Patents Examined by Ethan Whisenant
  • Electrodes linked via conductive oligomers to nucleic acids
    Patent number: 7384749
    Abstract: The invention relates to nucleic acids covalently coupled to electrodes via conductive oligomers. More particularly, the invention is directed to the site-selective modification of nucleic acids with electron transfer moieties and electrodes to produce a new class of biomaterials, and to methods of making and using them.
    Type: Grant
    Filed: January 30, 2006
    Date of Patent: June 10, 2008
    Assignee: Clinical Micro Sensors, Inc.
    Inventors: Jon F. Kayyem, Stephen D. O'Connor, Michael Gozin, Changjun Yu, Thomas J. Meade
  • Assays for drug discovery based on microcompetition with a foreign polynucleotide
    Patent number: 7381526
    Abstract: A recent discovery showed that microcompetition between a foreign polynucleotide and a cellular polynucleotide is a risk factor for some of the major chronic diseases. The invention uses this novel discovery to present assays for screening compounds based on their effectiveness in modulating such microcompetition. The effective compounds can be used in treatment of these chronic diseases. The invention also presents assays for screening compounds that can be used in treatment of chronic diseases resulting from other foreign polynucleotide-type disruptions.
    Type: Grant
    Filed: August 1, 2002
    Date of Patent: June 3, 2008
    Inventor: Hanan Polansky
  • Electrodes linked via oligomers to nucleic acids
    Patent number: 7381533
    Abstract: The invention relates to nucleic acids covalently coupled to electrodes via conductive oligomers. More particularly, the invention is directed to the site-selective modification of nucleic acids with electron transfer moieties and electrodes to produce a new class of biomaterials, and to methods of making and using them.
    Type: Grant
    Filed: December 6, 2005
    Date of Patent: June 3, 2008
    Assignee: Clinical Micro Sensors, Inc.
    Inventors: Jon F. Kayyem, Stephen D. O'Connor, Michael Gozin, Changjun Yu, Thomas J. Meade
  • Compositions and methods for the detection of a nucleic acid using a cleavage reaction
    Patent number: 7381532
    Abstract: The invention relates to a method of generating a signal indicative of the presence of a target nucleic acid sequence in a sample, where the method includes forming a cleavage structure by incubating a sample containing a target nucleic acid sequence with a nucleic acid polymerase and cleaving the cleavage structure with a nuclease to generate a cleaved nucleic acid fragment. The invention also relates to methods of detecting or measuring a target nucleic acid sequence, where the method includes forming a cleavage structure by incubating a target nucleic acid sequence with a nucleic acid polymerase, cleaving the cleavage structure with a nuclease and detecting or measuring the release of a fragment.
    Type: Grant
    Filed: November 23, 2005
    Date of Patent: June 3, 2008
    Assignee: Stratagene California
    Inventor: Joseph A. Sorge
  • Method and apparatus for determining base sequence of nucleic acid molecule
    Patent number: 7371532
    Abstract: Disclosed herein is a method and apparatus for determining the base sequence of a nucleic acid molecule by cleaving a nucleic acid molecule of interest while controlling the cleavage site, measuring the change in mass which occurs in the nucleic acid molecule after the cleavage step, and acquiring the base information of the cleaved nucleic acid molecule from the data about the change in mass. The method and apparatus are based on the principle which is entirely different from that used for the conventional technique.
    Type: Grant
    Filed: September 22, 2005
    Date of Patent: May 13, 2008
    Assignee: Sony Corporation
    Inventors: Takayoshi Mamine, Atsumi Tsujimoto, Takuro Yamamoto
  • Methods of cloning and producing fragment chains with readable information content
    Patent number: 7371851
    Abstract: The present invention provides a method of attaching a fragment of a first nucleic acid molecule to a second nucleic acid molecule using adapters to mediate the binding particularly in methods of cloning, methods of producing fragment chains with a readily readable information content, particularly comprising fragments corresponding to code, such as alphanumeric code, the nucleic acid molecules thus produced and kits for performing such methods.
    Type: Grant
    Filed: June 27, 2000
    Date of Patent: May 13, 2008
    Assignee: Complete Genomics AS
    Inventor: Preben Lexow
  • Use of an extraction control in a method of extracting nucleic acids
    Patent number: 7371531
    Abstract: The present invention relates to a method of ensuring the effectiveness of the extraction workup from a biological sample of nucleic acid. The inventive method is able to distinguish between possible defects in the extraction of nucleic acid from a sample and possible defects in a subsequent amplification step. The present invention also relates to a packaged array for extracting nucleic acid from a biological sample.
    Type: Grant
    Filed: April 25, 2005
    Date of Patent: May 13, 2008
    Assignee: Becton, Dickinson and Company
    Inventors: Tobin Hellyer, Thomas Fort, Ray A. McMillian
  • Methods and apparati using single polymer analysis
    Patent number: 7371520
    Abstract: The invention relates to methods for analyzing and characterizing single polymers such as nucleic acid molecules. In preferred embodiments, the single molecules are analyzed using single molecule detection and analysis systems.
