Patents Examined by Scott W. Houtteman
  • Patent number: 6613508
    Abstract: Tags and linkers specifically designed for a wide variety of nucleic acid reactions are disclosed, which are suitable for a wide variety of nucleic acid reactions wherein separation of nucleic acid molecules based upon size is required.
    Type: Grant
    Filed: July 22, 1997
    Date of Patent: September 2, 2003
    Assignee: Qiagen Genomics, Inc.
    Inventors: Jeffrey Van Ness, John C. Tabone, J. Jeffry Howbert, John T. Mulligan
  • Patent number: 6444428
    Abstract: Methods are provided for enhancing nucleic acid polymerase reactions. The methods comprise use of a polymerase and a polymerase enhancing composition.
    Type: Grant
    Filed: August 4, 2000
    Date of Patent: September 3, 2002
    Assignee: Stratagene
    Inventor: Holly Hogrefe
  • Patent number: 6410225
    Abstract: Compositions and methods are disclosed which facilitate purification of oligomers and other compounds. The disclosed compositions are silyl compositions that can be directly coupled, or coupled through a linking group, to a compound of interest, preferably to an oligomer at the end of oligomer synthesis. The silicon atom includes between one and three sidechains that function as capture tags. In one embodiment, the capture tags are lipophilic, which allows a derivatized oligomer to be separated from failure sequences by reverse phase chromatography. In another embodiment, the capture tags are compounds with a known affinity for other compounds, which other compounds are preferably associated with a solid support to allow chromatographic separation. Examples include haptens, antibodies, and ligands. Biotin, which can bind to or interact with a streptavidin-bound solid support, is a preferred capture tag of this type.
    Type: Grant
    Filed: June 27, 1997
    Date of Patent: June 25, 2002
    Assignees: Yale University, Ribozyme Pharmaceuticals, Inc.
    Inventor: Brian S. Sproat
  • Patent number: 6395524
    Abstract: The present invention provides a method for identifying a thermostable polymerase having altered fidelity. The method consists of generating a random population of polymerase mutants by mutating at least one amino acid residue of a thermostable polymerase and screening the population for one or more active polymerase mutants by genetic selection. For example, the invention provides a method for identifying a thermostable polymerase having altered fidelity by mutating at least one amino acid residue in an active site O-helix of a thermostable polymerase. The invention also provides thermostable polymerases and nucleic acids encoding thermostable polymerases having altered fidelity, for example, high fidelity polymerases and low fidelity polymerases. The invention additionally provides a method for identifying one or more mutations in a gene by amplifying the gene with a high fidelity polymerase.
    Type: Grant
    Filed: November 26, 1997
    Date of Patent: May 28, 2002
    Assignee: University of Washington
    Inventors: Lawrence A. Loeb, Leroy Hood, Motoshi Suzuki
  • Patent number: 6379553
    Abstract: Novel extracts, proteins, and complexes are identified, purified, and analyzed, which improve the polymerization activity of nucleic acid polymerases. Included within the aspects of the invention are methods for identifying compositions with a polymerase enhancing activity, methods for purifying and using these compositions, and specific extracts, proteins, and complexes that function to enhance polymerase activity. Implications for numerous assays and techniques are described. For example, the invention can be used to enhance polymerase activity in a PCR process and to increase the sensitivity of a PCR-based assay.
