Patents Examined by Gary Benzion
  • Biomolecule substrate, and test and diagnosis methods and apparatuses using the same
    Patent number: 7833701
    Abstract: An object of the present invention is to provide a test apparatus for testing a DNA substrate on which a plurality of DNA fragments for testing are arranged, wherein absolute precision is not required. The above-described problem was solved by providing a substrate on which a plurality of biomolecule spots containing a group of biomolecules (e.g., DNA, etc.) of a specific type are formed, where the pattern or position of the DNA spot is changed depending on specific data so that information of the specific data is recorded on the substrate.
    Type: Grant
    Filed: May 10, 2002
    Date of Patent: November 16, 2010
    Assignee: Panasonic Corporation
    Inventor: Mitsuaki Oshima
  • Cleavage of nucleic acids
    Patent number: 7829314
    Abstract: 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: Grant
    Filed: June 2, 2009
    Date of Patent: November 9, 2010
    Assignee: Third Wave Technologies, Inc.
    Inventors: James R. Prudent, Jeff G. Hall, Victor I. Lyamichev, Mary Ann D. Brow, James E. Dahlberg
  • Identification and quantification of a plurality of biological (micro)organisms or their components
    Patent number: 7829313
    Abstract: Disclosed is a system and method conducting real-time PCR. Capture molecules of a specific design are immobilized on a solid support, and contacted with amplicons produced in one or more PCR cycles. Detection of amplicons may take place during or between the PCR cycles while the solid support is in fluidic contact with the PCR solution. In an alternate embodiment detection of the amplicons takes place when the solid support is not in fluidic contact with the PCR solution. The method is suitable for the simultaneous detection and quantification of closely homologous target molecules.
    Type: Grant
    Filed: May 24, 2006
    Date of Patent: November 9, 2010
    Assignee: Eppendorf Array Technologies
    Inventors: Isabelle Alexandre, Sylvain Margaine, Dieter Husar, Nathalie Zammatteo, Heinz Koehn, José Remacle
  • Methods for relative quantification of specific nucleic acid sequences
    Patent number: 7829312
    Abstract: This invention relates generally to a method for quantifying the number of occurrences of a specific nucleic acid sequence within a nucleic acid sample in order to circumvent the shortcomings of the methods currently available and to provide reliable quantification of a specific nucleic acid sequence within a nucleic acid sample. The present invention provides a method of assessing an amount of a known target nucleic acid sequence in a sample comprising co-amplifying said target nucleic acid sequence and a known amount of a known control nucleic acid sequence to produce respective target and control amplicons, wherein said control nucleic acid sequence is different than said target nucleic acid sequence; and determining relative amounts of said respective amplicons by determining relative quantities of a primer extension reaction using each of said respective amplicons as a template.
    Type: Grant
    Filed: April 11, 2003
    Date of Patent: November 9, 2010
    Assignee: DNA Landmarks, Inc.
    Inventors: Martin Laforest, Nathalie Hubert, Benoît S. Landry
  • Method of error reduction in nucleic acid populations
    Patent number: 7820412
    Abstract: A method is disclosed for the direct synthesis of double stranded DNA molecules of a variety of sizes and with any desired sequence. The DNA molecule to be synthesis is logically broken up into smaller overlapping DNA segments. A maskless microarray synthesizer is used to make a DNA microarray on a substrate in which each element or feature of the array is populated by DNA of a one of the overlapping DNA segments. The complement of each segment is also made in the microarray. The DNA segments are released from the substrate and held under conditions favoring hybridization of DNA, under which conditions the segments will hybridize to form duplexes. The duplexes are then separated using a DNA binding agent which binds to improperly formed DNA helixes to remove errors from the set of DNA molecules. The segments can then be hybridized to each other to assemble the larger target DNA sequence.
    Type: Grant
    Filed: August 29, 2005
    Date of Patent: October 26, 2010
    Assignee: Wisconsin Alumni Research Foundation
    Inventors: Peter Jeremy Belshaw, Michael R. Sussman, Franco Cerrina, James Howard Kaysen, Brock F. Binkowski, Kathryn E. Richmond
  • Method of detecting target molecule by using aptamer
    Patent number: 7807351
    Abstract: An aptamer-probe complex for detecting the presence of a target molecule is disclosed. The complex of the present invention contains an aptamer moiety which is able to bind to an indicator protein and change the properties of the indicator protein, and a probe moiety which is able to bind to a target molecule, wherein the aptamer moiety and the probe moiety are combined in such a manner that the binding mode between the aptamer moiety and the indicator protein changes when the probe moiety binds to the target molecule. A target molecule can be detected with combination of an aptamer which binds to a certain protein, and a probe which binds to the target molecule, utilizing the properties of that protein as an indicator.
    Type: Grant
    Filed: November 22, 2004
    Date of Patent: October 5, 2010
    Assignee: Techno Medica Co., Ltd.
