Patents Represented by Attorney Stephen C. Macevicz
  • Patent number: 5856093
    Abstract: The invention provides a method of nucleic acid sequence analysis based on repeated cycles of ligation to and cleavage of probes at the terminus of a target polynucleotide. At each such cycle one or more terminal nucleotides are identified and one or more nucleotides are removed from the end of the target polynucleotide, such that further cycles of ligation and cleavage can take place. At each cycle the target sequence is shortened by one or more nucleotides until the nucleotide sequence of the target polynucleotide is determined. The method obviates electrophoretic separation of similarly sized DNA fragments and eliminates the difficulties associated with the detection and analysis of spatially overlapping bands of DNA fragments in a gel, or like medium. The invention further obviates the need to generate DNA fragments from long single stranded templates with a DNA polymerase.
    Type: Grant
    Filed: June 7, 1995
    Date of Patent: January 5, 1999
    Assignee: Lynx Therapeutics, Inc.
    Inventor: Sydney Brenner
  • Patent number: 5846719
    Abstract: The invention provides a method of tracking, identifying, and/or sorting classes or subpopulations of molecules by the use of oligonucleotide tags. Oligonucleotide tags of the invention comprise oligonucleotides selected from a minimally cross-hybridizing set. Preferably, such oligonucleotides each consist of a plurality of subunits 3 to 9 nucleotides in length. A subunit of a minimally cross-hybridizing set forms a duplex or triplex having two or more mismatches with the complement of any other subunit of the same set. The number of oligonucleotide tags available in a particular embodiment depends on the number of subunits per tag and on the length of the subunit. An important aspect of the invention is the use of the oligonucleotide tags for sorting polynucleotides by specifically hybridizing tags attached to the polynucleotides to their complements on solid phase supports.
    Type: Grant
    Filed: June 6, 1996
    Date of Patent: December 8, 1998
    Assignee: Lynx Therapeutics, Inc.
    Inventors: Sydney Brenner, Glenn Albrecht, Stephen C. Macevicz
  • Patent number: 5831065
    Abstract: The invention provides a method of nucleic acid sequence analysis based on repeated cycles of ligation to and cleavage of probes at the terminus of a target polynucleotide. At each such cycle one or more terminal nucleotides are identified and one or more nucleotides are removed from the end of the target polynucleotide, such that further cycles of ligation and cleavage can take place. At each cycle the target sequence is shortened by one or more nucleotides until the nucleotide sequence of the target polynucleotide is determined. The method obviates electrophoretic separation of similarly sized DNA fragments and eliminates the difficulties associated with the detection and analysis of spatially overlapping bands of DNA fragments in a gel, or like medium. The invention further obviates the need to generate DNA fragments from long single stranded templates with a DNA polymerase.
    Type: Grant
    Filed: September 11, 1996
    Date of Patent: November 3, 1998
    Assignee: Lynx Therapeutics, Inc.
    Inventor: Sydney Brenner
  • Patent number: 5830658
    Abstract: The invention provides methods and compositons for convergent synthesis of branched polymers useful as molecular probes. The invention also includes several novel branched polymeric structures particularly useful for detecting target polynucleotides. Branched polymers of the invention comprise at least two branches: at least one branch is a target binding moiety capable of specifically binding to a target molecule of interest and one or more branches are signal generation moities capable of directly or indirectly generating a detectable signal. In accordance with the method of the invention branched polymers are assembled from components having phosphorothioate groups and/or haloacyl- or haloalkylamino groups. The phosphorothioate and haloacyl- or haloalkylamino groups react rapidly and efficiently when brought into contact to form thiophosphorylacyl- or thiophosphorylalkylamino bridges which complete the assembly of a branched polymer.
    Type: Grant
    Filed: August 15, 1996
    Date of Patent: November 3, 1998
    Assignee: Lynx Therapeutics, Inc.
