Patents by Inventor Nicolaas M. J. Vermeulen

Nicolaas M. J. Vermeulen 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).

  • Hybridization-triggered fluorescent detection of nucleic acids
    Patent number: 7297495
    Abstract: Compositions and methods for fluorescent detection of nucleic acids are provided. The compositions can be detected by fluorescence when hybridized to a nucleic acid containing a target sequence, but are non-fluorescent in the non-hybridized state. Alternatively, the fluorescence properties of the compositions change in a detectable manner upon hybridization to a nucleic acid containing a target sequence. Methods for synthesis and methods of use of the compositions are also provided.
    Type: Grant
    Filed: October 3, 2005
    Date of Patent: November 20, 2007
    Assignee: Epoch Biosciences, Inc.
    Inventors: Robert O. Dempcy, Irina Aleksandrovna Afonina, Nicolaas M. J. Vermeulen
  • Compounds and methods for fluorescent labeling
    Patent number: 7112684
    Abstract: Dye reagents useful in labeling biological materials are provided along with methods for their use.
    Type: Grant
    Filed: December 22, 2004
    Date of Patent: September 26, 2006
    Assignee: Epoch Biosciences, Inc.
    Inventors: Eugeny A. Lukhtanov, Alexei V. Vorobiev, Michael W. Reed, Nicolaas M. J. Vermeulen
  • Modified oligonucleotides for mismatch discrimination
    Patent number: 7045610
    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: February 28, 2001
    Date of Patent: May 16, 2006
    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
  • Compounds and methods for fluorescent labeling
    Patent number: 6972339
    Abstract: Dye reagents useful in labeling biological materials are provided along with methods for their use.
    Type: Grant
    Filed: December 21, 2001
    Date of Patent: December 6, 2005
    Assignee: Epoch Biosciences, Inc.
    Inventors: Eugeny A. Lukhtanov, Alexei V. Vorobiev, Michael W. Reed, Nicolaas M. J. Vermeulen
  • Non-aggregating non-quenching oligomer comprising nucelotide analogs, method of synthesis and use thereof
    Patent number: 6972328
    Abstract: The invention provides compositions and methods for improved hybridization analysis utilizing DNA, RNA, PNA and chimeric oligomers in which one or more purine bases are substituted by a pyrazolo[5,4-d]pyrimidine or by a 7-deazapurine purine analogue. Reduced self-aggregation and reduced fluorescence quenching are obtained when the oligomers are used in various methods involving hybridization. Methods of synthesis, as well as novel synthetic precursors, are also provided.
    Type: Grant
    Filed: November 4, 2003
    Date of Patent: December 6, 2005
    Assignee: Epoch Biosciences, Inc.
    Inventors: Alexander A. Gall, Igor V. Kutyavin, Nicolaas M. J. Vermeulen, Robert O. Dempcy
  • Hybridization-triggered fluorescent detection of nucleic acids
    Patent number: 6951930
    Abstract: Compositions and methods for fluorescent detection of nucleic acids are provided. The compositions can be detected by fluorescence when hybridized to a nucleic acid containing a target sequence, but are non-fluorescent in the non-hybridized state. Alternatively, the fluorescence properties of the compositions change in a detectable manner upon hybridization to a nucleic acid containing a target sequence. Methods for synthesis and methods of use of the compositions are also provided.
    Type: Grant
    Filed: August 21, 2002
    Date of Patent: October 4, 2005
    Assignee: Epoch Biosciences, Inc.
    Inventors: Robert O. Dempcy, Irina Aleksandrovna Afonina, Nicolaas M. J. Vermeulen
  • Fluorescent quenching detection reagents and methods
    Patent number: 6790945
    Abstract: Oligonucleotide probes containing two labels are provided and are useful in hybridization assays. The probes can also contain a minor groove binding group.
    Type: Grant
    Filed: June 6, 2001
    Date of Patent: September 14, 2004
    Assignee: Epoch Biosciences, Inc.
    Inventors: Eugeny A. Lukhtanov, Alexander A. Gall, Robert O. Dempcy, Nicolaas M. J. Vermeulen
  • Non-aggregating non-quenching oligomer comprising nucelotide analogs, method of synthesis and use thereof
    Publication number: 20040116689
    Abstract: The invention provides compositions and methods for improved hybridization analysis utilizing DNA, RNA, PNA and chimeric oligomers in which one or more purine bases are substituted by a pyrazolo[5,4-d]pyrimidine or by a 7-deazapurine purine analogue. Reduced self-aggregation and reduced fluorescence quenching are obtained when the oligomers are used in various methods involving hybridization. Methods of synthesis, as well as novel synthetic precursors, are also provided.
    Type: Application
    Filed: November 4, 2003
    Publication date: June 17, 2004
    Applicant: Epoch Biosciences, Inc.
    Inventors: Alexander A. Gall, Igor V. Kutyavin, Nicolaas M.J. Vermeulen, Robert O. Dempcy
  • Fluorescent quenching detection reagents and methods
    Publication number: 20040081959
    Abstract: Oligonucleotide probes containing two labels are provided and are useful in hybridization assays. The probes can also contain a minor groove binding group.
    Type: Application
    Filed: March 29, 2002
    Publication date: April 29, 2004
    Applicant: Epoch Biosciences, Inc.
    Inventors: Michael W. Reed, Eugeny Alexander Lukhtanov, Alexander A. Gall, Robert O. Dempcy, Nicolaas M.J. Vermeulen
  • Tm leveling methods
    Patent number: 6683173
    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: December 21, 2001
    Date of Patent: January 27, 2004
    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
  • Systems and methods for predicting oligonucleotide melting temperature (TmS)
    Publication number: 20030235822
    Abstract: Software systems and methods for predicting the melting temperature (Tm) and other characteristics of oligonucleotides, including modified oligonucleotides. 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: Application
    Filed: June 18, 2002
    Publication date: December 25, 2003
    Applicant: Epoch Biosciences, Inc.
