Patents Represented by Attorney, Agent or Law Firm Scott R. Bortner
  • Patent number: 7897738
    Abstract: The present teachings relate to DNA polymerases that have an F667Y mutation as defined with respect to Taq DNA polymerase and exhibit reduced discrimination against labeled nucleotides into polynucleotides. The teachings also include kits comprising the subject DNA polymerases and numerous methods of using the subject DNA polymerases, including uses for chain termination sequencing and PCR. The present teachings relate to DNA polymerases that have an F667Y mutation as defined with respect to Taq DNA polymerase and exhibit reduced discrimination against labeled nucleotides into polynucleotides. The teachings also include kits comprising the subject DNA polymerases and numerous methods of using the subject DNA polymerases, including uses for chain termination sequencing and PCR.
    Type: Grant
    Filed: December 9, 2005
    Date of Patent: March 1, 2011
    Assignee: Applied Biosystems, LLC
    Inventors: John Brandis, Curtis Bloom, John H. Richards
  • Patent number: 7378260
    Abstract: The present invention provides products and methods of reducing dye artifacts from chain extension reactions.
    Type: Grant
    Filed: April 1, 2005
    Date of Patent: May 27, 2008
    Assignee: Applera Corporation
    Inventors: Michael P. Harrold, Kevin M. Hennessy, Aldrich N. K. Lau, Sean Matthew Desmond
  • Patent number: 7211385
    Abstract: The invention provides a method for reducing stutter in the amplification of a microsatellite comprising the steps of providing a sample comprising a microsatellite having a G+C content of 50% or less; contacting the sample with at least one enzyme having nucleic acid polymerase activity; and incubating the sample with the enzyme for a sufficient amount of time and under conditions sufficient to amplify the microsatellite; wherein the incubation is performed in the presence of an amount of betaine, sorbitol or mixtures thereof, effective to reduce stutter relative to the amount of stutter observed in the absence of betaine and/or sorbitol. The invention also provides compositions containing betaine and/or sorbitol, kits for amplifying microsatellites having a G+C content of 50% or less, and methods of using all of the foregoing.
    Type: Grant
    Filed: August 8, 2003
    Date of Patent: May 1, 2007
    Assignee: Applera Corporation
    Inventors: Sulekha Rao Coticone, Will Bloch
  • Patent number: 7153658
    Abstract: The present invention relates to methods and kits for detecting the presence or absence of (or quantitating) target nucleic acid sequences using ligation and amplification. The invention also relates to methods, reagents, and kits that employ addressable portions and labeled probes.
    Type: Grant
    Filed: September 19, 2003
    Date of Patent: December 26, 2006
    Assignee: Applera Corporation
    Inventors: Mark R. Andersen, Michael W. Hunkapiller, Kenneth J. Livak, Eugene G. Spier, H. Michael Wenz
  • Patent number: 7148340
    Abstract: The invention provides novel nucleic acid polymerases from strains GK24 and RQ-1 of Thermus thermophilus, and nucleic acids encoding those polymerases, as well as methods for using the polymerases and nucleic acids.
    Type: Grant
    Filed: November 22, 2002
    Date of Patent: December 12, 2006
    Assignee: Applera Corporation
    Inventors: James E. Rozzelle, Elena V. Bolchakova
  • Patent number: 7056668
    Abstract: A method is provided for purifying a desired polynucleotide product by removing unincorporated oligonucleotides from a polymerase or ligase reaction mixture.
    Type: Grant
    Filed: July 23, 2002
    Date of Patent: June 6, 2006
    Assignee: Applera Corporation
    Inventors: Lawrence Greenfield, Douglas A. Bost
  • Patent number: 7052877
    Abstract: The invention provides nucleic acids and polypeptides for nucleic acid polymerases from a thermophilic organism, Thermus brockianus. The invention also provides methods for using these nucleic acids and polypeptides.