    Inventor: Sergei M. Gryaznov
  • Patent number: 5824793
    Abstract: The invention provides a method of synthesizing oligonucleotide N3'.fwdarw.P5' phosphoramidates using an amine-exchange reaction of phosphoramidites in which a deprotected 3'-amino group of a solid phase supported oligonucleotide chain is exhanged for the amino portion of a 5'-phosphoramidite of an incoming monomer which has a protected 3'-amino group. The resulting internucleotide phosphoramidite linkage is then oxidized to form a stable protected phosphoramidate linkage. The method of the invention greatly improves product yields and reduces reagent usage over currently available methods for synthesizing the above class of compound.
    Type: Grant
    Filed: June 14, 1996
    Date of Patent: October 20, 1998
    Assignee: Lynx Therapeutics, Inc.
    Inventors: Bernard L. Hirschbein, Karen L. Fearon, Sergei M. Gryaznov, Sarah N. McCurdy, Jeffery S. Nelson, Ronald G. Schultz
  • Patent number: 5817795
    Abstract: Compounds referred to herein as oligonucleotide clamps are provided that stably bind to target polynucleotides in a sequence-specific manner. The oligonucleotide clamps comprise one or more oligonucleotide moieties capable of specifically binding to a target polynucleotide and one or more pairs of binding moieties covalently linked to the oligonucleotide moieties. In accordance with the invention, upon annealing of the oligonucleotide moieties to the target polynucleotide, the binding moieties of a pair are brought into juxtaposition so that they form a stable covalent or non-covalent linkage or complex. The interaction of the binding moieties of the one or more pairs effectively clamps the specifically annealed oligonucleotide moieties to the target polynucleotide.
    Type: Grant
    Filed: September 17, 1996
    Date of Patent: October 6, 1998
    Assignee: Lynx Therapeutics, Inc.
    Inventors: Sergei M. Gryaznov, David H. Lloyd
  • Patent number: 5780231
    Abstract: A novel "primer walking" method for DNA sequencing is provided that comprises repeated cycles nucleotide identification by selective extension and primer advancement along a template by template mutation. An important feature of the invention is providing a set of primers, referred to herein as "rolling primers" that contain complexity-reducing nucleotides for reducing the number of primers required for annealing to every possible primer binding site on a sequencing template. Another important feature of the invention is the systematic replacement of at least one of the four nucleotides in the target polynucleotide with its cognate complexity-reducing nucleotide or complement thereof. Sequencing is initiated by annealing rolling primers differing only in their terminal nucleotides to a primer binding site of a sequencing template so that only the rolling primer whose terminal nucleotide forms a perfect complement with the template leads to the formation of an extension product.
    Type: Grant
    Filed: March 5, 1996
    Date of Patent: July 14, 1998
    Assignee: Lynx Therapeutics, Inc.
    Inventor: Sydney Brenner
  • Patent number: 5763175
    Abstract: The invention provides a method for sequencing each polynucleotide of a population by using an oligonucleotide tag assigned to each such polynucleotide for transfering sequence information to a tag complement located on a spatially addressable array of such complements. That is, a unique tag is attached to each polynucleotide of a population which can be copied and used to shuttle sequence information to its complement at a fixed position on an array of such complements. After a tag hybridizes with its complement, a signal is generated that is indicative of the transferred sequence information. Sequences of the tagged polynucleotides are determined by repeated cycles of information transfer and signal detection at the positions of the corresponding tag complements.
    Type: Grant
    Filed: November 17, 1995
    Date of Patent: June 9, 1998
    Assignee: Lynx Therapeutics, Inc.
    Inventor: Sydney Brenner
  • Patent number: 5759369
    Abstract: An electrophoresis separation medium is disclosed comprising a matrix of a copolymer composed of a linear hydrophilic polymer segment having a selected substantially uniform segment length and hydrophobic polymer segments carried on each end. Also disclosed is an electrophoresis method employing the separation medium which permits high resolution separation of polynucleotides, especially in DNA sequencing operations.
    Type: Grant
    Filed: March 24, 1995
    Date of Patent: June 2, 1998
    Assignee: The Perkin-Elmer Corporation
    Inventors: Steven Michael Menchen, Mitchell A. Winnik, Ben F. Johnson
  • Patent number: 5756342
    Abstract: A method of treating EBV infections is provided. The method comprises administering an effective amount of an monoclonal antibody antagonist to the EBV protein, BCRF1. Preferably, the antagonist is a blocking monoclonal antibody specific for BCRF1, or a fragment or binding composition derived therefrom.
