Patents Examined by Eggerton Campbell
  • Patent number: 6413723
    Abstract: The invention provides a method of identifying nucleic acid molecules that contain cis acting nucleic acid elements. Also provided is a method of isolating nucleic acid binding factors. The invention also provides methods of identifying compounds that are cis acting nucleic acid element analogs, compounds that are nucleic acid binding factor analogs, compounds that selectively bind cis acting nucleic acid elements and compounds that selectively displace binding between a nucleic acid binding factor and a cis acting nucleic acid element or between nucleic acid binding factors. Also provided is a method of determining a binding state of a nucleic acid. Pluralities of isolated nucleic acid molecules containing cis acting nucleic acid elements, of isolated cis acting nucleic acid elements and of isolated nucleic acid binding factors are also provided.
    Type: Grant
    Filed: September 1, 2000
    Date of Patent: July 2, 2002
    Assignee: Cistem Molecular Corporation
    Inventors: Stuart A. Kauffman, Marc Ballivet
  • Patent number: 6410277
    Abstract: A formulation and kit of thermostable or other DNA polymerases comprising at least one thermostable or other DNA polymerase which lacks 3′-exonuclease activity, and at least one thermostable DNA polymerase exhibiting 3′-exonuclease activity. Also provided is an improved method for enzymatic extension of DNA strands, especially while, but not limited to, amplifying nucleic acid sequences by polymerase chain reaction wherein the above formulation is made and used to catalyze primer extension.
    Type: Grant
    Filed: September 16, 1997
    Date of Patent: June 25, 2002
    Assignee: Takara Shuzo Co., Ltd.
    Inventor: Wayne M. Barnes
  • Patent number: 6410232
    Abstract: Novel FMCP polypeptides, proteins, and nucleic acid molecules are disclosed. In addition to isolated, full-length FMCP proteins, the invention further provides isolated FMCP fussion proteins, antigenic peptides and anti-FMCP antibodies. The invention also provides FMCP nucleic acid molecules, recombinant expression vectors containing a nucleic acid molecule of the invention, host cells into which the expression vectors have been introduced and non-human transgenic animals in which a FMCP gene has been introduced or disrupted. Diagnostic, screening and therapeutic methods utilizing compositions of the invention are also provided.
    Type: Grant
    Filed: March 12, 1999
    Date of Patent: June 25, 2002
    Assignee: Millennium Pharmaceuticals, Inc.
    Inventor: Douglas A. Holtzman
  • Patent number: 6410239
    Abstract: Methods are described for detecting protein-protein interactions, among two populations of proteins, each having a complexity of at least 100. Encoded proteins are fused either to the DNA-binding domain of a transcriptional activator or to the activation domain of a transcriptional activator. Two yeast strains, of the opposite mating type and carrying one type each of the fusion proteins are mated together. Productive interactions between the two halves due to protein-protein interactions lead to the reconstitution of the transcriptional activator, which in turn leads to the activation of a reporter gene containing a binding site for the DNA-binding domain. This analysis can be carried out for two or more populations of proteins.
    Type: Grant
    Filed: December 14, 1999
    Date of Patent: June 25, 2002
    Assignee: CuraGen Corporation
    Inventors: Krishnan Nandabalan, Jonathan Marc Rothberg, Meijia Yang, James Robert Knight, Theodore Samuel Kalbfleisch
  • Patent number: 6406854
    Abstract: Disclosed are methods and compositions for estimating the crossover point of a molecular separation system.
    Type: Grant
    Filed: September 14, 2000
    Date of Patent: June 18, 2002
    Assignee: MJ Research
    Inventor: Daniel E. Sullivan
  • Patent number: 6403308
    Abstract: This invention describes novel purified and isolated nucleic acid molecules or the fragments thereof, extracted from nematode or arthropod pests or recombinant, which encode P-glycoprotein homologs and regulate resistance to the macrocyclic lactone compounds. The invention further relates to the new P-glycoprotein homolog expression product of these nucleic acids. Also described herein are methods for detecting the gene encoding for resistance to the macrocyclic lactone compounds in nematode or arthropod pests which comprise comparing the nucleic acids extracted from a pest specimen to the nucleic acids encoding for resistance and the nucleic acids encoding for susceptibility to the macrocyclic lactone compounds.
    Type: Grant
    Filed: April 28, 1998
    Date of Patent: June 11, 2002
    Assignee: McGill University
    Inventors: Roger K. Prichard, Ming Xu, Ana Paula Ribeiro, William J. Blackhall, Robin N. Beech, Marcelo Molento, Hao Yuan Liu
  • Patent number: 6403320
    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: October 5, 2000
    Date of Patent: June 11, 2002
    Assignee: Affymetrix, Inc.
