides a novel method for nucleic acid amplification.
    Type: Application
    Filed: June 28, 2007
    Publication date: July 10, 2008
    Applicant: Epoch Biosciences, Inc.
    Inventors: Igor V. Kutyavin, David Milesi, Merl F. Hoekstra
  • Patent number: 7381818
    Abstract: Minor groove binder-oligonucleotide probes are provided along with methods for their use wherein the probes have an attached fluorophore which, in an unhybridized form exhibits very low background signal.
    Type: Grant
    Filed: October 27, 2004
    Date of Patent: June 3, 2008
    Assignee: Epoch Biosciences, Inc.
    Inventors: Sergey Lokhov, Eugene Lukhtanov
  • Patent number: 7368549
    Abstract: Modified oligonucleotides are provided containing bases selected from unsubstituted and 3-substituted pyrazolo[3,4-d]pyrimidines and 5-substituted pyrimidines, and optionally have attached minor groove binders and reporter groups.
    Type: Grant
    Filed: April 19, 2005
    Date of Patent: May 6, 2008
    Assignee: Epoch Biosciences, Inc.
    Inventors: Robert O. Dempcy, Alexander A Gall, Sergey G. Lokhov, Irina A. Afonina, Michael J. Singer, Igor V. Kutyavin, Nicolaas M. J. Vermeulen
  • Patent number: 7348146
    Abstract: Methods and probes are provided for the analysis of target sequences having two or more polymorphisms wherein one of the polymorphisms is to be distinguished and another polymorphism is to be masked.
    Type: Grant
    Filed: September 29, 2004
    Date of Patent: March 25, 2008
    Assignee: Epoch Biosciences, Inc.
    Inventors: Yevgeniy Belousov, Robert O. Dempcy, Sergey G. Lokhov, Alexei Vorobiev
  • Patent number: 7319022
    Abstract: Methods are provided for amplification and monitoring of oligonucleotide amplification in which a primer has an overlap with one or more bases of a detection probe.
    Type: Grant
    Filed: August 11, 2005
    Date of Patent: January 15, 2008
    Assignee: Epoch Biosciences, Inc.
    Inventors: Walt Mahoney, Nicolaas M. J. Vermeulen, Irina Afonina