    Type: Grant
    Filed: May 28, 2003
    Date of Patent: May 13, 2008
    Assignee: U.S. Genomics, Inc.
    Inventors: Xiaojian (David) Zhao, Jeffrey D. Randall, Bijit Kundu, Jessica Kesty, Steve R. Gullans, Eugene Y. Chan, Martin Fuchs
  • Methods for separation of polymeric compounds
    Patent number: 7371533
    Abstract: Recently two techniques using free solution electrophoresis to separate charged-uncharged polymer conjugates have proven successful: End Labeled Free Solution Electrophoresis (ELFSE) for DNA sequencing, and Free Solution Conjugate Electrophoresis (FSCE) for molar mass profiling of uncharged polymers. Previous attempts have been made to analyze experimental data generated by these new techniques for the electrophoresis of molecules with varying charge distributions. However, the importance of the ends of the polymers in determining the polymer's overall mobility was neglected in previous work. Through a careful investigation and a reanalysis of the experimental data, it is determined here that this “end effect” critically impacts the behavior of polymers and charged-uncharged polymer conjugates during electrophoresis.
    Type: Grant
    Filed: October 4, 2005
    Date of Patent: May 13, 2008
    Assignees: University of Ottawa, Northwestern University
    Inventors: Gary W. Slater, Laurette C. McCormick, Annelise E Barron, Robert J. Meagher
  • Method and kits for multiplex hybridization assays
    Patent number: 7368242
    Abstract: The invention provides a method for genotyping interfering polymorphic loci in a target polynucleotide, such as a strand of genomic DNA, in a multiplex hybridization-based assay. The invention also provides nucleic acid standards for validating the performance of such hybridization-based assays. In one aspect, the method of the invention is carried out by providing for each interfering polymorphic locus one or more probes so that at least one probe is capable of forming a perfectly match duplex at the locus regardless of the characteristic sequence of an adjacent polymorphism.
    Type: Grant
    Filed: June 14, 2005
    Date of Patent: May 6, 2008
    Assignee: Affymetrix, Inc.
    Inventors: Xin Miao, James Ireland, Paul Hardenbol, Thomas Matthew Daly, Dong-Jing Fu, Richard D. Hockett
  • Short GCG expansions in the PAB II gene for oculopharyngeal muscular dystrophy and diagnostic thereof
    Patent number: 7364852
    Abstract: The present invention relates to a human PAB II gene containing transcribed polymorphic GCG repeat, which comprises a sequence as set forth in SEQ ID NO:3, which includes introns and flanking genomic sequence. The allelic variants of GCG repeat of the human PAB II gene are associated with a disease related with protein accumulation in nucleus, such as polyalanine accumulation, a disease related with swallowing difficulties, such as oculopharyngeal muscular dystrophy. The present invention also relates to a method for the diagnosis of a disease with protein accumulation in nucleus, which comprises the steps of: a) obtaining a nucleic acid sample of said patient; and b) determining allelic variants of GCG repeat of the gene of claim 1, and wherein long allelic variants are indicative of a disease related with protein accumulation in nucleus.
    Type: Grant
    Filed: July 12, 2004
    Date of Patent: April 29, 2008
    Assignee: McGill University
    Inventors: Guy A. Rouleau, Bernard Brais
  • Treatment of substrates for immobilizing biomolecules
    Patent number: 7364849
    Abstract: A method of treating a substrate for immobilizing a biomolecule and substrates produced by the method are disclosed. The method includes contacting at least a portion of a substrate with a reducing agent such as a hydride. Treatment with an appropriate reducing agent substantially eliminates autofluorescence on substrates.
    Type: Grant
    Filed: December 5, 2003
    Date of Patent: April 29, 2008
    Assignee: Corning Incorporated
    Inventors: Yijia Bao, Guangshan Li, Nalini Raghavachari, Mingqian He, Xinying Xie, Yuming Xie
  • Methods and kits for methylation detection
    Patent number: 7364855
    Abstract: Ligation-based methods and kits are disclosed for determining the degree of methylation of one or more target nucleotides. In certain embodiments, the methylation status of one or more target nucleotides is determined by generating misligation products. In certain embodiments, at least one target nucleotide is amplified prior to the ligation reaction. In certain embodiments, at least one ligation product, at least one ligation product surrogate, at least one misligation product, at least one misligation product surrogate, or combinations thereof are amplified. In certain embodiments, one or more ligation probes comprise at least one nucleotide analog, at least one Modification, at least one mismatched nucleotide, or combinations thereof.
    Type: Grant
    Filed: May 2, 2005
    Date of Patent: April 29, 2008
    Assignee: Applera Corporation
    Inventors: Mark R. Andersen, Jer-Kang Chen, Michael W. Hunkapiller, Steven M. Menchen
  • Methods for detection of a target nucleic acid by capture
    Patent number: 7361467
    Abstract: The invention relates to a method of generating a signal indicative of the presence of a target nucleic acid in a sample, where the method includes forming a cleavage structure by incubating a sample comprising a target nucleic acid with a probe having a secondary structure that changes upon binding of the probe to the target nucleic acid and further comprising a binding moiety. The invention also includes the steps of cleaving the cleavage structure with a nuclease to release a nucleic acid fragment to generate a signal, wherein generation of the signal is indicative of the presence of a target nucleic acid in a sample, and detecting and/or measuring the amount of the fragment captured by binding of a binding moiety to a capture element on a solid support.