    Inventors: Koji Sode, Kazunori Ikebukuro
  • Labeled nucleotide composition
    Patent number: 7807356
    Abstract: Embodiments of labeled nucleotide compositions are described. Methods are described in which a sample containing RNA is contacted with an enzyme having an RNA ligation activity in the presence of a labeled nucleotide composition to provide labeled RNA. Methods of performing an array analysis of a labeled RNA sample are also described.
    Type: Grant
    Filed: March 9, 2006
    Date of Patent: October 5, 2010
    Assignee: Agilent Technologies, Inc.
    Inventors: Jeffrey R. Sampson, Hui Wang
  • Methods and kits for the detection of nucleotide mutations using peptide nucleic acid as both PCR clamp and sensor probe
    Patent number: 7803543
    Abstract: Disclosed herein is a method for determining whether a target polynucleotide sequence contained in a nucleic acid sample has nucleotide variation(s) in a selected region thereof, the steps of which involve the use of a pair of primers that allows the formation of a PCR product having a sequence covering that of the selected region of the target polynucleotide sequence via a PCR process, and a peptide nucleic acid (PNA) that acts as a PCR clamp as well as a sensor probe. Also disclosed herein is a kit for use in determining the presence of nucleotide variation(s) in the target polynucleotide sequence, which includes the pair of primers and the PNA.
    Type: Grant
    Filed: January 19, 2007
    Date of Patent: September 28, 2010
    Assignee: Chang Gung University
    Inventors: Chiuan-Chian Chiou, Ji-Dung Luo
  • Alkaline shock-based preparation of nucleic acids
    Patent number: 7803581
    Abstract: Method of preparing a biological sample appropriate for use in a subsequent in vitro nucleic acid amplification reaction. The method involves a rapid, transient exposure to alkaline conditions which can be achieved by mixing an alkaline solution with a pH-buffered solution that includes a detergent and the biological sample to be tested for the presence of particular nucleic acid species using in vitro amplification. The invented method advantageously can improve detection of some target nucleic acids without substantially compromising detectability of others. The method is particularly useful for simultaneously preparing RNA and DNA templates that can be used in multiplex amplification reactions.
    Type: Grant
    Filed: March 24, 2009
    Date of Patent: September 28, 2010
    Assignee: Gen-Probe Incorporated
    Inventors: Kui Gao, Michael M. Becker, Wen Wu, Jeffrey M. Linnen
  • Method for amplification of RNA sequences
    Patent number: 7794986
    Abstract: The invention relates to a method for amplification of a target RNA sequence, wherein the first primer comprises a hybridizing sequence of 7 to 14 nucleotides, which is capable of binding to a first segment of the target RNA sequence, a transcription enhancing sequence, and an anchor which is capable of binding to a second segment of the target RNA sequence, and/or wherein the second primer comprises a hybridizing sequence of 7 to 14 nucleotides, an amplification enhancing sequence and an anchor which is capable of binding to a second segment of the first single stranded cDNA. The invention further relates to primers for the amplification of target RNA sequences and to a kit comprising one or more of the primers.
    Type: Grant
    Filed: October 27, 2004
    Date of Patent: September 14, 2010
    Assignee: Biomerieux B.V.
    Inventors: Birgit Alberta Louisa Maria Deiman, Arnoldina Margaretha Wilhelmina Strijp
  • Template-dependent nucleic acid polymerization using oligonucleotide triphosphates building blocks
    Patent number: 7794984
    Abstract: A novel use of a template-dependent polymerase. The novel use is effected by employing the template-dependent polymerase for incorporating at least one oligonucleotide triphosphate onto a nascent oligonucleotide-3?-OH in a template-dependent manner.
    Type: Grant
    Filed: December 26, 2007
    Date of Patent: September 14, 2010
    Assignee: Yeda Research and Development Co. Ltd.
    Inventor: Hadar Kless
  • Amplification methods and compositions
    Patent number: 7790393
    Abstract: The present invention provides methods and routines for developing and optimizing nucleic acid detection assays for use in basic research, clinical research, and for the development of clinical detection assays. In particular, the present invention provides methods for designing oligonucleotide primers to be used in multiplex amplification reactions. The present invention also provides methods to optimize multiplex amplification reactions.
    Type: Grant
    Filed: July 16, 2008
    Date of Patent: September 7, 2010
    Assignee: Third Wave Technologies, Inc.
    Inventors: Victor I. Lyamichev, Andrew A. Lukowiak, Nancy Jarvis, David Kurensky
  • Genotyping by amplicon melting curve analysis
    Patent number: 7785776
    Abstract: Methods for analyzing a target nucleic acid are provided. A fluorescent label attached to a nucleic acid is incorporated into at least one strand of the target nucleic acid and the methods include monitoring change in fluorescence emission resulting from dissociation of the labeled strand of the amplification product from its complementary strand.
