Patents Examined by Ethan Whisenant
  • Hybridization and mismatch discrimination using oligonucleotides conjugated to minor groove binders
    Patent number: 7794945
    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: July 14, 2008
    Date of Patent: September 14, 2010
    Assignee: Elitech Holding B.V.
    Inventors: Joel Hedgpeth, Irina A. Afonina, Igor V. Kutyavin, Eugeny A. Lukhtanov, Evgeniy S. Belousov, Rich B. Meyer, Jr.
  • Methods and compositions for cellular and metabolic engineering
    Patent number: 7795030
    Abstract: The present invention is generally directed to the evolution of new metabolic pathways and the enhancement of bioprocessing through a process herein termed recursive sequence recombination. Recursive sequence recombination entails performing iterative cycles of recombination and screening or selection to “evolve” individual genes, whole plasmids or viruses, multigene clusters, or even whole genomes. Such techniques do not require the extensive analysis and computation required by conventional methods for metabolic engineering.
    Type: Grant
    Filed: January 28, 2008
    Date of Patent: September 14, 2010
    Assignee: Maxygen, Inc.
    Inventors: Jeremy Minshull, Willem P. C. Stemmer
  • Method for creating polynucleotide and polypeptide sequences
    Patent number: 7790381
    Abstract: The invention provides methods for evolving a polynucleotide toward acquisition of a desired property. Such methods entail incubating a population of parental polynucleotide variants under conditions to generate annealed polynucleotides comprising heteroduplexes. The heteroduplexes are then exposed to a cellular DNA repair system to convert the heteroduplexes to parental polynucleotide variants or recombined polynucleotide variants. The resulting polynucleotides are then screened or selected for the desired property.
    Type: Grant
    Filed: December 7, 2006
    Date of Patent: September 7, 2010
    Assignee: California Institute of Technology
    Inventors: Frances Arnold, Zhixin Shao, Alexander Volkov
  • Method for analyzing nucleic acid
    Patent number: 7790368
    Abstract: A method is provided for analyzing nucleic acid comprising the steps of extracting, amplifying and detecting the nucleic acid of interest, wherein one or more internal control nucleic acids which can be detected and discriminated from the nucleic acid of interest are added for each step to a sample prior to the performance of each step, and the success or failure of each step is judged from the detection results obtained for the respective internal control nucleic acids in the detection step. The internal control nucleic acids added prior to each step can be discriminated from each other.
    Type: Grant
    Filed: September 22, 2000
    Date of Patent: September 7, 2010
    Assignee: Hitachi, Ltd.
    Inventor: Shinichi Fukuzono
  • Abasic site endonuclease assay
    Patent number: 7790385
    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: Grant
    Filed: June 28, 2007
    Date of Patent: September 7, 2010
    Assignee: Elitech Holding B.V.
    Inventors: Igor V. Kutyavin, David Milesi, Merl F. Hoekstra
  • Detection of oligonucleotides by dual hybridization
    Patent number: 7785784
    Abstract: The invention provides methods and compositions for detecting and/or quantifying modified nucleic acid oligonucleotides. These methods and compositions are useful for detecting and quantifying diagnostic and/or therapeutic synthetic modified oligonucleotides, such as aptamers, RNAi, siRNA, antisense oligonucleotides or ribozymes in a biological sample.
    Type: Grant
    Filed: July 21, 2005
    Date of Patent: August 31, 2010
    Assignee: Eyetech, Inc.
    Inventors: David T. Shima, Pericles Calias, Gregory S. Robinson, John P. Wing, Lori M. Mullin, Lillian M. Smith, Ervin Sinani
  • Methods and compositions for polypeptide engineering
    Patent number: 7776598
    Abstract: Methods are provided for the evolution of proteins of industrial and pharmaceutical interest, including methods for effecting recombination and selection. Compositions produced by these methods are also disclosed.
    Type: Grant
    Filed: February 5, 2008
    Date of Patent: August 17, 2010
    Assignee: Maxygen, Inc.
    Inventors: Phillip A. Patten, Willem P. C. Stemmer
  • Methods and compositions for rapid light-activated isolation and detection of analytes
    Patent number: 7771947
    Abstract: The present invention relates to novel methods for isolating a target molecule from a sample suspected of containing the target molecule. The methods of the present invention utilize solid substrates as a means for capturing, separating, and releasing target molecules, such as chemical or biological compounds. The present invention is specifically directed to novel approaches for capturing, separating and releasing such target molecules.