    Type: Grant
    Filed: August 4, 2000
    Date of Patent: April 30, 2002
    Assignee: Stratagene
    Inventor: Holly Hogrefe
  • Patent number: 6355418
    Abstract: A chimaeric oligonucleotide library for use in identifying an antisense binding site in a target mRNA, comprising a plurality of distinct chimaeric oligonucleotides capable of hybridizing to mRNA to form a duplex, the nucleotide sequences of which each have a common length of 7 to 20 bases and are generated randomly or generated from information characterizing the sequence of the target mRNA, wherein substantially all the nucleotide sequences of said common length which are present as sub-sequences in the target mRNA are present in the library, and wherein each nucleotide sequence comprises: a) a recognition region comprising a sequence of nucleotides which is recognizable by a duplex-cutting RNAase when hybridized to the mRNA, and b) a flanking region comprising a sequence of chemically-modified nucleotides which binds to the mRNA sufficiently tightly to stabilize the duplex for cutting of the mRNA in the duplex by the duplex-cutting RNAase, wherein the nucleotides constituting the flanking region are differ
    Type: Grant
    Filed: March 13, 1998
    Date of Patent: March 12, 2002
    Assignee: Xzillion GmbH & Co. KG
    Inventor: Gunter Schmidt
  • Patent number: 6348574
    Abstract: DNA sequences encoding seven novel seven transmembrane receptors and variants thereof are disclosed as well as materials and methods for production of the same by recombinant techniques. Antibody substances specific for each of the seven transmembrane receptors are disclosed as useful for the modulation of the ligand/receptor binding reactions of the receptors.
    Type: Grant
    Filed: June 1, 1998
    Date of Patent: February 19, 2002
    Assignee: ICOS Corporation
    Inventors: Ronald Godiska, Patrick W. Gray, Vicki Louise Schweickart
  • Patent number: 6344554
    Abstract: The present invention provides RBT1 polynucleotides, including RBT1 polynucleotides encoding Rbt1, and Rbt1 polypeptides, from Candida albicans. Expression of the RBT1 gene is upregulated by the inactivation of the TUP1 gene and by environmental conditions that induce filamentous growth. Disruption of TUP1 finction in C. albicans is associated with filament fonnation as well as low infectivity. These RBT1 polynucleotide and Rbtl polypeptide sequences (and anti-Rbt1 antibodies derived from Rbt1 polypeptides) may be used in methods of detecting C. albicans sequences in a biological sample. Further, the invention provides methods for screening agents which may control C. albicans virulence and compositions comprising these agents.
    Type: Grant
    Filed: October 1, 1998
    Date of Patent: February 5, 2002
    Assignee: Regents of the University of California
    Inventors: Alexander D. Johnson, Burkhard Braun
  • Patent number: 6344316
    Abstract: The present invention provides a simplified method for identifying differences in nucleic acid abundances (e.g., expression levels) between two or more samples. The methods involve providing an array containing a large number (e.g. greater than 1,000) of arbitrarily selected different oligonucleotide probes where the sequence and location of each different probe is known. Nucleic acid samples (e.g. mRNA) from two or more samples are hybridized to the probe arrays and the pattern of hybridization is detected. Differences in the hybridization patterns between the samples indicates differences in expression of various genes between those samples. This invention also provides a method of end-labeling a nucleic acid. In one embodiment, the method involves providing a nucleic acid, providing a labeled oligonucleotide and then enzymatically ligating the oligonucleotide to the nucleic acid. Thus, for example, where the nucleic acid is an RNA, a labeled oligoribonucleotide can be ligated using an RNA ligase.
    Type: Grant
    Filed: June 25, 1997
    Date of Patent: February 5, 2002
    Assignee: Affymetrix, Inc.
    Inventors: David J. Lockhart, Mark Chee, Kevin Gunderson, Lai Chaoqiang, Lisa Wodicka, Maureen T. Cronin, Danny Lee, Huu M. Tran, Hajime Matsuzaki
  • Patent number: 6337188
    Abstract: The present invention describes a novel nucleic acid sequencing reagent which consists of a capture moiety, a spacer region and a sequence specific hybridizing region of 4-8 bases. The nucleic acid sequencing reagent of the present invention can also contain an attachment moiety. The nucleic acid sequencing reagent can be arranged into a nested array. This array configuration can then be used to sequence a given template without prior knowledge (de novo) of the wild type or expected sequence in conjunction with primer extension in the presence of a labeled chain terminating nucleotide.
    Type: Grant
    Filed: August 25, 2000
    Date of Patent: January 8, 2002
    Assignee: Orchid BioSciences, Inc.