    Type: Grant
    Filed: June 5, 1995
    Date of Patent: May 26, 1998
    Assignee: Schering Corporation
    Inventor: Kevin W. Moore
  • Patent number: 5750341
    Abstract: Method and compositions are provided for analyzing nucleic acid sequences based on repeated cycles of duplex extension along a single stranded template. Preferably, such extension starts from a duplex formed between an initializing oligonucleotide and the template. The initializing oligonucleotide is extended in an initial extension cycle by ligating an oligonucleotide probe to its end to form an extended duplex. The extended duplex is then repeatedly extended by subsequent cycles of ligation. During each cycle, the identity of one or more nucleotides in the template is determined by a label on, or associated with, a successfully ligated oligonucleotide probe. Preferably, the oligonucleotide probe has a blocking moiety, e.g. a chain-terminating nucleotide, in a terminal position so that only a single extension of the extended duplex takes place in a single cycle. The duplex is further extended in subsequent cycles by removing the blocking moiety and regenerating an extendable terminus.
    Type: Grant
    Filed: April 17, 1995
    Date of Patent: May 12, 1998
    Assignee: Lynx Therapeutics, Inc.
    Inventor: Stephen C. Macevicz
  • Patent number: 5747255
    Abstract: A method for detecting a target polynucleotide is provided which relies on the exponential amplification of oligonucleotide fragments. Separated populations of oligonucleotides are provided that contain complementary sequences to one another and that contain at least one scissile linkage which is cleaved whenever a perfectly matched duplex is formed containing the linkage. When a target polynucleotide contacts a first oligonucleotide cleavage occurs and a first fragment is produced which can hybridize with a second oligonucleotide. Upon such hybridization, the second oligonucleotide is cleaved releasing a second fragment that can, in turn, hybridize with a first oligonucleotide in a manner similar to that of the target polynucleotide.
    Type: Grant
    Filed: September 29, 1995
    Date of Patent: May 5, 1998
    Assignee: Lynx Therapeutics, Inc.
    Inventor: Sydney Brenner
  • Patent number: 5741643
    Abstract: Compounds referred to herein as oligonucleotide clamps are provided that stably bind to target polynucleotides in a sequence-specific manner. The oligonucleotide clamps comprise one or more oligonucleotide moieties capable of specifically binding to a target polynucleotide and one or more pairs of binding moieties covalently linked to the oligonucleotide moieties. In accordance with the invention, upon annealing of the oligonucleotide moieties to the target polynucleotide, the binding moieties of a pair are brought into juxtaposition so that they form a stable covalent or non-covalent linkage or complex. The interaction of the binding moieties of the one or more pairs effectively clamps the specifically annealed oligonucleotide moieties to the target polynucleotide.
    Type: Grant
    Filed: June 5, 1995
    Date of Patent: April 21, 1998
    Assignee: Lynx Therapeutics, Inc.
    Inventors: Sergei M. Gryaznov, David H. Lloyd
  • Patent number: 5736390
    Abstract: BCRF1 proteins are provided for treating conditions associated with excessive production of IFN-.gamma.. Also provided are expression vectors for producing BCRF1 proteins. Compositions of the invention are useful in treating a variety of disorders, including allergy, psoriasis, tissue rejection, and MHC-linked autoimmune diseases.
    Type: Grant
    Filed: June 6, 1995
    Date of Patent: April 7, 1998
    Assignee: Schering Corporation
    Inventors: Kevin W. Moore, Robert A. Kastelein
  • Patent number: 5726297
    Abstract: Modified oligodeoxyribonucleotide 3'--NHP (O) (O.sup.-) O-5' phosphoramidates were synthesized on a solid phase support. The phosphoramidate analogs were found to have significantly increased resistance toward phosphodiesterase digestion. Thermal dissociation experiments demonstrated that these compounds form more stable duplexes than phosphodiesters with complementary DNA and particularly RNA strands. Further, the phosphoramidate analogs can also form stable triplexes with double-stranded DNA target, where under similar conditions parent phosphodiester compounds failed to do so.