    Type: Grant
    Filed: November 22, 2002
    Date of Patent: May 30, 2006
    Assignee: Applera Corporation
    Inventors: James E. Rozzelle, Elena V. Bolchakova
  • Patent number: 6821402
    Abstract: The invention relates to methods, compositions, and systems for calibrating a fluorescent polynucleotide separation apparatus. One aspect of the invention is multiple color calibration standards and their use. A multiple color calibration standard is a mixture of at least two polynucleotides of different length, wherein each of the polynucleotides is labeled with a spectrally distinct fluorescent dye. Another aspect of the invention is to produce total emission temporal profiles of multiple color calibration standards for use in calibrating fluorescent polynucleotide separation apparatus. The peaks corresponding to the fluorescently labeled polynucleotides in the total emission temporal profile may be detected using a peak detector that is driven by changes in the slopes of the total emission temporal profile.
    Type: Grant
    Filed: September 16, 1998
    Date of Patent: November 23, 2004
    Assignee: Applera Corporation
    Inventors: Muhammad A. Sharaf, Maria C. Roque-Biewer
  • Patent number: 6787310
    Abstract: The present invention provides methods and kits for isolating one strand of a double-stranded target nucleic acid. The method capitalizes on the differences in the kinetics and thermodynamic stabilities between conventional DNA/DNA, DNA/RNA and RNA/RNA duplexes and heteroduplexes in which one strand of the heteroduplexe is a nucleobase polymer having a net positively charged or net neutral backbone, such as a PNA.
    Type: Grant
    Filed: July 18, 2001
    Date of Patent: September 7, 2004
    Assignee: Applera Corporation
    Inventors: Claudia Chiesa, Gary P. Schroth, Michael Egholm
  • Patent number: 6783940
    Abstract: The invention provides methods for reducing non-specific amplification DNA in a polymerase chain reaction comprising providing a sample comprising a target DNA sequence of interest; contacting the sample with at least one enzyme having nucleic acid polymerase activity; and incubating the sample with said enzyme for a time and under conditions sufficient to amplify the target DNA sequence, forming amplified target sequence; wherein the incubation is performed in the presence of an amount of sorbitol, or sorbitol and DMSO effective to reduce the non-specific amplification relative to the amount of non-specific amplification observed in the absence of sorbitol, or sorbitol and DMSO. The methods are suitable for amplification of ribosomal DNA, particularly from clinical samples. Compositions and kits containing sorbitol, or sorbitol and DMSO for reducing non-specific amplification are also provided.
    Type: Grant
    Filed: October 31, 2001
    Date of Patent: August 31, 2004
    Assignee: Applera Corporation
    Inventors: Ian J. McLaughlin, Sulekha Rao Coticone, Will Bloch
  • Patent number: 6780588
    Abstract: The invention provides a method for reducing stutter in the amplification of a microsatellite comprising the steps of providing a sample comprising a microsatellite having a G+C content of greater than 50%; contacting the sample with at least one enzyme having nucleic acid polymerase activity; and incubating the sample with the enzyme for a sufficient amount of time and under conditions sufficient to amplify the microsatellite; wherein the incubation is performed in the presence of an amount of sorbitol effective to reduce stutter relative to the amount of stutter observed in the absence of sorbitol. The invention also provides compositions containing sorbitol, kits for amplifying microsatellites having a G+C content of greater than 50%, and methods of using all of the foregoing.
    Type: Grant
    Filed: May 7, 2001
    Date of Patent: August 24, 2004
    Assignee: Applera Corporation
    Inventors: Sulekha Rao Coticone, Will Bloch
  • Patent number: 6777189
    Abstract: One embodiment of the invention is a method of producing an oligonucleotide extended by a single nucleotide base. An oligonucleotide and an extension terminating nucleotide are mixed with an enzyme having terminal transferase activity. The reaction produces an oligonucleotide extended by a single base. The extended oligonucleotide may be used as a size standard for single base extension reactions. Another embodiment of the invention is a method of producing a mixture of oligonucleotides extended by different single bases. An oligonucleotide, a first extension terminating nucleotide, and a second extension terminating nucleotide are mixed with an enzyme having terminal transferase activity. The first and second extension terminating nucleotides comprise different nucleotide bases and are labeled with different labels. The identity of the different extension terminating nucleotides (and hence the extended oligonucleotides) may be ascertained by reference to the specific label incorporated.
