Patents Examined by Stephanie W. Zitomer
  • Patent number: 6743586
    Abstract: The present invention is a method of identifying ligands that interact will cellular processes involved in the life-cycle of HIV. In particular, an oligonucleotide, corresponding to specific RNA sequence within an infected cell, is modified by the substitution of 2-aminopurine. As a result, interactions between the oligonucleotide and the ligand can be measured via fluorescence. This technique can be use to find inhibitors of binding between rev and its response element (RRE), dimerization initiation sequences, and topoisomerases and DNA.
    Type: Grant
    Filed: October 25, 2001
    Date of Patent: June 1, 2004
    Assignee: The United States of America as represented by the Secretary of the Commerce
    Inventors: John P. Marino, James T. Stivers, Karen Lacourciere
  • Patent number: 6727070
    Abstract: Many proteins, when produced recombinantly, suffer from improper processing, folding and lack normal solubility. Modified proteins, including those indicative of disease states, also can have such defects. The present invention is directed to methods of identifying proper and improper protein folding, aberrant processing and/or insolubility. The method relies on the use of two components: a specialized fusion protein and structural complementation. The fusion protein contains sequences from the protein of interest and one portion of a marker protein that, by itself, is not active. A host cell then provides the remainder of the marker protein that serves to “complement” the function of the fused marker protein such that their association restores activity, permitting detection.
    Type: Grant
    Filed: January 31, 2001
    Date of Patent: April 27, 2004
    Assignees: The Board of Regents, The University of Texas System, The Trustees of Columbia University in the City of New York
    Inventors: Philip Jordan Thomas, John F. Hunt, William Christian Wigley, Rhesa D. Stidham
  • Patent number: 6716810
    Abstract: Described are methods and compositions for regulating body weight and/or regulating the rate of weight gain or loss, and particularly, for treating or preventing obesity. Specifically, methods of administering varying levels of circulating proopiomelanocortin peptides or analogs thereof to an animal, alone or in combination with leptin or other body weight regulating agents are disclosed. Methods and compositions for treating a variety of disorders associated with or caused by undesirable body weight are also described.
    Type: Grant
    Filed: December 9, 1999
    Date of Patent: April 6, 2004
    Assignees: Eleanor Roosevelt Institute, Oklahoma Medical Research Foundation
    Inventors: Miles B. Brennan, Ute Hochgeschwender
  • Patent number: 6706479
    Abstract: A method detects binding of molecules, advantageously without tagging molecules in the sample. A sensor is used in which is included a single stranded nucleic acid sequence and a photoluminescent material in respective layers. After the sensor is exposed to a biological sample for sufficient time for its single stranded nucleic acid sequence to bind to a material of interest, photoluminescence from the sensor can be measured. An apparatus for tagging-free detection of binding of molecules also is provided. Methods of making tagging-free sensors are provided. Also, tagging-free methods to detect binding of antigens and related devices are disclosed.
    Type: Grant
    Filed: June 1, 2001
    Date of Patent: March 16, 2004
    Assignee: Virginia Tech Intellectual Properties, Inc.
    Inventors: Ravi F. Saraf, Sanjun Niu
  • Patent number: 6696252
    Abstract: Methods are described for the identification and preparation of nucleic acid ligand ligands to vascular endothelial growth factor (VEGF). Included in the invention are specific RNA ligands to VEGF identified by the SELEX method.
    Type: Grant
    Filed: May 18, 2001
    Date of Patent: February 24, 2004
    Assignee: Gilead Sciences, Inc.
    Inventors: Larry Gold, Nebojsa Janjic
  • Patent number: 6653071
    Abstract: A method of identifying cellular regulatory circuits which employ at least one component of a subcomplex of regulatory proteins within the RNA II polymerase holoenzyme which behaves as a signal processor for gene-specific regulators (at least one component of a eukaryotic transcription initiation apparatus) and of determining the set of components of the apparatus which are responsible for regulation of each gene and the set of genes which are coordinately controlled by each transcription factor.
    Type: Grant
    Filed: June 4, 1999
    Date of Patent: November 25, 2003
    Assignee: Whitehead Institute for Biomedical Research
    Inventors: Frank C. P. Holstege, Richard A. Young
  • Patent number: 6653072
    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: June 24, 1999
    Date of Patent: November 25, 2003
    Assignee: Maxygen, Inc.