    Inventors: J. Leighton Read, Stephen P. A. Fodor, Lubert Stryer, Michael C. Pirrung
  • Patent number: 6401267
    Abstract: Disclosed are novel methods and compositions for rapid and highly efficient nucleic acid sequencing based upon hybridization with two sets of small oligonucleotide probes of known sequences. Extremely large nucleic acid molecules, including chromosomes and non-amplified RNA, may be sequenced without prior cloning or subcloning steps. The methods of the invention also solve various current problems associated with sequencing technology such as, for example, high noise to signal ratios and difficult discrimination, attaching many nucleic acid fragments to a surface, preparing many, longer or more complex probes and labelling more species.
    Type: Grant
    Filed: March 18, 1999
    Date of Patent: June 11, 2002
    Inventor: Radoje Drmanac
  • Patent number: 6399755
    Abstract: A human gene has been discovered which is genetically altered in human tumor cells. The genetic alteration is gene amplification and leads to a corresponding increase in gene products. Detecting that the gene, designated hMDM2, has become amplified or detecting increased expression of gene products is diagnostic of tumorigenesis. Human MDM2 protein binds to human p53 and allows the cell to escape from p53-regulated growth.
    Type: Grant
    Filed: October 13, 1998
    Date of Patent: June 4, 2002
    Assignee: The Johns Hopkins University
    Inventors: Kenneth W. Kinzler, Bert Vogelstein
  • Patent number: 6399334
    Abstract: The present invention relates generally to methods for producing normalized nucleic acid libraries in which each member of the library can be isolated with approximately equivalent probability. In particular, the present methods comprise subtractive hybridization of a nucleic acid library with haptenylated (e.g., biotinylated, avidinated or streptavidinated) nucleic acid molecules that are complementary to one or more of the nucleic acid molecules of the library, such that the variation in the abundances of the individual nucleic acid molecules in the library is reduced. The invention also relates to production of normalized nucleic acid libraries (particularly cDNA libraries) in which contaminating nucleic acid molecules have been reduced or eliminated, and to normalized nucleic acid libraries produced by such methods.
    Type: Grant
    Filed: September 23, 1998
    Date of Patent: June 4, 2002
    Assignee: Invitrogen Corporation
    Inventors: Wu-Bo Li, Paul E. Nisson, Joel Jessee
  • Patent number: 6391539
    Abstract: The invention concerns human papillomavirus (HPV) DNA and more particularly the probes derived from these papillomaviruses, as well as the methods of detecting HPV using these probes. These human papillomaviruses are designated as HPV-2d, HPV-10b, HPV-14a, HPV-14b, HPV-15, HPV-17a, HPV-17b, HPV-19, HPV-20, HPV-21, HPV-22, HPV-23, HPV-24, HPV-28, HPV-29, HPV-31, HPV-32, HPV-IP2 and HPV-IP4.
    Type: Grant
    Filed: September 22, 1997
    Date of Patent: May 21, 2002
    Assignees: Institut Pasteur, Institut National de la Sante Fe et de la Rechereche Medicale
    Inventors: Gerard Orth, Sylvie Beaudenon, Michel Favre, Dina Kremsdorf, Odile Croissant, Gerard Pehau-Arnaudet
  • Patent number: 6391548
    Abstract: The invention provides improved methods of introducing site-directed mutations into circular DNA molecules of interest by means of mutagenic primer pairs. The mutagenic primer pairs are also selected so as to be either completely complementary or partially complementary to each other, wherein the mutation site (or sites) is located within the region of complementarity. A mutagenic primer pair is annealed to opposite strands of a circular DNA molecule containing the DNA sequence to be mutagenized. After annealing, first and second mutagenized DNA strands, each incorporating a member of the mutagenic oligonucleotide primer pair is synthesized by a linear cyclic amplification reaction. After the linear cyclic amplification mediated synthesis step is completed, the reaction mixture is treated with a selection enzyme that digests the parental template strands. After the digesting step, a double-stranded circular DNA intermediate is formed.
    Type: Grant
    Filed: March 23, 1999
    Date of Patent: May 21, 2002
    Assignees: Stratagene, Children's Medical Center Corp.
    Inventors: John C. Bauer, Dowain A. Wright, Jeffrey Carl Braman, Raif S. Geha
  • Patent number: 6387623
    Abstract: Materials and methods are disclosed for identifying chemical compounds having desired binding properties towards a binding partner of pharmaceutical interest. The method employs transponders associated with the solid phase material used in the assay and a scanner to encode and decode data stored electronically on the transponder. The data stored on the transponder identifies the monomeric building blocks added during the synthesis. The structural identification of synthesized compounds bound to the solid phase is done by decoding the transponder.
