Patents by Inventor Thomas M. Brennan

Thomas M. Brennan has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).

  • Patent number: 8084245
    Abstract: A polymer synthesis apparatus (20) for building a polymer chain including a head assembly (21) having an array of nozzles (22) with each nozzle coupled to a reservoir (23) of liquid reagent (24), and a base assembly (25) having an array of reaction wells (26). A transport mechanism (27) aligns the reaction wells (26) and selected nozzles (22) for deposition of the liquid reagent (24) into selected reaction wells (26). A sliding seal (30) is positioned between the head assembly (21) and the base assembly (25) to form a common chamber (31) enclosing both the reaction well (26) and the nozzles (22) therein. A gas inlet (70) into the common chamber (31), upstream from the nozzles (22), and a gas outlet (71) out of the common chamber (31), downstream from the nozzles (22), sweeps the common chamber (31) of toxic fumes emitted by the reagents.
    Type: Grant
    Filed: November 19, 2010
    Date of Patent: December 27, 2011
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventor: Thomas M. Brennan
  • Publication number: 20110124529
    Abstract: A polymer synthesis apparatus (20) for building a polymer chain including a head assembly (21) having an array of nozzles (22) with each nozzle coupled to a reservoir (23) of liquid reagent (24), and a base assembly (25) having an array of reaction wells (26). A transport mechanism (27) aligns the reaction wells (26) and selected nozzles (22) for deposition of the liquid reagent (24) into selected reaction wells (26). A sliding seal (30) is positioned between the head assembly (21) and the base assembly (25) to form a common chamber (31) enclosing both the reaction well (26) and the nozzles (22) therein. A gas inlet (70) into the common chamber (31), upstream from the nozzles (22), and a gas outlet (71) out of the common chamber (31), downstream from the nozzles (22), sweeps the common chamber (31) of toxic fumes emitted by the reagents.
    Type: Application
    Filed: November 19, 2010
    Publication date: May 26, 2011
    Applicant: The Board of Trustees of the Leland Stanford Junior University
    Inventor: Thomas M. Brennan
  • Patent number: 7858364
    Abstract: The invention concerns a polymer synthesis apparatus (20) for building a polymer chain including a head assembly (21) having an array of nozzles (22) with each nozzle coupled to a reservoir (23) of liquid reagent (24), and a base assembly (25) having an array of reaction wells (26). A transport mechanism (27) aligns the reaction wells (26) and selected nozzles (22) for deposition of the liquid reagent (24) into selected reaction wells (26). A sliding seal (30) is positioned between the head assembly (21) and the base assembly (25) to form a common chamber (31) enclosing both the reaction well (26) and the nozzles (22) therein.
    Type: Grant
    Filed: July 22, 2008
    Date of Patent: December 28, 2010
    Assignee: The Board of Trustees of Leland Junior Stanford University
    Inventor: Thomas M. Brennan
  • Publication number: 20090054605
    Abstract: A polymer synthesis apparatus (20) for building a polymer chain including a head assembly (21) having an array of nozzles (22) with each nozzle coupled to a reservoir (23) of liquid reagent (24), and a base assembly (25) having an array of reaction wells (26). A transport mechanism (27) aligns the reaction wells (26) and selected nozzles (22) for deposition of the liquid reagent (24) into selected reaction wells (26). A sliding seal (30) is positioned between the head assembly (21) and the base assembly (25) to form a common chamber (31) enclosing both the reaction well (26) and the nozzles (22) therein. A gas inlet (70) into the common chamber (31), upstream from the nozzles (22), and a gas outlet (71) out of the common chamber (31), downstream from the nozzles (22), sweeps the common chamber (31) of toxic fumes emitted by the reagents.
    Type: Application
    Filed: July 22, 2008
    Publication date: February 26, 2009
    Applicant: The Board of Trustees of the Leland Stanford Junior University
    Inventor: Thomas M. Brennan
  • Patent number: 6921636
    Abstract: The invention provides apparatus and methods for determining the nucleotide sequence of target nucleic acids using hybridization to arrays of oligonucleotides. The invention further provides apparatus and methods for identifying the amino acid sequence of peptides that bind to biologically active macromolecules, by specifically binding biologically active macromolecules to arrays of peptides or peptide mimetics.
    Type: Grant
    Filed: November 16, 2000
    Date of Patent: July 26, 2005
    Assignee: Metrigen, Inc.
    Inventor: Thomas M. Brennan
  • Publication number: 20030232382
    Abstract: The present invention relates to a method and apparatus for performing a large number of reactions using array assembly. In particular, the present invention features a method and apparatus for performing a large number of chemical and biological reactions by bringing two arrays into close apposition and allowing reactants on the surfaces of two arrays to come into contact. The present invention is exemplified by performing a large number of polynucleotide amplification reactions using array assembly. In addition, the present invention features a method and apparatus for coupling the amplification of polynucleotides and the detection of sequence variations, expression levels, and functions thereof.
