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
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
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
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.
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
Abstract: The present invention provides amide-substituted xanthene fluorescent dyes and reagent for the introduction of phosphonate or sulfo groups into the fluorescent dyes.
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
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
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.
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
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.
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
Abstract: Reagents are provided for the introduction of phosphonate groups into fluorescent dyes. Methods are also provided for preparing dye conjugates.
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
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.
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
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
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