    Inventors: Steven R. Head, Philip Goelet, Jonathan Karn, Michael Boyce-Jacino
  • Patent number: 6335184
    Abstract: The extensive synthesis (“amplification”) of a nucleic acid sequence of interest is attained through a linked series of multi-cycle primer extension reactions (LLA). The primers used in each of the primer extension reactions of the process contain non-replicable and/or cleavable elements that halt nucleic acid synthesis and thereby prevent the synthesized molecules from serving as templates in subsequent cycles. Synthesized molecules accumulate during primer extension in a mathematically linear fashion, thereby rendering the process relatively insensitive to contaminating nucleic acids. Multiple primer sets are employed, and simultaneously included in the reaction mixture, thereby ensuring the accumulation of a large number of copies of the nucleic acid sequence of interest. The invention also provides for the detection of an amplified nucleic acid sequence of interest, as well as reagent kits for carrying out the reaction.
    Type: Grant
    Filed: January 11, 1999
    Date of Patent: January 1, 2002
    Assignee: Bio-Rad Laboratories, Inc.
    Inventors: Antonio Arevalo Reyes, Robert Bruce Wallace, Luis A. Ugozzoli
  • Patent number: 6335440
    Abstract: Novel linkers for linking a donor dye to an acceptor dye in an energy transfer fluorescent dye are provided. These linkers faciliate the efficient transfer of energy between a donor and acceptor dye in an energy transfer dye. One of these linkers for linking a donor dye to an acceptor dye in an energy transfer fluorescent dye has the general structure R21Z1C(O)R22R26 where R21 is a C1-5 alkyl attached to the donor dye, C(O) is a carbonyl group, Z1 is either NH, sulfur or oxygen, R22 is a substituent which includes an alkene, diene, alkyne, a five and six membered ring having at least one unsaturated bond or a fused ring structure which is attached to the carbonyl carbon, and R28 includes a functional group which attaches the linker to the acceptor dye.
    Type: Grant
    Filed: March 18, 1999
    Date of Patent: January 1, 2002
    Assignee: PE Corporation (NY)
    Inventors: Linda G. Lee, Sandra L. Spurgeon, Barnett Rosenblum
  • Patent number: 6333165
    Abstract: Methods are provided for identifying the presence or absence of compositions with polymerase-enhancing activity.
    Type: Grant
    Filed: August 4, 2000
    Date of Patent: December 25, 2001
    Assignee: Stratagene
    Inventor: Holly Hogrefe
  • Patent number: 6329146
    Abstract: The present invention provides methods for the determination of the structure of biomolecular targets, as well as the site and nature of the interaction between ligands and biomolecular targets. The present invention also provides methods for the determination of the relative affinity of a ligand for the biomolecular target it interacts with. Also provided are methods for screening ligand or combinatorial libraries of compounds against one or more than one biological target molecules. The methods of the invention also allow determination of the relative binding affinity of combinatorial and other compounds for a biomolecular target. The present invention further provides methods for the use of mass modifying tags for screening multiple biomolecular targets. In a preferred embodiment, ligands which have great specificity and affinity for molecular interaction sites on biomolecules, especially RNA can be identified.
    Type: Grant
    Filed: March 2, 1999
    Date of Patent: December 11, 2001
    Assignee: ISIS Pharmaceuticals, Inc.
    Inventors: Stanley T. Crooke, Richard Griffey, Steven Hofstadler
  • Patent number: 6326487
    Abstract: Novel oligonucleotide analogs of the formulae I and II in which A, B, D, R1, R2, T, U, V, W, X, Y, Z, a, b, m, m′, n and n′ have the meanings stated in the description, with valuable physical, biological and pharmacological properties, and a process for the preparation thereof are described. Application thereof relates to the use as inhibitors of gene expression (antisense oligonucleotides, ribozymes, sense oligonucleotides and triplex forming oligonucleotides), as probes for detecting nucleic acids and as aids in molecular biology.