    Type: Grant
    Filed: March 29, 2000
    Date of Patent: May 14, 2002
    Assignee: Pharmaseq
    Inventor: Wlodek Mandecki
  • Patent number: 6387628
    Abstract: A process for determining the identity of a target polypeptide using mass spectroscopy is provided. Depending on the target polypeptide to be identified, a process as disclosed can be used, for example, to diagnose a genetic disease or chromosomal abnormality, a predisposition to a disease or condition, or infection by a pathogenic organism; or for determining identity or heredity. Kits for performing the disclosed processes also are provided.
    Type: Grant
    Filed: September 18, 2000
    Date of Patent: May 14, 2002
    Assignee: Sequenom, Inc.
    Inventors: Daniel Little, Hubert Köster, G. Scott Higgins, David Lough
  • Patent number: 6383784
    Abstract: A nucleoprotein based nanoprocessor is described. The nanoprocessor includes one or more chimelic fusion proteins linked to a DNA scaffold. Both components of the fusion protein are enzymes.
    Type: Grant
    Filed: December 3, 1999
    Date of Patent: May 7, 2002
    Assignee: City of Hope
    Inventor: Steven S. Smith
  • Patent number: 6379899
    Abstract: Methods and compositions are provided for performing isothermal amplification of a nucleic acid target employing probes characterized by having a masked RNA polymer promoter unable to bind to a complementary initiator oligonucleotide and RNA polymerase and initiate transcription, a dsDNA sequence which when invaded by the target nucleic acid exposes the masked promoter to initiate transcription, and a template sequence, a portion of which is normally included in the dsDNA region, which when copied produces a product that can reinitiate the process of invading the dsDNA region and initiating transcription of another copy.
    Type: Grant
    Filed: March 13, 2001
    Date of Patent: April 30, 2002
    Assignee: Discoverx
    Inventors: Edwin Ullman, Ming Wu
  • Patent number: 6380369
    Abstract: The present invention discloses three human DNA repair proteins and DNA (RNA) encoding such proteins. The DNA repair proteins which may be produced by recombinant DNA techniques. One of the human DNA repair proteins, hMLH1, has been mapped to chromosome 3 while hMLH2 has been mapped to chromosome 2 and hMLH3 has been mapped to chromosome 7. The polynucleotide sequences of the DNA repair proteins may be used for diagnosis of a hereditary susceptibility to cancer.
    Type: Grant
    Filed: August 23, 1994
    Date of Patent: April 30, 2002
    Assignee: Human Genome Sciences, Inc.
    Inventors: Mark D. Adams, Robert D. Fleischmann, Claire M. Fraser, Rebecca A. Fuldner, Ewen F. Kirkness, William A. Haseltine, Craig A. Rosen, Steve Ruben, Ying-Fei Wei
  • Patent number: 6379898
    Abstract: This invention discloses methods, compositions and kits for the detection of extremely low levels of nucleic acid, cells and cellular material in biological samples. The nucleic acid detection systems utilize either the pyrophosphorolysis reaction catalyzed by various polymerases or nuclease digestion coupled with pyrophosphorylation catalyzed by phosphoribosylpyrophosphate synthetase to produce either deoxyribonucleoside triphosphates or ribonucleoside triphosphates. dNTPs are transformed to ATP by the action of nucleoside diphosphate kinase. The ATP produced by these reactions may be detected by luciferase or NADH based detection systems. If more sensitive detection is required, schemes for the amplification of NTPs and dNTPS are provided. A detection system for cells or cellular material in a sample is provided wherein AMP and a high energy phosphate donor added to a sample are converted to ATP by the action of endogenous enzymes, followed by detection of the ATP.
    Type: Grant
    Filed: January 9, 2001
    Date of Patent: April 30, 2002
    Inventors: John W. Shultz, Michelle A. Nelson, Donna M. Leippe, Martin K. Lewis, Lisa S. Nelson
  • Patent number: 6380370
    Abstract: The invention provides isolated polypeptide and nucleic acid sequences derived from Staphylococcus epidermidis that are useful in diagnosis and therapy of pathological conditions; antibodies against the polypeptides; and methods for the production of the polypeptides. The invention also provides methods for the detection, prevention and treatment of pathological conditions resulting from bacterial infection.
    Type: Grant
    Filed: August 13, 1998
    Date of Patent: April 30, 2002
    Assignee: Genome Therapeutics Corporation
    Inventors: Lynn A. Doucette-Stamm, David Bush
  • Patent number: 6379895
    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: September 1, 2000
    Date of Patent: April 30, 2002
    Assignee: Affymetrix, Inc.
    Inventors: Stephen P. A. Fodor, J. Leighton Read, Lubert Stryer, Michael C. Pirrung