    Type: Grant
    Filed: June 5, 1995
    Date of Patent: March 10, 1998
    Assignee: Lynx Therapeutics, Inc.
    Inventors: Sergei M. Gryaznov, Ronald G. Schultz, Jer-Kang Chen
  • Patent number: 5714330
    Abstract: The invention provides a method of nucleic acid sequence analysis based on repeated cycles of ligation to and cleavage of probes at the terminus of a target polynucleotide. At each such cycle one or more terminal nucleotides are identified and one or more nucleotides are removed from the end of the target polynucleotide, such that further cycles of ligation and cleavage can take place. At each cycle the target sequence is shortened by one or more nucleotides until the nucleotide sequence of the target polynucleotide is determined. The method obviates electrophoretic separation of similarly sized DNA fragments and eliminates the difficulties associated with the detection and analysis of spatially overlapping bands of DNA fragments in a gel, or like medium. The invention further obviates the need to generate DNA fragments from long single stranded templates with a DNA polymerase.
    Type: Grant
    Filed: June 21, 1996
    Date of Patent: February 3, 1998
    Assignee: Lynx Therapeutics, Inc.
    Inventors: Sydney Brenner, Robert B. DuBridge
  • Patent number: 5684143
    Abstract: A new class of oligonucleotide N3'.fwdarw.P5' phosphoramidates having 2' fluoro substituents are provided that have superior acid stability. The invention includes oligo-2'-fluoronucleotide N3'.fwdarw.P5' phosphoramidates, methods of synthesis, and duplexes and triplexes formed with DNA and RNA. Compounds of the invention are useful where the formation of stable and specific duplex and/or triplex structures is desired, including antisense and/or anti-gene pharmaceuticals, branched DNA components, DNA and/or RNA capture agents, components of DNA-based diagnostic assays, and the like.
    Type: Grant
    Filed: February 21, 1996
    Date of Patent: November 4, 1997
    Assignee: Lynx Therapeutics, Inc.
    Inventors: Sergei Gryaznov, Ronald G. Schultz
  • Patent number: 5676940
    Abstract: A method of reducing immunoglobulin E responses associated with certain immune disorders is provided. The method comprises administering an effective amount of an antagonist to human interleukin-4. Preferably, the antagonist is a blocking monoclonal antibody specific for human interleukin-4, or a fragment or binding composition derived therefrom.
    Type: Grant
    Filed: March 17, 1994
    Date of Patent: October 14, 1997
    Assignee: Schering Corporation
    Inventors: Robert L. Coffman, Jan Egbert de Vries
  • Patent number: 5654413
    Abstract: The invention provides a method of tracking, identifying, and/or sorting classes or subpopulations of molecules by the use of oligonucleotide tags. Oligonucleotide tags of the invention each consist of a plurality of subunits 3 to 6 nucleotides in length selected from a minimally cross-hybridizing set. A subunit of a minimally cross-hybridizing set forms a duplex or triplex having two or more mismatches with the complement of any other subunit of the same set. The number of oligonucleotide tags available in a particular embodiment depends on the number of subunits per tag and on the length of the subunit. An important aspect of the invention is the use of the oligonucleotide tags for sorting polynucleotides by specifically hybridizing tags attached to the polynucleotides to their complements on solid phase supports.
    Type: Grant
    Filed: June 7, 1995
    Date of Patent: August 5, 1997
    Assignee: Spectragen, Inc.
    Inventor: Sydney Brenner
  • Patent number: 5654442
    Abstract: Long wavelength, narrow emission bandwidth fluorecein dyes are provided for detecting spacially overlapping target substances. The dyes comprise 4,7-dichlorofluoresceins, and particularly 2',4',5',7'-tetrachloro-4,7-dichloro-5- (and 6-) carboxyfluoresceins. Methods and kits for using the dyes in DNA analysis are provided.
    Type: Grant
    Filed: March 8, 1995
    Date of Patent: August 5, 1997
    Assignee: The Perkin-Elmer Corporation
    Inventors: Steven M. Menchen, Linda G. Lee, Charles R. Connell, N. Davis Hershey, Vergine Chakerian, Sam L. Woo, Steven Fung