Patents by Inventor Stephen J. Benkovic

Stephen J. Benkovic 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).

  • Publication number: 20140308673
    Abstract: A method for replicating and amplifying a target nucleic acid sequence is described. A method of the invention involves the formation of a recombination intermediate without the prior denaturing of a nucleic acid duplex through the use of a recombination factor. The recombination intermediate is treated with a high fidelity polymerase to permit the replication and amplification of the target nucleic acid sequence. In preferred embodiments, the polymerase comprises a polymerase holoenzyme. In further preferred embodiments, the recombination factor is bacteriophage T4 UvsX protein or homologs from other species, and the polymerase holoenzyme comprises a polymerase enzyme, a clamp protein and a clamp loader protein, derived from viral, bacteriophage, prokaryotic, archaebacterial, or eukaryotic systems.
    Type: Application
    Filed: June 24, 2014
    Publication date: October 16, 2014
    Inventors: Stephen J BENKOVIC, Frank Salinas
  • Publication number: 20140234910
    Abstract: A method for replicating and amplifying a target nucleic acid sequence is described. A method of the invention involves the formation of a recombination intermediate without the prior denaturing of a nucleic acid duplex through the use of a recombination factor. The recombination intermediate is treated with a high fidelity polymerase to permit the replication and amplification of the target nucleic acid sequence. In preferred embodiments, the polymerase comprises a polymerase holoenzyme. In further preferred embodiments, the recombination factor is bacteriophage T4 UvsX protein or homologs from other species, and the polymerase holoenzyme comprises a polymerase enzyme, a clamp protein and a clamp loader protein, derived from viral, bacteriophage, prokaryotic, archaebacterial, or eukaryotic systems.
    Type: Application
    Filed: May 2, 2014
    Publication date: August 21, 2014
    Inventors: Stephen J. BENKOVIC, Frank Salinas
  • Publication number: 20140221631
    Abstract: This invention relates to compounds useful for treating fungal infections, more specifically topical treatment of onychomycosis and/or cutaneous fungal infections. This invention is directed to compounds that are active against fungi and have properties that allow the compound, when placed in contact with a patient, to reach the particular part of the skin, nail, hair, claw or hoof infected by the fungus. In particular the present compounds have physiochemical properties that facilitate penetration of the nail plate.
    Type: Application
    Filed: March 7, 2014
    Publication date: August 7, 2014
    Applicant: Anacor Pharmaceuticals, Inc.
    Inventors: Stephen J. BAKER, Tsutomu Akama, Michael Richard Kevin Alley, Stephen J. Benkovic, Michael Dipierro, Vincent S. Hernandez, Karin M. Hold, Isaac Kennedy, Igor Likhotvorik, Weimin Mao, Kirk Maples, Jacob J. Plattner, Fernando Rock, Virginia Sanders, Aaron M. Stemphoski, George Petros Yiannikouros, Siead Zagar, Yong-Kang Zhang, Huchen Zhou
  • Publication number: 20140187443
    Abstract: Inhibitors of the tmRNA pathway have antibacterial activity with broad species specificity, including B. anthracis and other pathogens of military and civilian interest. Identified cyclic or linear peptides are further selected by in vivo selection methods, kill bacterial pathogens when added exogenously, and/or eliminate plasmids carrying antibiotic resistance or virulence genes. The molecular target of each cyclic peptide is in the tmRNA pathway and the tmRNA pathway is inhibited in vitro and in vivo by the addition of the peptides.
    Type: Application
    Filed: December 20, 2013
    Publication date: July 3, 2014
    Applicant: The Penn State Research Foundation
    Inventors: Kenneth C. KEILER, Stephen J. Benkovic
  • Patent number: 8765374
    Abstract: A method for replicating and amplifying a target nucleic acid sequence is described. A method of the invention involves the formation of a recombination intermediate without the prior denaturing of a nucleic acid duplex through the use of a recombination factor. The recombination intermediate is treated with a high fidelity polymerase to permit the replication and amplification of the target nucleic acid sequence. In preferred embodiments, the polymerase comprises a polymerase holoenzyme. In further preferred embodiments, the recombination factor is bacteriophage T4 UvsX protein or homologs from other species, and the polymerase holoenzyme comprises a polymerase enzyme, a clamp protein and a clamp loader protein, derived from viral, bacteriophage, prokaryotic, archaebacterial, or eukaryotic systems.