    Type: Grant
    Filed: February 20, 2008
    Date of Patent: August 10, 2010
    Assignee: Investigen, Inc.
    Inventors: Rachel Anne Holmes-Davis, Heather Koshinsky, Miaomiao Wang, Brian David Warner
  • Compositions for detection of a target nucleic acid sequence
    Patent number: 7767396
    Abstract: The invention relates to compositions for generating a signal indicative of the presence of a target nucleic acid in a sample, where the compositions include a probe having a 5? region and a 3? flap and a P. furiosus polymerase having 3? exonuclease activity.
    Type: Grant
    Filed: May 25, 2006
    Date of Patent: August 3, 2010
    Assignee: Hologic, Inc.
    Inventor: Joseph A. Sorge
  • Method for assessing cancerous state
    Patent number: 7763422
    Abstract: The present invention relates to a method for assessing a cancerous state of a mammal-derived specimen, which comprises: (1) a first step of measuring a methylation frequency of Fibrillin2 gene contained in a mammal-derived specimen or an index value having the correlation therewith, and (2) a second step of determining a cancerous state of the specimen based on a difference obtained by comparing the measured methylation frequency or the index value having the correlation therewith, with a control; and the like.
    Type: Grant
    Filed: September 15, 2004
    Date of Patent: July 27, 2010
    Assignees: Sumitomo Chemical Company, Limited, Japan as Represented by President of National Cancer Center
    Inventors: Toshikazu Ushijima, Atsushi Hagihara
  • Method for obtaining subtraction polynucleotide
    Patent number: 7749707
    Abstract: The present invention provides a method for obtaining or amplifying a polynucleotide (a tester-specific polynucleotide), in which an amount existing in a sample (tester) is larger than the amount existing in another sample (driver), easily and within a short time as well as with high efficiency, a polynucleotide obtained (amplified) by such method, a method for identifying gene mutation in the tester, and a kit to be used in such methods.
    Type: Grant
    Filed: February 27, 2006
    Date of Patent: July 6, 2010
    Assignee: Wako Pure Chemical Industries, Ltd.
    Inventor: Yukinobu Hayashida
  • Method for identifying the sequence of one or more variant nucleotides in a nucleic acid molecule
    Patent number: 7749708
    Abstract: The invention relates to methods for identifying the sequence of one or more variant nucleotides in a nucleic acid molecule. The method involves cleaving a double-stranded nucleic acid molecule containing a mismatch with a mismatch-specific endonuclease which cleaves on the 3? side of the mismatch, and preserving the integrity of the variant nucleotide by ligating a double-stranded linker with a 3?-overhang to said variant nucleotide. Because the variant nucleotide is immediately adjacent to the linker, PCR and/or sequence-by-synthesis analysis can be readily carried out.
    Type: Grant
    Filed: September 12, 2007
    Date of Patent: July 6, 2010
    Assignee: Transgenomic, Inc.
    Inventors: Paul D. Taylor, Gary F. Gerard, Reyes Candau
  • Methods for sequencing of a necleic acid
    Patent number: 7745129
    Abstract: Improved labeled molecule probes for use in biomedical applications including the sequencing of nucleic acid molecules and methods and apparatuses for their use are detailed. Labeled-probe-assemblies, comprising a probe element, for binding to a target molecule, attached to a label-assembly further comprising a linear series of information encoded structures and means for spatially separating these structures, are presented together with methods for extending the label assemblies such that the information encoded structures can be individually resolved, substantially simultaneously, by a readout device.
    Type: Grant
    Filed: July 11, 2007
    Date of Patent: June 29, 2010
    Inventor: Kenneth David Schatz
  • Hybridization method
    Patent number: 7745124
    Abstract: A hybridization method is provided in which an efficient hybridization reaction can be carried out. Further, there are provided, using this hybridization method, a method for detecting a target gene with high sensitivity and a signal amplifying method for markedly improving the detection sensitivity of the target gene. There is provided a hybridization method comprising the use of oligonucleotides in a reaction solution, the method comprising forming partially a reaction temperature region in the reaction solution and performing a hybridization reaction in the reaction temperature region.
    Type: Grant
    Filed: April 28, 2005
    Date of Patent: June 29, 2010
    Assignee: Eisai R&D Management Co., Ltd.
