Patents by Inventor James Prudent
James Prudent 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).
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Patent number: 7892796Abstract: Solid support assays using non-standard bases are described. A capture oligonucleotide comprising a molecular recognition sequence is attached to a solid support and hybridized with a target oligonucleotide. In some instances, the molecular recognition sequence includes one or more non-standard bases and hybridizes to a complementary tagging sequence of the target oligonucleotide. In other instances, incorporation of a non-standard base (e.g., via PCR or ligation) is used in the assay.Type: GrantFiled: November 19, 2005Date of Patent: February 22, 2011Assignee: EraGen Biosciences, Inc.Inventors: James Prudent, David Marshall, Christopher Sherrill, Eric Roesch, Craig Richmond, Christopher Scherrer, Jennifer Grenier, Jerod Ptacin
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Publication number: 20070292856Abstract: The present invention provides novel cleavage agents and polymerases for the cleavage and modification of nucleic acid. The cleavage agents and polymerases find use, for example, for the detection and characterization of nucleic acid sequences and variations in nucleic acid sequences. In some embodiments, the 5? nuclease activity of a variety of enzymes is used to cleave a target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.Type: ApplicationFiled: July 19, 2006Publication date: December 20, 2007Applicant: Third Wave Technologies, Inc.Inventors: Victor Lyamichev, Michael Kaiser, Natalie Lyamichev, Jeff Hall, James Prudent, Mary Brow
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Publication number: 20070264694Abstract: The present methods relate to generating nucleic acid molecules using non-natural nucleotides. In some methods, the nucleic acid molecules may be generated by hybridizing a plurality of oligonucleotides comprising one or more non-natural nucleotides and using a polymerase and/or a coupling agent to link the hybridized oligonucleotides. The methods also relate to the use of proximity effects to generate nucleic acid molecules using non-natural nucleotides. Furthermore, the methods relate to the use of at least one non-natural base in a DNA template in order to generate a replicate of the DNA template in which the non-natural base has been replaced with a natural base.Type: ApplicationFiled: April 9, 2007Publication date: November 15, 2007Inventor: James Prudent
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Publication number: 20070105099Abstract: The present invention provides methods, kits and compositions for high fidelity nucleic acid amplification reactions of target nucleic acids such that specific amplification products that incorporate non-standard bases are produced. The amplification reactions can either be linear or exponential. In some embodiments, the fidelity of the amplification reaction is high enough such that a majority of the amplification products maintain non-standard bases at specific sites designated by the user after a specified number of amplification cycles. In some embodiments, the ratio of non-standard nucleoside triphosphates is greater than the amount of standard nucleoside triphosphates initially present in the reaction mixture.Type: ApplicationFiled: January 17, 2004Publication date: May 10, 2007Applicant: EraGen Biosciences, Inc.Inventors: James Prudent, Scott Johnson, Michael Moser, David Marshall
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Publication number: 20070087361Abstract: Solid support assays using non-standard bases are described. A capture oligonucleotide comprising a molecular recognition sequence is attached to a solid support and hybridized with a target. In some instances, the molecular recognition sequence includes one or more non-standard bases and hybridizes to a complementary tagging sequence of the target oligonucleotide. In other instances, incorporation of a non-standard base (e.g., via PCR or ligation) is used in the assay.Type: ApplicationFiled: July 20, 2006Publication date: April 19, 2007Inventors: Jennifer Grenier, David Marshall, James Prudent, Craig Richmond, Eric Roesch, Christopher Scherrer, Christopher Sherrill, Jerod Ptacin
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Publication number: 20070065815Abstract: The present invention relates to methods and compositions for analyzing nucleic acids. In particular, the present invention provides methods and compositions for the detection and characterization of nucleic acid sequences and sequence changes. The methods of the present invention permit the detection and/or identification of genetic polymorphism such as those associated with human disease and permit the identification of pathogens (e.g., viral and bacterial strain identification).Type: ApplicationFiled: September 5, 2006Publication date: March 22, 2007Inventors: Fang Dong, Victor Lyamichev, James Prudent, Lance Fors, Bruce Neri, Mary Brow, Todd Anderson, James Dahlberg
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Publication number: 20070059686Abstract: Disclosed are methods and kits for identifying a virus in a sample, which may include a coronavirus capable of causing Severe Acute Respiratory Syndrome (“SARS”) or SARS-like symptoms. The virus may be a SARS-Associated Coronavirus (“SARS-CoV”). Typically, the methods may include reacting a mixture that includes, in addition to nucleic acid isolated from the sample, at least one oligonucleotide capable of specifically hybridizing to SARS-CoV nucleic acid where the oligonucleotide includes at least one non-natural base. In addition, the mixture may include control nucleic acid.Type: ApplicationFiled: July 28, 2006Publication date: March 15, 2007Inventors: Michael Moser, James Prudent
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Publication number: 20070031885Abstract: Assays using non-natural bases are described. In one embodiment, the method involves contacting a sample suspected of containing the target nucleic acid with a polymerase and first and second primers; amplifying the target nucleic acid, if present in the sample, by PCR using the first and second primers to generate an amplification product having a double-stranded region and a single-stranded region that comprises the non-natural base; contacting the sample with a reporter comprising a label and a non-natural base that is complementary to the non-natural base of the single-stranded region; annealing at least a portion of the reporter to the single-stranded region of the amplification product; and correlating a signal of the label with the presence of the target nucleic acid in the sample. The invention also provides corresponding kits for use in detecting target nucleic acids in a sample.Type: ApplicationFiled: October 12, 2006Publication date: February 8, 2007Inventors: David Marshall, James Prudent, Christopher Sherrill, Gideon Shapiro, Jennifer Grenier, Craig Richmond, Simona Jurczyk, Jerod Ptacin