    Type: Application
    Filed: June 23, 2003
    Publication date: December 18, 2003
    Inventors: Thomas M. Brennan, Francois Chatelain, Mark Berninger
  • Patent number: 6632641
    Abstract: The present invention relates to a method and apparatus for performing a large number of reactions using array assembly. In particular, the present invention features a method and apparatus for performing a large number of chemical and biological reactions by bringing two arrays into close apposition and allowing reactants on the surfaces of two arrays to come into contact. The present invention is exemplified by performing a large number of polynucleotide amplification reactions using array assembly. In addition, the present invention features a method and apparatus for coupling the amplification of polynucleotides and the detection of sequence variations, expression levels, and functions thereof.
    Type: Grant
    Filed: October 10, 2000
    Date of Patent: October 14, 2003
    Assignee: Metrigen, Inc.
    Inventors: Thomas M. Brennan, Francois Chatelain, Mark Berninger
  • Publication number: 20030186226
    Abstract: The present invention relates to a cost-effective method of assembling long DNA sequences from short synthetic oligonucleotides. More specifically, short oligonucleotides are synthesized in situ on a solid support and subsequently cleaved from the solid support prior to or during the assembly into the full-length DNA sequences.
    Type: Application
    Filed: March 7, 2000
    Publication date: October 2, 2003
    Inventors: Thomas M. Brennan, Herbert L. Heyneker
  • Patent number: 6589726
    Abstract: The present invention relates to methods for fabricating solid supports. More specifically, the present invention features methods for fabricating solid supports for in situ synthesis and for carrying out large numbers of reactions. The present invention also features solid supports with in situ synthesized long polynucleotides.
    Type: Grant
    Filed: August 23, 2000
    Date of Patent: July 8, 2003
    Assignee: Metrigen, Inc.
    Inventors: John H. Butler, Thomas M. Brennan
  • Publication number: 20030069411
    Abstract: A polymer synthesis apparatus (20) for building a polymer chain including a head assembly (21) having an array of nozzles (22) with each nozzle coupled to a reservoir (23) of liquid reagent (24), and a base assembly (25) having an array of reaction wells (26). A transport mechanism (27) aligns the reaction wells (26) and selected nozzles (22) for deposition of the liquid reagent (24) into selected reaction wells (26). A sliding seal (30) is positioned between the head assembly (21) and the base assembly (25) to form a common chamber (31) enclosing both the reaction well (26) and the nozzles (22) therein. A gas inlet (70) into the common chamber (31), upstream from the nozzles (22), and a gas outlet (71) out of the common chamber (31), downstream from the nozzles (22), sweeps the common chamber (31) of toxic fumes emitted by the reagents.
    Type: Application
    Filed: June 12, 2002
    Publication date: April 10, 2003
    Inventor: Thomas M. Brennan
  • Publication number: 20030068643
    Abstract: The present invention relates to a method for synthesizing and assembling long DNA sequences from short synthetic oligonucleotides. More specifically, the present invention is a cost-effective method for producing large segments of DNA of interest.
    Type: Application
    Filed: November 14, 2002
    Publication date: April 10, 2003
    Inventors: Thomas M. Brennan, Herbert L. Heyneker
  • Patent number: 6337393
    Abstract: A method for reducing evaporation of a liquid reagent solution during solid phase, micro-scale chemical synthesis of a molecule comprising sub-units on an open environment solid support surface. The method includes the steps of providing an open solid support surface including at least one binding site which is functionalized with a reactive chemical moiety; and depositing a substantially controlled and minute volume of liquid reagent solution onto the support surface, and in contact with the binding site. The reagent solution includes reactants contained in at least one relatively high boiling point solvent, in contrast to standard organic solvents for such reagents. Application of a high boiling point solvent substantially reduces evaporation of the reagent solution in the open environment during synthesis on the solid support while enabling the maintenance of a substantially high reaction yield.
    Type: Grant
    Filed: September 14, 2000
    Date of Patent: January 8, 2002
    Assignee: Protogene Laboratories, Inc.
    Inventors: Thomas M. Brennan, Albrecht W. Frauendorf
  • Patent number: 6210894
    Abstract: The invention provides apparatus and methods for making arrays of functionalized binding sites on a support surface. The invention further provides apparatus and methods for sequencing oligonucleotides and for identifying the amino acid sequence of peptides that bind to biologically active macromolecules, by specifically binding biologically active macromolecules to arrays of peptides or peptide mimetics.
    Type: Grant
    Filed: May 18, 1999
    Date of Patent: April 3, 2001
    Assignee: Protogene Laboratories, Inc.
    Inventor: Thomas M. Brennan
  • Patent number: 6177558
    Abstract: A method for reducing evaporation of a liquid reagent solution during solid phase, micro-scale chemical synthesis of a molecule comprising sub-units on an open environment solid support surface. The method includes the steps of providing an open solid support surface including at least one binding site which is functionalized with a reactive chemical moiety; and depositing a substantially controlled and minute volume of liquid reagent solution onto the support surface, and in contact with the binding site. The reagent solution includes reactants contained in at least one relatively high boiling point solvent, in contrast to standard organic solvents for such reagents. Application of a high boiling point solvent substantially reduces evaporation of the reagent solution in the open environment during synthesis on the solid support while enabling the maintenance of a substantially high reaction yield.