    Type: Grant
    Filed: March 27, 2002
    Date of Patent: August 17, 2004
    Assignee: Applera Corporation
    Inventors: Dong Wei, Danielle Bishop
  • Patent number: 6514699
    Abstract: The invention relates to methods and compositions for simultaneously generating a plurality of polynucleotide sequencing ladders or PCR amplification products. Each sequencing ladder is generated from a recoverable primer, i.e., an oligonucleotide primer comprising a recovery tag. The recovery tag may be an oligonucleotide. Each sequencing ladder has a unique recovery tag. After the generation of the multiple sequencing ladders, the different sequencing ladders are separated from one another, i.e., purified, by binding to recovery tag binding compounds that have been immobilized on one or more solid supports. The recovery tag binding compounds are immobilized on the solid support in an addressable manner, i.e., the recovery tag binding compounds have distinct locations on the solid support. The binding of the sequencing ladders to the recovery tag binding compounds serves to separate the different polynucleotide sequencing ladders present in a given solution.
    Type: Grant
    Filed: June 13, 2000
    Date of Patent: February 4, 2003
    Assignee: PE Corporation (NY)
    Inventors: Roger A. O'Neill, Jer-Kang Chen, Claudia Chiesa, George Fry
  • Patent number: 6447777
    Abstract: Polymers and polymer conjugates comprising crosslinked Staphylococcal protein A, or crosslinked protein A-superantigen, or crosslinked functional derivatives thereof ranging in size from 12kDa to 1O,OOOkDa are useful in the treatment of autoimmune diseases, such as rheumatoid arthritis and ITP as well as neoplastic diseases. Compositions and pharmaceutical composition comprising chemically crosslinked polymers of protein A alone or protein A and bacterial enterotoxins, optionally further complexed with immunoglobulins and complement components, are disclosed, as are methods for making and using these compositions in the treatment of diseases. Plasma perfusates of protein A immunadsorbent columns in clinical use are shown to act through the leaching of polymers of protein A and protein A-Staphylococcal enterotoxin B having a broad range of molecular masses.
    Type: Grant
    Filed: March 28, 1997
    Date of Patent: September 10, 2002
    Inventors: David Stephen Terman, Raoul F. Reiser
  • Patent number: 6265193
    Abstract: The present invention relates to mutant DNA polymerases that exhibit reduced discrimination against labeled nucleotides into polynucleotides. The DNA polymerases of the invention have at least one mutation in the nucleotide label interaction region of the enzyme such the mutation results in reduced discrimination against labeled nucleotides. The nucleotide label interaction regions is located at portions of the O-helix, (ii) the K helix, and (iii) the inter O-P helical loop of Taq DNA polymerase or analogous positions in other DNA polymerases. In addition to providing novel mutant DNA polymerases, the invention also provides polynucleotides encoding the subject mutant DNA polymerases. The polynucleotides provided may comprise expression vectors for the recombinant production of the mutant polymerases. The invention also provide host cells containing the subject polynucleotides.
    Type: Grant
    Filed: March 12, 1998
    Date of Patent: July 24, 2001
    Assignees: PE Corporation (NY), California Institute of Technology
    Inventors: John Brandis, Curtis Bloom, John H. Richards
  • Patent number: 6258539
    Abstract: The present invention relate to methods and compositions for simultaneously analyzing multiple different polynucleotides of a polynucleotide composition comprising multiple diverse polynucleotide sequences. The subject methods and compositions may also be applied to analyze or identify single polynucleotides; however, the subject methods and compositions are particularly useful for analyzing large diverse populations of polynucleotides, e.g., cDNA libraries. Most embodiments of the invention involve hybridizing terminus probes (of known base sequence) to adapter-modified restriction fragment generated from polynucleotide for analysis, and subsequently joining the terminus probes and internal fragment probes to each other. The terminus probe hybridizes to bases of restriction endonuclease recognition site present at the terminus of a restriction fragment generated from the polynucleotide for analysis.