    Type: Grant
    Filed: May 8, 2003
    Date of Patent: August 31, 2010
    Assignees: Idaho Technology, Inc., University of Utah Research Foundation
    Inventors: Carl T. Wittwer, Cameron Gundry, Richard David Abbott, Derek Allen David
  • Methods for rapid identification of pathogens in humans and animals
    Patent number: 7781162
    Abstract: The present invention provides methods of: identifying pathogens in biological samples from humans and animals, resolving a plurality of etiologic agents present in samples obtained from humans and animals, determining detailed genetic information about such pathogens or etiologic agents, and rapid detection and identification of bioagents from environmental, clinical or other samples.
    Type: Grant
    Filed: September 11, 2003
    Date of Patent: August 24, 2010
    Assignee: Ibis Biosciences, Inc.
    Inventors: David J. Ecker, Richard H. Griffey, Rangarajan Sampath, Steven A. Hofstadler, John McNeil, Stanley T. Crooke
  • Micro-channel long molecule manipulation system
    Patent number: 7775368
    Abstract: Laminar flow of a carrier liquid and polymeric molecules through micro-channels is used to straighten, align, separate, and/or sort the polymeric molecules. The polymeric molecules may be analyzed and/or manipulated in the carrier liquid or attached to a wall of the micro-channel for subsequent treatment and analysis. Micro-channels can be manufactured using an elastic molding material. One micro-channel embodiment provides fluid flow using a standard laboratory centrifuge.
    Type: Grant
    Filed: October 17, 2003
    Date of Patent: August 17, 2010
    Assignee: Wisconsin Alumni Research Foundation
    Inventors: David Charles Schwartz, Eileen T. Dimalanta, Juan J. de Pablo
  • Methods for analysis of molecular events
    Patent number: 7776524
    Abstract: Methods and compositions are provided for detecting the presence of nucleic acid sequence variants in a subpopulation of nucleic acid molecules in a biological sample. These methods are particularly useful for identifying individuals with mutations indicative of cancer.
    Type: Grant
    Filed: February 18, 2003
    Date of Patent: August 17, 2010
    Assignee: Genzyme Corporation
    Inventors: Anthony P. Shuber, Lisa Kann, Duncan Whitney
  • Methods and compositions for generation of multiple copies of nucleic acid sequences and methods of detection thereof
    Patent number: 7771934
    Abstract: The present invention provides novel isothermal methods of generating multiple copies of, detecting and/or quantifying nucleic acid sequences of interest based on limited primer extension or attachment of oligonucleotide pairs using composite RNA/DNA primers. Methods for generating multiple copies of and/or detecting and/or quantifying nucleic acid sequences, wherein products of primer extension or attachment of oligonucleotide pairs comprising a cleavable portion are generated, and wherein cleavage of the products results in dissociation of cleaved products from target polynucleotides, are provided. The invention further provides compositions, kits and systems for practicing these methods.
    Type: Grant
    Filed: May 28, 2004
    Date of Patent: August 10, 2010
    Assignee: NuGEN Technologies, Inc.
    Inventor: Nurith Kurn
  • Homogeneous multiplex screening kits
    Patent number: 7771949
    Abstract: Kits for highly multiplexed homogeneous in vitro screening assays for numerous possible nucleic acid targets, any of which might be present in a sample, that utilize fluorescent hybridization probes that are combinatorially coded from a panel of fluorophores by subdividing each probe into portions and differently labeling each portion such that, when portions are combined, each probe has a unique code. The kits may include reagents and primers for target amplification and real-time detection.
    Type: Grant
    Filed: May 7, 2008
    Date of Patent: August 10, 2010
    Inventor: Fred R. Kramer
  • Localized temperature control for spatial arrays of reaction media
    Patent number: 7771933
    Abstract: Individual temperature control in multiple reactions performed simultaneously in a spatial array such as a multi-well plate is achieved by thermoelectric modules with individual control, with each module supplying heat to or drawing heat from a single region within the array, the region containing either a single reaction vessel or a group of reaction vessels.
    Type: Grant
    Filed: May 21, 2004
    Date of Patent: August 10, 2010
    Assignee: Bio-Rad Laboratories, Inc.
    Inventors: German Arciniegas, Jeff Ceremony, Daniel Y. Chu, Charles W. Ragsdale
  • Purification process for plasmid DNA
    Patent number: 7767399
    Abstract: Methods of isolating clinical-grade plasmid DNA from manufacturing processes, including large-scale fermentation regimes, are disclosed which encompass alternatives to two core unit operations common to plasmid DNA purification processes. The novel upstream and downstream purification processes disclosed herein provide for reduced production costs and increase process robustness. Either or both of the purification processes disclosed herein may be used in combination with additional purification steps known in the art that are associated with DNA plasmid purification technology.
    Type: Grant
    Filed: January 27, 2006
    Date of Patent: August 3, 2010
    Assignee: Merck & Co., Inc.
    Inventors: Jason C. Murphy, David B. Boyd, Adam Joel Kristopeit, Russel Jackson Lander, Michael Albert Winters