    Type: Grant
    Filed: November 13, 1997
    Date of Patent: January 23, 2001
    Assignee: Protogene Laboratories, Inc.
    Inventors: Thomas M. Brennan, Albrecht W. Frauendorf
  • Patent number: 6001311
    Abstract: A chemical synthesis apparatus (20) for building chemical compounds includes a head assembly (21) having an array of nozzles (22) with each nozzle or plurality of nozzles coupled to a reservoir (23) of liquid reagent (24), and a base assembly (25) having an array of reaction wells (26). A transport mechanism (27) aligns the reaction wells (26) and selected nozzles (22) in a longitudinal X-direction for deposition of liquid reagent (24) into selected reaction wells (26). A plurality of independently controllable sliders (100) move nozzle columns (41) in a lateral Y-direction for deposition of liquid reagent (24) into selected reaction wells (26). A first sliding seal (30) is positioned between the head assembly (21) and the base assembly (25) to form a common chamber (31) enclosing both the reaction well (26) and the nozzles (22) therein. A plurality of second sliding seals (120) is positioned between head assembly (21) and sliders (100).
    Type: Grant
    Filed: February 5, 1997
    Date of Patent: December 14, 1999
    Assignee: Protogene Laboratories, Inc.
    Inventor: Thomas M. Brennan
  • Patent number: 5985551
    Abstract: The invention provides apparatus and methods for making arrays of functionalized binding sites on a support surface. The invention further provides apparatus and methods for sequencing oligonucleotides and for identifying the amino acid sequence of peptides that bind to biologically active macromolecules, by specifically binding biologically active macromolecules to arrays of peptides or peptide mimetics.
    Type: Grant
    Filed: June 6, 1995
    Date of Patent: November 16, 1999
    Assignee: Protogene Laboratories, Inc.
    Inventor: Thomas M. Brennan
  • Patent number: 5837858
    Abstract: A polymer synthesis apparatus (20) for building a polymer chain including a head assembly (21) having an array of nozzles (22) with each nozzle coupled to a reservoir (23) of liquid reagent (24), and a base assembly (25) having an array of reaction wells (26). A transport mechanism (27) aligns the reaction wells (26) and selected nozzles (22) for deposition of the liquid reagent (24) into selected reaction wells (26). A sliding seal (30) is positioned between the head assembly (21) and the base assembly (25) to form a common chamber (31) enclosing both the reaction well (26) and the nozzles (22) therein. A gas inlet (70) into the common chamber (31), upstream from the nozzles (22), and a gas outlet: (71) out of the common chamber (31), downstream from the nozzles (22), sweeps the common chamber (31) of toxic fumes emitted by the reagents.
    Type: Grant
    Filed: May 30, 1995
    Date of Patent: November 17, 1998
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventor: Thomas M. Brennan
  • Patent number: 5814700
    Abstract: A method of synthesis for building a polymer chain, oligonucleotides in particular, by sequentially adding monomer units to at least one solid support for growing and immobilizing a polymer chain thereon in a liquid reagent solution. The method includes the step of: A) depositing a liquid reagent in a reaction well (26) in contact with at least one solid support and at least one monomer unit of the polymer chain affixed to the solid support. The well (26) includes at least one orifice (74) extending into the well (26), and is of a size and dimension to form a capillary liquid seal to retain the reagent solution in the well (26) to enable polymer chain growth on the solid support. The method further includes the step of B) expelling the reagent solution from the well (26), while retaining the polymer chain therein.
    Type: Grant
    Filed: May 30, 1995
    Date of Patent: September 29, 1998
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventor: Thomas M. Brennan
  • Patent number: 5636573
    Abstract: A method for vertically aligning the color plate cylinders of a press, which prints a two-color image on paper, in order to eliminate the vertical misalignment of the colors in the image printed. The method requires the use of a cylinder positioner that is releasably mounted on the press and involves operating the press to initially print the image, detaching the cylinder positioner from the press, adjusting the position of a positioner stop on the cylinder positioner based on the amount of misalignment in the printed image, reattaching the cylinder positioner, decoupling a color plate cylinder from normal operation, rotating the press's blanket cylinder until it impacts the positioner stop on the cylinder positioner, recoupling the color plate cylinder and then operating the press to correctly print the image.
    Type: Grant
    Filed: July 11, 1996
    Date of Patent: June 10, 1997
    Inventor: Thomas M. Brennan
  • Patent number: 5546669
    Abstract: A cylinder positioner apparatus for offset presses and duplicators which provides for rapid and efficient alignment of plate cylinders of single-color and multicolor presses. A detachable adjustment member is placed on printed images and a micrometer adjustment is used to accurately set the instrument for removing vertical misalignment or to change the vertical positioning of the plate cylinders of the press. The positioner can be used on two-color presses, single stations of multi-station color presses and single-color presses.
    Type: Grant
    Filed: July 12, 1994
    Date of Patent: August 20, 1996
    Inventor: Thomas M. Brennan