    Type: Grant
    Filed: April 30, 1999
    Date of Patent: July 10, 2001
    Assignee: The Perkin-Elmer Corporation
    Inventors: Michael W. Hunkapiller, John H. Richards
  • Patent number: 6232067
    Abstract: The present invention relate to methods and compositions for simultaneously analyzing multiple different polynucleotides of a polynucleotide composition comprising multiple diverse polynucleotide sequences. The subject methods and compositions may also be applied to analyze or identify single polynucleotides; however, the subject methods and compositions are particularly useful for analyzing large diverse populations of polynucleotides, e.g., cDNA libraries. Most embodiments of the invention involve hybridizing terminus probes (of known base sequence) and internal fragment probes (of known base sequence) at adjacent positions on an adapter-modified restriction fragment generated from polynucleotide for analysis, and subsequently joining the terminus probes and internal fragment probes to each other. The terminus probe hybridizes to bases of restriction endonuclease recognition site present at the terminus of a restriction fragment generated from the polynucleotide for analysis.
    Type: Grant
    Filed: August 17, 1998
    Date of Patent: May 15, 2001
    Assignee: The Perkin-Elmer Corporation
    Inventors: Michael W. Hunkapiller, John H. Richards
  • Patent number: 6168701
    Abstract: The invention relates to improved methods and compositions for loading samples into an analytical instrument having a plurality of sample receiving loading ports. In a principle embodiment of the invention, first and second sample markers are added to sample to be loaded onto an analytical instrument having a plurality of sample receiving loading ports. The first and second samples are compounds are selected so as to produce a distinctive signal upon combination thus a sample containing a first sample marker and a sample containing a second marker are mistakenly loaded into the same sample receiving loading port, a detectable signal indicative of the misloading is produced.
    Type: Grant
    Filed: April 30, 1999
    Date of Patent: January 2, 2001
    Assignee: The Perkins-Elmer Corporation
    Inventors: Shiaw-Min Chen, Cheryl R. Heiner, Adam L. Lowe
  • Patent number: 6124092
    Abstract: The invention relates to methods and compositions for simultaneously generating a plurality of polynucleotide sequencing ladders or PCR amplification products. Each sequencing ladder is generated from a recoverable primer, i.e., an oligonucleotide primer comprising a recovery tag. The recovery tag may be an oligonucleotide. Each sequencing ladder has a unique recovery tag. After the generation of the multiple sequencing ladders, the different sequencing ladders are separated from one another, i.e., purified, by binding to recovery tag binding compounds that have been immobilized on one or more solid supports. The recovery tag binding compounds are immobilized on the solid support in an addressable manner, i.e., the recovery tag binding compounds have distinct locations on the solid support. The binding of the sequencing ladders to the recovery tag binding compounds serves to separate the different polynucleotide sequencing ladders present in a given solution.
    Type: Grant
    Filed: June 12, 1997
    Date of Patent: September 26, 2000
    Assignee: The Perkin-Elmer Corporation
    Inventors: Roger A. O'Neill, Jer-Kang Chen, Claudia Chiesa, George Fry
  • Patent number: 6107061
    Abstract: The present invention relates to assays for the detection of nucleotide bases at predetermined locations on polynucleotides of interest. The embodiments of the invention include techniques relating to methods in which a primer extension reaction is designed to only extend a single nucleotide base. The invention, in part, relates to the improvement of adding corresponding non-labeled chain terminators to a primer extension reaction so as to increase the accuracy and reliability of nucleotide base determinations made by the assay. The invention is particularly useful when applied to assay methods in which the primer extension reaction is detected by a fluorescent dyes conjugated to chain terminators incorporated in the extension reactions. A first embodiment of the invention relates to methods for identifying a nucleotide base at the predetermined location on a polynucleotide of interest.
    Type: Grant
    Filed: September 18, 1999
    Date of Patent: August 22, 2000
    Assignee: The Perkin-Elmer Corporation
    Inventor: Martin D. Johnson