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Publication number: 20070003942Abstract: The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.Type: ApplicationFiled: July 15, 2005Publication date: January 4, 2007Inventors: James Prudent, Jeff Hall, Victor Lyamichev, Mary Ann Brow, James Dahlberg
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Publication number: 20060292580Abstract: The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.Type: ApplicationFiled: July 15, 2005Publication date: December 28, 2006Inventors: James Prudent, Jeff Hall, Victor Lyamichev, Mary Ann Brow, James Dahlberg
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Publication number: 20060252091Abstract: Assays using non-natural bases are described. In one embodiment, the method involves contacting a sample suspected of containing the target nucleic acid with a polymerase and first and second primers; amplifying the target nucleic acid, if present in the sample, by PCR using the first and second primers to generate an amplification product having a double-stranded region and a single-stranded region that comprises the non-natural base; contacting the sample with a reporter comprising a label and a non-natural base that is complementary to the non-natural base of the single-stranded region; annealing at least a portion of the reporter to the single-stranded region of the amplification product; and correlating a signal of the label with the presence of the target nucleic acid in the sample. The invention also provides corresponding kits for use in detecting target nucleic acids in a sample.Type: ApplicationFiled: July 14, 2006Publication date: November 9, 2006Inventors: David Marshall, James Prudent, Christopher Sherrill, Gideon Shapiro, Jennifer Grenier, Craig Richmond, Simona Jurczyk, Jerod Ptacin
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Publication number: 20060177835Abstract: The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.Type: ApplicationFiled: July 15, 2005Publication date: August 10, 2006Inventors: James Prudent, Jeff Hall, Victor Lyamichev, Mary Brow, James Dahlberg
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Publication number: 20060154269Abstract: The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.Type: ApplicationFiled: July 15, 2005Publication date: July 13, 2006Inventors: James Prudent, Jeff Hall, Victor Lyamichev, Mary Ann Brow, James Dahlberg
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Publication number: 20060110750Abstract: The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.Type: ApplicationFiled: September 9, 2005Publication date: May 25, 2006Inventors: James Prudent, Jeff Hall, Victor Lyamichev, Mary Brow, James Dahlberg
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Publication number: 20060078936Abstract: Solid support assays using non-standard bases are described. A capture oligonucleotide comprising a molecular recognition sequence is attached to a solid support and hybridized with a target oligonucleotide. In some instances, the molecular recognition sequence includes one or more non-standard bases and hybridizes to a complementary tagging sequence of the target oligonucleotide. In other instances, incorporation of a non-standard base (e.g., via PCR or ligation) is used in the assay.Type: ApplicationFiled: November 19, 2005Publication date: April 13, 2006Inventors: Jennifer Grenier, David Marshall, James Prudent, Craig Richmond, Eric Roesch, Christopher Scherrer, Christopher Sherrill, Jerod Ptacin
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Publication number: 20060040294Abstract: The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.Type: ApplicationFiled: July 15, 2005Publication date: February 23, 2006Inventors: James Prudent, Jeff Hall, Victor Lyamichev, Mary Brow, James Dahlberg
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Publication number: 20050181435Abstract: The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.Type: ApplicationFiled: April 12, 2005Publication date: August 18, 2005Applicant: Third Wave Technologies, Inc.Inventors: James Prudent, Jeff Hall, Victor Lyamichev, Mary Brow, James Dahlberg
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Publication number: 20050130179Abstract: The present invention relates to novel phosphoramidites, including positive and neutrally charged compounds. The present invention also provides charge tags for attachment to materials including solid supports and nucleic acids, wherein the charge tags increase or decrease the net charge of the material. The present invention further provides methods for separating and characterizing molecules based on the charge differentials between modified and unmodified materials.Type: ApplicationFiled: June 23, 2004Publication date: June 16, 2005Applicant: Third Wave Technologies, Inc.Inventors: Victor Lyamichev, Zbigniev Skrzypczynski, Hatim Allawi, Sarah Wayland, Tsetska Takova, Bruce Neri, James Prudent, Jeff Hall
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Publication number: 20050014163Abstract: The present invention relates to methods and compositions for analyzing nucleic acids. In particular, the present invention provides methods and compositions for the detection and characterization of nucleic acids and sequence changes. The methods of the present invention permit the detection and/or identification of genetic polymorphism such as those associated with human disease and permit the identification of pathogens (e.g., viral and bacterial strain identification).Type: ApplicationFiled: September 4, 2003Publication date: January 20, 2005Inventors: Fang Dong, Victor Lyamichev, James Prudent, Lance Fors, Bruce Neri, Mary Ann Brow, Todd Anderson, James Dahlberg
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Publication number: 20020187484Abstract: Modified hairpin-forming oligonucleotide to continuously assess nucleotide cleavage by enediynes and other nucleic acid cleavage agents are provided. These oligonucleotide probes, which are also referred to herein as “molecular break lights,” are also useful for continuous assessment of protection of nucleotides from cleavage agents. Probes according to the present invention are useful in assays; improved assays, including multiplexed assays, utilizing such pairs of molecules or moieties; and assay kits that include such pairs. Methods of using the probes are also provided.Type: ApplicationFiled: November 27, 2001Publication date: December 12, 2002Inventors: Jon Thorson, James Prudent