    Type: Grant
    Filed: December 20, 2012
    Date of Patent: July 1, 2014
    Assignee: The Penn State Research Foundation
    Inventors: Stephen J Benkovic, Frank Salinas
  • Publication number: 20140178941
    Abstract: A method for replicating and amplifying a target nucleic acid sequence is described. A method of the invention involves the formation of a recombination intermediate without the prior denaturing of a nucleic acid duplex through the use of a recombination factor. The recombination intermediate is treated with a high fidelity polymerase to permit the replication and amplification of the target nucleic acid sequence. In preferred embodiments, the polymerase comprises a polymerase holoenzyme. In further preferred embodiments, the recombination factor is bacteriophage T4 UvsX protein or homologs from other species, and the polymerase holoenzyme comprises a polymerase enzyme, a clamp protein and a clamp loader protein, derived from viral, bacteriophage, prokaryotic, archaebacterial, or eukaryotic systems.
    Type: Application
    Filed: December 16, 2013
    Publication date: June 26, 2014
    Applicant: THE PENN STATE RESEARCH FOUNDATION
    Inventors: Stephen J. BENKOVIC, Frank Salinas
  • Patent number: 8759000
    Abstract: A method for replicating and amplifying a target nucleic acid sequence is described. A method of the invention involves the formation of a recombination intermediate without the prior denaturing of a nucleic acid duplex through the use of a recombination factor. The recombination intermediate is treated with a high fidelity polymerase to permit the replication and amplification of the target nucleic acid sequence. In preferred embodiments, the polymerase comprises a polymerase holoenzyme. In further preferred embodiments, the recombination factor is bacteriophage T4 UvsX protein or homologs from other species, and the polymerase holoenzyme comprises a polymerase enzyme, a clamp protein and a clamp loader protein, derived from viral, bacteriophage, prokaryotic, archaebacterial, or eukaryotic systems.
    Type: Grant
    Filed: December 20, 2012
    Date of Patent: June 24, 2014
    Assignee: The Penn State Research Foundation
    Inventors: Stephen J Benkovic, Frank Salinas
  • Patent number: 8722917
    Abstract: This invention relates to compounds useful for treating fungal infections, more specifically topical treatment of onychomycosis and/or cutaneous fungal infections. This invention is directed to compounds that are active against fungi and have properties that allow the compound, when placed in contact with a patient, to reach the particular part of the skin, nail, hair, claw or hoof infected by the fungus. In particular the present compounds have physiochemical properties that facilitate penetration of the nail plate.
    Type: Grant
    Filed: January 23, 2012
    Date of Patent: May 13, 2014
    Assignee: Anacor Pharmaceuticals, Inc.
    Inventors: Stephen J. Baker, Tsutomu Akama, Michael Richard Kevin Alley, Stephen J. Benkovic, Michael Dipierro, Vincent S. Hernandez, Karin M. Hold, Isaac Kennedy, Igor Likhotvorik, Weimin Mao, Kirk Maples, Jacob J. Plattner, Fernando Rock, Virginia Sanders, Aaron M. Stemphoski, George Petros Yiannikouros, Siead Zagar, Yong-Kang Zhang, Huchen Zhou
  • Patent number: 8673561
    Abstract: A method for replicating and amplifying a target nucleic acid sequence is described. A method of the invention involves the formation of a recombination intermediate without the prior denaturing of a nucleic acid duplex through the use of a recombination factor. The recombination intermediate is treated with a high fidelity polymerase to permit the replication and amplification of the target nucleic acid sequence. In preferred embodiments, the polymerase comprises a polymerase holoenzyme. In further preferred embodiments, the recombination factor is bacteriophage T4 UvsX protein or homologs from other species, and the polymerase holoenzyme comprises a polymerase enzyme, a clamp protein and a clamp loader protein, derived from viral, bacteriophage, prokaryotic, archaebacterial, or eukaryotic systems.
    Type: Grant
    Filed: December 20, 2012
    Date of Patent: March 18, 2014
    Assignee: The Penn State Research Foundation
    Inventors: Stephen J Benkovic, Frank Salinas
  • Patent number: 8637267
    Abstract: Inhibitors of the tmRNA pathway have antibacterial activity with broad species specificity, including B. anthracis and other pathogens of military and civilian interest. Identified cyclic or linear peptides are further selected by in vivo selection methods, kill bacterial pathogens when added exogenously, and/or eliminate plasmids carrying antibiotic resistance or virulence genes. The molecular target of each cyclic peptide is in the tmRNA pathway and the tmRNA pathway is inhibited in vitro and in vivo by the addition of the peptides.
    Type: Grant
    Filed: April 28, 2008
    Date of Patent: January 28, 2014
    Assignee: The Penn State Research Foundation
    Inventors: Kenneth C. Keiler, Stephen J. Benkovic
  • Patent number: 8637243
    Abstract: A method for replicating and amplifying a target nucleic acid sequence is described. A method of the invention involves the formation of a recombination intermediate without the prior denaturing of a nucleic acid duplex through the use of a recombination factor. The recombination intermediate is treated with a high fidelity polymerase to permit the replication and amplification of the target nucleic acid sequence. In preferred embodiments, the polymerase comprises a polymerase holoenzyme. In further preferred embodiments, the recombination factor is bacteriophage T4 UvsX protein or homologs from other species, and the polymerase holoenzyme comprises a polymerase enzyme, a clamp protein and a clamp loader protein, derived from viral, bacteriophage, prokaryotic, archaebacterial, or eukaryotic systems.