    Inventors: Sergey G. Lokhov, Igor V. Kutyavin, Robert O. Dempcy, Alexander A. Gall, Irina A. Afonina, Michael J. Singer, Nicolaas M.J. Vermeulen
  • Non-aggregating, non-quenching oligomers comprising nucleotide analogues; methods of synthesis and use thereof
    Patent number: 6660845
    Abstract: The invention provides compositions and methods for improved hybridization analysis utilizing DNA, RNA, PNA and chimeric oligomers in which one or more purine bases are substituted by a pyrazolo[5,4-d]pyrimidine or by a 7-deazapurine purine analogue. Reduced self-aggregation and reduced fluorescence quenching are obtained when the oligomers are used in various methods involving hybridization. Methods of synthesis, as well as novel synthetic precursors, are also provided.
    Type: Grant
    Filed: November 23, 1999
    Date of Patent: December 9, 2003
    Assignee: Epoch Biosciences, Inc.
    Inventors: Alexander A. Gall, Igor V. Kutyavin, Nicolaas M. J. Vermeulen, Robert O. Dempcy
  • TMLEVELING METHODS
    Publication number: 20030224359
    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: Application
    Filed: December 21, 2001
    Publication date: December 4, 2003
    Applicant: 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
  • Fluorescent quenching detection reagents and methods
    Patent number: 6653473
    Abstract: Oligonucleotide probes containing two labels are provided and are useful in hybridization assays. The probes can also contain a minor groove binding group.
    Type: Grant
    Filed: February 26, 2002
    Date of Patent: November 25, 2003
    Assignee: Epoch Biosciences, Inc.
    Inventors: Michael W. Reed, Eugeny Alexander Lukhtanov, Alexander A. Gall, Robert O. Dempcy, Nicolaas M. J. Vermeulen
  • S-adenosyl methionine regulation of metabolic pathways and its use in diagnosis and therapy
    Patent number: 6596701
    Abstract: A new paradigm of disease centers around the metabolic pathways of S-adenosyl-L-methionine (SAM), the intermediates of these pathways and other metabolic pathways influenced by the SAM pathways. Methods are provided to analyze and modulate SAM pathways associated with a disease or condition. Such methods permit identification and utilization of diagnostic and therapeutic protocols and agents for such disease states and conditions.
    Type: Grant
    Filed: March 16, 1998
    Date of Patent: July 22, 2003
    Assignee: MediQuest Therapeutics, Inc.
    Inventors: Dennis E. Schwartz, Nicolaas M. J. Vermeulen, Christine L. O'Day
  • Hybridization-triggered fluorescent detection of nucleic acids
    Publication number: 20030113765
    Abstract: Compositions and methods for fluorescent detection of nucleic acids are provided. The compositions can be detected by fluorescence when hybridized to a nucleic acid containing a target sequence, but are non-fluorescent in the non-hybridized state. Alternatively, the fluorescence properties of the compositions change in a detectable manner upon hybridization to a nucleic acid containing a target sequence. Methods for synthesis and methods of use of the compositions are also provided.
    Type: Application
    Filed: August 21, 2002
    Publication date: June 19, 2003
    Applicant: Epoch Biosciences, Inc.
    Inventors: Robert O. Dempcy, Irina Aleksandrovna Afonina, Nicolaas M.J. Vermeulen
  • Fluorescent quenching detection reagents and methods
    Publication number: 20030096254
    Abstract: Oligonucleotide probes containing two labels are provided and are useful in hybridization assays. The probes can also contain a minor groove binding group.
    Type: Application
    Filed: March 29, 2002
    Publication date: May 22, 2003
    Applicant: Epoch Biosciences, Inc.
    Inventors: Michael W. Reed, Eugeny Alexander Lukhtanov, Alexander A. Gall, Robert O. Dempcy, Nicolaas M.J. Vermeulen
  • Fluorescent quenching detection reagents and methods
    Publication number: 20030008304
    Abstract: Oligonucleotide probes containing two labels are provided and are useful in hybridization assays. The probes can also contain a minor groove binding group.
    Type: Application
    Filed: February 26, 2002
    Publication date: January 9, 2003
    Applicant: Epoch Biosciences, Inc.
    Inventors: Michael W. Reed, Eugeny Alexander Lukhtanov, Alexander A. Gall, Robert O. Dempcy, Nicolaas M.J. Vermeulen
  • Hybridization-triggered fluorescent detection of nucleic acids
    Patent number: 6472153
    Abstract: Compositions and methods for fluorescent detection of nucleic acids are provided. The compositions can be detected by fluorescence when hybridized to a nucleic acid containing a target sequence, but are non-fluorescent in the non-hybridized state. Alternatively, the fluorescence properties of the compositions change in a detectable manner upon hybridization to a nucleic acid containing a target sequence. Methods for synthesis and methods of use of the compositions are also provided.
    Type: Grant
    Filed: October 26, 1999
    Date of Patent: October 29, 2002
    Assignee: Epoch Biosciences, Inc.
    Inventors: Robert O. Dempcy, Irina Aleksandrovna Afonina, Nicolaas M. J. Vermeulen
  • Fluorescent quenching detection reagents and methods
    Publication number: 20020034754
    Abstract: Oligonucleotide probes containing two labels are provided and are useful in hybridization assays. The probes can also contain a minor groove binding group.
    Type: Application
    Filed: June 6, 2001
    Publication date: March 21, 2002
    Inventors: Michael W. Reed, Eugeny Alexander Lukhtanov, Alexander A. Gall, Robert O. Dempcy, Nicolaas M.J. Vermeulen