    Type: Grant
    Filed: July 17, 1997
    Date of Patent: December 4, 2001
    Assignee: Aventis Pharma Deutschland GmbH
    Inventors: Anuschirwan Peyman, Eugen Uhlmann, Carolin Carolus
  • Patent number: 6326485
    Abstract: The present invention is directed to oligonucleotides used as amplification primers and assay probes for species-specific detection and identification of the protozoan Perkinsus in shellfish. The oligonucleotides are designed to preferentially hybridize to what has been found to be a species-unique sequence in the target organism's genome. Preferential hybridization means, for example, that the inventive primers amplify the target sequence in P. marinus with little or no detectable amplification of target sequences of other species of protozoa such as P. atlanticus thereby making the assay species specific.
    Type: Grant
    Filed: July 25, 1997
    Date of Patent: December 4, 2001
    Assignee: University of Maryland Biotechnology Institute
    Inventors: Gerardo Vasta, Adam G. Marsh, Joséto A. Fernández-Robledo, Cathleen A. Coss, Anita C. Wright
  • Patent number: 6326142
    Abstract: A method is described by which the association between an oligonucleotide labeled by attachment of a fluorophore and another macromolecule such as a protein or nucleic acid may be determined quantitatively in solution accurately and with high sensitivity. In the performance of this method the polarization of fluorescence of an extrinsic fluorescence probe that is covalently coupled to the oligonucleotide is determined. Changes in fluorescence polarization are related directly to the degree of association between the labeled oligonucleotide and another macromolecule and may be used to quantify the association. Because of its high sensitivity and accuracy, this method may be used to make reliable quantitative measurements of very small amounts of complexes formed between labeled oligonucleotides and proteins, nucleic acids or other macromolecules. The method also allows the accurate calculation of important biochemical parameters such as dissociation constants.
    Type: Grant
    Filed: February 18, 1998
    Date of Patent: December 4, 2001
    Assignee: PanVera Corporated
    Inventor: Catherine A. Royer
  • Patent number: 6322974
    Abstract: The present invention demonstrates that mitochondrial DNA damage occurs prior to, or simultaneous with, atherosclerotic lesion development, that aortic mitochondrial DNA damage increases with age, and that genotype and diet both influence the level of mitochondrial DNA damage. Hence, the present invention demonstrates that mitochondrial DNA damage occurs early in atherosclerosis, and may be an initiating event in atherogenesis, and provides methods to predict coronary atherosclerotic heart disease based upon the amount of mitochondrial DNA damage.
    Type: Grant
    Filed: January 14, 1999
    Date of Patent: November 27, 2001
    Assignee: Research Development Foundation
    Inventors: Marschall S. Runge, Scott W. Ballinger, Bennett VanHouten
  • Patent number: 6322966
    Abstract: The present invention relates to identification of the features of an RNA template that provide for efficient “copy-back” self-priming activity of hepatitis C virus replicase. This activity can be used to screen for anti-HCV replicase compounds, or to characterize the biological relevance of lead compounds that have already been identified. The specific features of the optimal RNA templates can be used for developing a system to characterize HCV NS5B polymerase mechanistically and kinetically, and for designing small RNA molecules to co-crystallize with HCV NS5B polymerase.
    Type: Grant
    Filed: May 11, 1999
    Date of Patent: November 27, 2001
    Inventors: Weidong Zhong, Zhi Hong, Johnson Y. N. Lau
  • Patent number: 6322968
    Abstract: The present invention describes a novel nucleic acid sequencing reagent which consists of a capture moiety, a spacer region and a sequence specific hybridizing region of 4-8 bases. The nucleic acid sequencing reagent of the present invention can also contain an attachment moiety. The nucleic acid sequencing reagent can be arranged into a nested array. This array configuration can then be used to sequence a given template without prior knowledge (de novo) of the wild type or expected sequence in conjunction with primer extension in the presence of a labeled chain terminating nucleotide.
    Type: Grant
    Filed: November 21, 1997
    Date of Patent: November 27, 2001
    Assignee: Orchid BioSciences, Inc.
    Inventors: Steven R. Head, Philip Goelet, Jonathan Karn, Michael Boyce-Jacino