    Type: Grant
    Filed: December 20, 2012
    Date of Patent: January 28, 2014
    Assignee: The Penn State Research Foundation
    Inventors: Stephen J Benkovic, Frank Salinas
  • Publication number: 20130330776
    Abstract: A method for replicating and amplifying a target nucleic acid sequence is described. A method of the invention involves the formation of a recombination intermediate without the prior denaturing of a nucleic acid duplex through the use of a recombination factor. The recombination intermediate is treated with a high fidelity polymerase to permit the replication and amplification of the target nucleic acid sequence. In preferred embodiments, the polymerase comprises a polymerase holoenzyme. In further preferred embodiments, the recombination factor is bacteriophage T4 UvsX protein or homologs from other species, and the polymerase holoenzyme comprises a polymerase enzyme, a clamp protein and a clamp loader protein, derived from viral, bacteriophage, prokaryotic, archaebacterial, or eukaryotic systems.
    Type: Application
    Filed: December 20, 2012
    Publication date: December 12, 2013
    Applicant: THE PENN STATE RESEARCH FOUNDATION
    Inventors: Stephen J BENKOVIC, Frank SALINAS
  • Publication number: 20130330775
    Abstract: A method for replicating and amplifying a target nucleic acid sequence is described. A method of the invention involves the formation of a recombination intermediate without the prior denaturing of a nucleic acid duplex through the use of a recombination factor. The recombination intermediate is treated with a high fidelity polymerase to permit the replication and amplification of the target nucleic acid sequence. In preferred embodiments, the polymerase comprises a polymerase holoenzyme. In further preferred embodiments, the recombination factor is bacteriophage T4 UvsX protein or homologs from other species, and the polymerase holoenzyme comprises a polymerase enzyme, a clamp protein and a clamp loader protein, derived from viral, bacteriophage, prokaryotic, archaebacterial, or eukaryotic systems.
    Type: Application
    Filed: December 20, 2012
    Publication date: December 12, 2013
    Applicant: THE PENN STATE RESEARCH FOUNDATION
    Inventors: Stephen J BENKOVIC, Frank SALINAS
  • Publication number: 20130323792
    Abstract: A method for replicating and amplifying a target nucleic acid sequence is described. A method of the invention involves the formation of a recombination intermediate without the prior denaturing of a nucleic acid duplex through the use of a recombination factor. The recombination intermediate is treated with a high fidelity polymerase to permit the replication and amplification of the target nucleic acid sequence. In preferred embodiments, the polymerase comprises a polymerase holoenzyme. In further preferred embodiments, the recombination factor is bacteriophage T4 UvsX protein or homologs from other species, and the polymerase holoenzyme comprises a polymerase enzyme, a clamp protein and a clamp loader protein, derived from viral, bacteriophage, prokaryotic, archaebacterial, or eukaryotic systems.
    Type: Application
    Filed: December 20, 2012
    Publication date: December 5, 2013
    Applicant: THE PENN STATE RESEARCH FOUNDATION
    Inventors: Stephen J BENKOVIC, Frank SALINAS
  • Publication number: 20130137145
    Abstract: A method for replicating and amplifying a target nucleic acid sequence is described. A method of the invention involves the formation of a recombination intermediate without the prior denaturing of a nucleic acid duplex through the use of a recombination factor. The recombination intermediate is treated with a high fidelity polymerase to permit the replication and amplification of the target nucleic acid sequence. In preferred embodiments, the polymerase comprises a polymerase holoenzyme. In further preferred embodiments, the recombination factor is bacteriophage T4 UvsX protein or homologs from other species, and the polymerase holoenzyme comprises a polymerase enzyme, a clamp protein and a clamp loader protein, derived from viral, bacteriophage, prokaryotic, archaebacterial, or eukaryotic systems.
    Type: Application
    Filed: December 20, 2012
    Publication date: May 30, 2013
    Inventors: Stephen J Benkovic, Frank Salinas
  • Publication number: 20130064783
    Abstract: This invention relates to compounds useful for treating fungal infections, more specifically topical treatment of onychomycosis and/or cutaneous fungal infections. This invention is directed to compounds that are active against fungi and have properties that allow the compound, when placed in contact with a patient, to reach the particular part of the skin, nail, hair, claw or hoof infected by the fungus. In particular the present compounds have physiochemical properties that facilitate penetration of the nail plate.