    Inventors: Phillip A. Patten, Willem P. C. Stemmer
  • Patent number: 6639060
    Abstract: A DNA fragment distinct from the epidermal growth factor receptor (EGFR) and erbB-2 genes was detected by reduced stringency hybridization of v-erbB to normal genomic human DNA. Characterization of the cloned DNA fragment mapped the region of v-erbB homology to three exons with closest homology of 64% and 67% to a contiguous region within the tyrosine kinase domains of the EGFR and erbB-2 proteins, respectively. cDNA cloning revealed a predicted 148 kd transmembrane polypeptide with structural features identifying it as a member of the erbB family, prompting designation of the new gene as erbB-3. It was mapped to human chromosome 12q11-13 and was shown to be expressed as a 6.2 kb transcript in a variety of normal tissues of epithelial origin. Markedly elevated erbB-3 mRNA levels were demonstrated in certain human mammary tumor cell lines. These findings indicate that increased erbB-3 expression, as in the case of EGFR and erbB-2, plays a role in some human malignancies.
    Type: Grant
    Filed: October 13, 1998
    Date of Patent: October 28, 2003
    Assignee: The United States of America as represented by the Department of Health and Human Services
    Inventors: Matthias H. Kraus, Stuart A. Aaronson
  • Patent number: 6627456
    Abstract: Improvements are disclosed for in vitro selection methods that yield ligands and catalysts through partitioning libraries of oligonucleotides. These improvements all increase the diversity and amount of fuctionality available to the oligonucleotides, by incorporating into the oligonucleotide libraries non-standard nucleobase analogs and/or functionalized standard nucleobases, and/or incorporating into the selection mixture organic cofactors that deliver functional groups by binding non-covalently to oligonucleotides in the library.
    Type: Grant
    Filed: October 12, 1999
    Date of Patent: September 30, 2003
    Inventor: Steven Albert Benner
  • Patent number: 6613514
    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: April 27, 2000
    Date of Patent: September 2, 2003
    Assignee: Maxygen, Inc.
    Inventors: Phillip A. Patten, Willem P. C. Stemmer
  • Patent number: 6599707
    Abstract: The present invention provides methods of identifying hot-spot residues for one or both members of a receptor-ligand complex of interest. Further provided are methods of using receptor hot-spot residues to identify compounds that functionally bind a receptor in a manner that mimics the binding of a known ligand for the receptor.
    Type: Grant
    Filed: September 10, 1999
    Date of Patent: July 29, 2003
    Assignee: ExSAR Corporation
    Inventor: Virgil L. Woods, Jr.
  • Patent number: 6582908
    Abstract: The present invention provides a number of oligonucleotide sequences which can be used for a wide variety of analyses applicable to the diverse fields impacted by the nature of molecular interaction, including chemistry, biology, medicine, and medical diagnostics. In certain embodiments these oligonucleotides may be used as probes to be used in, for example, gene expression analysis.
    Type: Grant
    Filed: March 6, 2000
    Date of Patent: June 24, 2003
    Assignee: Affymetrix, Inc.
    Inventors: Stephen P.A. Fodor, Dennis W. Solas, William J. Dower, Xiaohua C. Huang
  • Patent number: 6576424
    Abstract: The present invention provides methods and apparatus for sequencing, fingerprinting and mapping biological macromolecules, typically biological polymers. The methods make use of a plurality of sequence specific recognition reagents which can also be used for classification of biological samples, and to characterize their sources.
    Type: Grant
    Filed: January 25, 2001
    Date of Patent: June 10, 2003
    Assignee: Affymetrix Inc.
    Inventors: Stephen P. A. Fodor, Dennis W. Solas, William J. Dower
  • Patent number: 6569620
    Abstract: The present invention includes a method and device for performing automated SELEX. The steps of the SELEX process are performed at one or more work stations on a work surface by a cartesian robotic manipulator controlled by a computer.
    Type: Grant
    Filed: January 19, 1999
    Date of Patent: May 27, 2003
    Assignee: SomaLogic, Inc.