    Inventors: Chikako Hakii, Mitsugu Usui
  • Methods of detection of a target nucleic acid sequence
    Patent number: 7736854
    Abstract: The present invention is directed to methods of generating a signal indicative of the presence of a target nucleic acid in a sample by forming a cleavage structure comprising duplex and single-stranded nucleic acid by incubating a sample comprising a target nucleic acid with a thermostable nucleic acid polymerase substantially lacking 5? to 3? exonuclease activity and cleaving said cleavage structure with a thermostable Fen nuclease lacking 5? to 3? synthetic activity to generate a signal.
    Type: Grant
    Filed: November 29, 2006
    Date of Patent: June 15, 2010
    Assignee: Hologic, Inc.
    Inventor: Joseph A. Sorge
  • Methods for detection of genetic disorders
    Patent number: 7727720
    Abstract: The invention provides a method useful for detection of genetic disorders. The method comprises determining the sequence of alleles of a locus of interest, and quantitating a ratio for the alleles at the locus of interest, wherein the ratio indicates the presence or absence of a chromosomal abnormality. The present invention also provides a non-invasive method for the detection of chromosomal abnormalities in a fetus. The invention is especially useful as a non-invasive method for determining the sequence of fetal DNA. The invention further provides methods of isolation of free DNA from a sample.
    Type: Grant
    Filed: August 26, 2005
    Date of Patent: June 1, 2010
    Assignee: Ravgen, Inc.
    Inventor: Ravinder S. Dhallan
  • Detection of HIV-1 by nucleic acid amplification
    Patent number: 7723040
    Abstract: Nucleic acid sequences and methods for detecting HIV-1 nucleic acid (LTR and pol sequences) in biological samples by detecting amplified nucleic acids are disclosed. Kits comprising nucleic acid oligomers for amplifying HIV-1 nucleic acid present in a biological sample and detecting the amplified nucleic acid are disclosed.
    Type: Grant
    Filed: September 4, 2008
    Date of Patent: May 25, 2010
    Assignee: Gen-Probe Incorporated
    Inventors: Gary G. Bee, Yeasing Y. Yang, Dan Kolk, Cristina Giachetti, Sherrol H. McDonough
  • Methods for detection of genetic disorders
    Patent number: 7718370
    Abstract: The invention provides a method useful for detection of genetic disorders. The method comprises determining the sequence of alleles of a locus of interest, and quantitating a ratio for the alleles at the locus of interest, wherein the ratio indicates the presence or absence of a chromosomal abnormality. The present invention also provides a non-invasive method for the detection of chromosomal abnormalities in a fetus. The invention is especially useful as a non-invasive method for determining the sequence of fetal DNA. The invention further provides methods of isolation of free DNA from a sample.
    Type: Grant
    Filed: December 28, 2006
    Date of Patent: May 18, 2010
    Assignee: Ravgen, Inc.
    Inventor: Ravinder S. Dhallan
  • Device, kit and method for pulsing biological samples with an agent and stabilising the sample so pulsed
    Patent number: 7700276
    Abstract: The present invention is related to a device, kit and method for pulsing a biological sample with a pulsing agent and subsequently stabilizing the biological sample so pulsed. The invention has application in the fields of medical diagnostics, particularly relating to immunity.
    Type: Grant
    Filed: July 10, 2003
    Date of Patent: April 20, 2010
    Assignee: Universite Libre de Bruxelles
    Inventors: Patrick Stordeur, Michel Goldman
  • Method for quantifying biomolecules conjugated to a nanoparticle
    Patent number: 7682789
    Abstract: Disclosed embodiments concern quantifying a biomolecule conjugated to a nanoparticle. Quantifying typically comprises determining the number of biomolecules per nanoparticle. Any suitable biomolecule can be used, including but not limited to, amino acids, peptides, proteins, haptens, nucleic acids, oligonucleotides, DNA, RNA, and combinations thereof. A single type of biomolecule may be conjugated to the nanoparticle, more than one biomolecule of a particular class may be conjugated to the nanoparticle, or two or more classes of biomolecules may be conjugated to the nanoparticle. Certain disclosed embodiments comprise enzymatically or chemically digesting a biomolecule conjugated to the nanoparticle, or displacing a biomolecule using ligand-exchange chemistry.
    Type: Grant
    Filed: May 4, 2007
    Date of Patent: March 23, 2010
    Assignee: Ventana Medical Systems, Inc.
    Inventors: Xiao-Bo Chen, Christopher Bieniarz, Michael Farrell