    Type: Application
    Filed: September 7, 2012
    Publication date: March 14, 2013
    Applicant: Anacor Pharmaceuticals, Inc.
    Inventors: Stephen J. Baker, Tsutomu Akama, Michael Richard Kevin Alley, Stephen J. Benkovic, Michael DiPierro, Vincent S. Hernandez, Karin M. Hold, Isaac Kennedy, Igor Likhotvorik, Weimin Mao, Kirk R. Maples, Jacob J. Plattner, Fernando Rock, Virginia Sanders, Aaron M. Stemphoski, George Petros Yiannikouros, Siead Zagar, Yong-Kang Zhang, Huchen Zhou
  • Publication number: 20130059803
    Abstract: This invention relates to compounds useful for treating fungal infections, more specifically topical treatment of onychomycosis and/or cutaneous fungal infections. This invention is directed to compounds that are active against fungi and have properties that allow the compound, when placed in contact with a patient, to reach the particular part of the skin, nail, hair, claw or hoof infected by the fungus. In particular the present compounds have physiochemical properties that facilitate penetration of the nail plate.
    Type: Application
    Filed: September 7, 2012
    Publication date: March 7, 2013
    Applicant: Anacor Pharmaceuticals, Inc.
    Inventors: Stephen J. Baker, Tsutomu Akama, Michael Richard Kevin Alley, Stephen J. Benkovic, Michael DiPierro, Vincent S. Hernandez, Karin M. Hold, Isaac Kennedy, Igor Likhotvorik, Weimin Mao, Kirk R. Maples, Jacob J. Plattner, Fernando Rock, Virginia Sanders, Aaron M. Stemphoski, George Petros Yiannikouros, Siead Zagar, Yong-Kang Zhang, Huchen Zhou
  • Publication number: 20130059802
    Abstract: This invention relates to compounds useful for treating fungal infections, more specifically topical treatment of onychomycosis and/or cutaneous fungal infections. This invention is directed to compounds that are active against fungi and have properties that allow the compound, when placed in contact with a patient, to reach the particular part of the skin, nail, hair, claw or hoof infected by the fungus. In particular the present compounds have physiochemical properties that facilitate penetration of the nail plate.
    Type: Application
    Filed: September 7, 2012
    Publication date: March 7, 2013
    Applicant: Anacor Pharmaceuticals, Inc.
    Inventors: Stephen J. Baker, Tsutomu Akama, Michael Richard Kevin Alley, Stephen J. Benkovic, Michael DiPierro, Vincent S. Hernandez, Karin M. Hold, Isaac Kennedy, Igor Likhotvorik, Weimin Mao, Kirk R. Maples, Jacob J. Plattner, Fernando Rock, Virginia Sanders, Aaron M. Stemphoski, George Petros Yiannikouros, Siead Zagar, Yong-Kang Zhang, Huchen Zhou
  • Patent number: 8389216
    Abstract: A method for replicating and amplifying a target nucleic acid sequence is described. A method of the invention involves the formation of a recombination intermediate without the prior denaturing of a nucleic acid duplex through the use of a recombination factor. The recombination intermediate is treated with a high fidelity polymerase to permit the replication and amplification of the target nucleic acid sequence. In preferred embodiments, the polymerase comprises a polymerase holoenzyme. In further preferred embodiments, the recombination factor is bacteriophage T4 UvsX protein or homologs from other species, and the polymerase holoenzyme comprises a polymerase enzyme, a clamp protein and a clamp loader protein, derived from viral, bacteriophage, prokaryotic, archaebacterial, or eukaryotic systems.
    Type: Grant
    Filed: May 24, 2010
    Date of Patent: March 5, 2013
    Assignee: The Penn State Research Foundation
    Inventors: Stephen J. Benkovic, Frank Salinas
  • Patent number: 8361718
    Abstract: A method for replicating and amplifying a target nucleic acid sequence is described. A method of the invention involves the formation of a recombination intermediate without the prior denaturing of a nucleic acid duplex through the use of a recombination factor. The recombination intermediate is treated with a high fidelity polymerase to permit the replication and amplification of the target nucleic acid sequence. In preferred embodiments, the polymerase comprises a polymerase holoenzyme. In further preferred embodiments, the recombination factor is bacteriophage T4 UvsX protein or homologs from other species, and the polymerase holoenzyme comprises a polymerase enzyme, a clamp protein and a clamp loader protein, derived from viral, bacteriophage, prokaryotic, archaebacterial, or eukaryotic systems.
    Type: Grant
    Filed: May 24, 2010
    Date of Patent: January 29, 2013
    Assignee: The Penn State Research Foundation
    Inventors: Stephen J. Benkovic, Frank Salinas