    Inventors: Larry Gold, Dominic A. Zichi, Robert D. Jenison, Daniel J. Schneider
  • Patent number: 6569630
    Abstract: The present invention concerns methods of preparing nucleic acid ligands against anthrax spores, compositions comprising anthrax specific nucleic acid ligands and methods of use of such ligands for detection and/or neutralization of anthrax spores.
    Type: Grant
    Filed: October 15, 2001
    Date of Patent: May 27, 2003
    Assignee: Conceptual MindWorks, Inc.
    Inventors: Jeevalatha Vivekananda, Johnathan L. Kiel
  • Patent number: 6551778
    Abstract: Nucleic acid sequences for detecting the presence of nucleic acids, particularly mRNA, encoding human prostate-associated genetic markers encoding prostate-specific antigen (PSA), prostate specific membrane antigen (PSMA) or human kallikrein 2 (hK2) are disclosed. Preferred combinations of nucleic acid sequences amplifying and detecting the prostate-associated genetic markers RNA, used in methods that include amplification of the target sequences and detection of the amplified sequences are disclosed. Methods of detecting the presence of prostate-associated genetic marker nucleic acids, particularly mRNA, in a biological sample of non-prostate origin are disclosed.
    Type: Grant
    Filed: January 28, 2000
    Date of Patent: April 22, 2003
    Assignee: Gen-Probe Incorporated
    Inventors: Richard C. Harvey, Thomas J. Clark, Jr.
  • Patent number: 6534265
    Abstract: A nucleic acid sequence encoding for oryzacystatin-I peptides and a signal peptide therefore is provided. The oryzacystatin-I peptide is approximately 12.6 kDa, and is approximately twelve amino acid residues longer than previously described oryzacystatin-I peptides. The nucleic acid sequences may be cloned into vectors, and used to transform plants conferring resistance to plant pests, including insects and nematodes, that utilize cysteine proteases, and to viruses with processing mechanisms involving cysteine proteases.
    Type: Grant
    Filed: February 15, 2000
    Date of Patent: March 18, 2003
    Assignee: New Mexico State University Technology Transfer Corporation
    Inventors: James S. Womack, Jennifer J. Randall, John D. Kemp
  • Patent number: 6528266
    Abstract: The present invention provides for the selective covalent modification of nucleic acids with redox active moieties such as transition metal complexes. Electron donor and electron acceptor moieties are covalently bound to the ribose-phosphate backbone of a nucleic acid at predetermined positions The resulting complexes represent a series of new derivatives that are bimolecular templates capable of transferring electrons over very large distances at extremely fast rates. These complexes possess unique structural features which enable the use of an entirely new class of bioconductors and photoactive probes.
    Type: Grant
    Filed: April 30, 2001
    Date of Patent: March 4, 2003
    Assignee: California Institute of Technology
    Inventors: Thomas J. Meade, Jon Faiz Kayyem, Scott E. Fraser
  • Patent number: 6521745
    Abstract: An isolated and purified nucleic acid molecule encoding an inclusion membrane protein C of a strain of Chlamydia, is useful for nucleic acid immunization of a host, including a human host, against disease caused by infection by a strain of Chlamydia, particularly C. pneumoniae.
    Type: Grant
    Filed: August 20, 1999
    Date of Patent: February 18, 2003
    Assignee: Aventis Pasteur Limited
    Inventors: Andrew D. Murdin, Pamela L. Dunn, Raymond P. Oomen
  • Patent number: 6518026
    Abstract: This invention relates to a method of incorporating an exo-sample nucleotide into the amplified product strands resulting from a nucleic acid amplification process. Once the product strands have been obtained and analyzed (e.g., by hybridization, Southern blot, etc.), the exo-sample strands can be selectively destroyed by acting on the incorporated exo-sample nucleotide. Two embodiments are presented. In a first embodiment, the exo-sample nucleotide is incorporated by carrying out the amplification reaction in the presence of an excess of exo-sample nucleotide triphosphate. In a second embodiment, the exo-sample nucleotide is incorporated by carrying out the amplification reaction in the presence of an oligonucleotide which has, as part of its sequence, one or more exo-sample nucleotides.
    Type: Grant
    Filed: February 14, 2001
    Date of Patent: February 11, 2003
    Assignee: Invitrogen Corporation
    Inventor: James L. Hartley