    Type: Grant
    Filed: June 10, 2005
    Date of Patent: April 22, 2008
    Assignee: Stratagene California
    Inventors: Joseph A. Sorge, Anne M. Whalen
  • Electrocatalytic nucleic acid hybridization detection
    Patent number: 7361470
    Abstract: The detection of specific DNA sequences using electrochemical readout would permit the rapid and inexpensive detection and identification of bacterial pathogens and the analysis of human genes. A new assay developed for this purpose is described that harnesses an electrocatalytic process to monitor DNA hybridization.
    Type: Grant
    Filed: November 11, 2005
    Date of Patent: April 22, 2008
    Assignee: Trustees of Boston College
    Inventors: Shana O. Kelley, Melissa Lapierre-Devlin, Meaghan O'Keefe
  • Nucleic acid archiving
    Patent number: 7361471
    Abstract: This invention is directed to a process for tightly binding nucleic acid to solid phase and corresponding processes for the utilization thereof. Nucleic acid is bound to solid phase matrices exhibiting sufficient hydrophilicity and electropositivity to tightly bind the nucleic acids from a sample. These processes include nucleic acid (double or single stranded DNA and RNA) capture from high volume and/or low concentration specimens, buffer changes, washes, and volume reductions, and enable the interface of solid phase bound nucleic acid with enzyme, hybridization or amplification strategies. The tightly bound nucleic acid may be used, for example, in repeated analyses to confirm results or test additional genes in both research and commercial applications. Further, a method is described for virus extraction, purification, and solid phase amplification from large volume plasma specimens.
    Type: Grant
    Filed: May 18, 2006
    Date of Patent: April 22, 2008
    Assignee: Applera Corporation
    Inventors: John C. Gerdes, Jeffery M. Marmaro, Jeffrey T. Ives, Christopher A. Roehl
  • High-throughput methods of screening DNA for deletions and other mutations
    Patent number: 7354715
    Abstract: The subject invention relates to high-throughput methods of screening DNA for mutations. These methods offer various unexpected advantages over current methods. In a preferred embodiment, the subject invention includes pooling DNA samples from many plants that were subjected to mutagenesis. Methods of the subject invention include highly sensitive means for detecting individual mutants, preferably deletions, in large pools or collections of DNA samples.
    Type: Grant
    Filed: May 21, 2004
    Date of Patent: April 8, 2008
    Assignee: Dow AgroSciences LLC
    Inventors: Avutu Sambi Reddy, Max Otto Ruegger, James Patrick Connell, Thomas Skokut
  • Label free analysis of nucleic acids
    Patent number: 7354720
    Abstract: A method is provided for label free analysis of nucleic acid materials. In accordance with the present invention, a fluorescent material is provided having a certain fluorescence emission without nucleic acids attached thereto. The fluorescent material of the present invention, has a greater emission upon the binding of a single stranded nucleic acid and an even greater emission upon the binding of a double stranded nucleic acid allowing detection of double stranded binding without using a label attached to the DNA.
    Type: Grant
    Filed: December 20, 2005
    Date of Patent: April 8, 2008
    Assignee: Affymetrix, Inc.
    Inventors: Andrea Cuppoletti, Handong Li
  • RNA detection and quantitation
    Patent number: 7354716
    Abstract: The present invention is directed to a highly sensitive method for direct detection of at least one specific RNA in a sample. The presence of a specific RNA provides a positive indicator of a pathogenic agent, contaminant, and/or normal or abnormal genes in the sample. Applications for which the method of the invention is particularly well suited include point-of-care disease diagnosis, detection of microbial contamination in food and/or water supplies, and pathogen detection in biodefense.
    Type: Grant
    Filed: August 5, 2004
    Date of Patent: April 8, 2008
    Assignee: Georgia State University Research Foundation, Inc.
    Inventor: Zhen Huang
  • Systems and methods for detecting and analyzing polymers
    Patent number: 7351538
    Abstract: A detection system and methods for improving the ability of the detection system to recognize labels that are disposed on a polymer. Embodiments of the invention include schemes for selecting emitters and labels used within the system in a manner that allows an increase in the number of distinct labels that can be used together in a system. In other embodiments, the detection system and methods are directed to identifying portions of a detection signal that may be associated with extra labels residing within a detection zone. In other embodiments, the detection system and methods relate to using wide field imaging detectors while reducing out of focus noise contributions to detection signals of the system. Still, other embodiments relate to the use of linear array detectors to detect labels.
    Type: Grant
    Filed: August 23, 2005
    Date of Patent: April 1, 2008
    Assignee: U.S. Genomics
    Inventors: Martin Fuchs, John Harris, Ray Meyers