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).
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Publication number: 20140308673Abstract: 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: ApplicationFiled: June 24, 2014Publication date: October 16, 2014Inventors: Stephen J BENKOVIC, Frank Salinas
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Publication number: 20140234910Abstract: 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: ApplicationFiled: May 2, 2014Publication date: August 21, 2014Inventors: Stephen J. BENKOVIC, Frank Salinas
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Publication number: 20140221631Abstract: 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: ApplicationFiled: March 7, 2014Publication date: August 7, 2014Applicant: 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
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Publication number: 20140187443Abstract: 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: ApplicationFiled: December 20, 2013Publication date: July 3, 2014Applicant: The Penn State Research FoundationInventors: Kenneth C. KEILER, Stephen J. Benkovic
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Patent number: 8765374Abstract: 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: GrantFiled: December 20, 2012Date of Patent: July 1, 2014Assignee: The Penn State Research FoundationInventors: Stephen J Benkovic, Frank Salinas
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Publication number: 20140178941Abstract: 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: ApplicationFiled: December 16, 2013Publication date: June 26, 2014Applicant: THE PENN STATE RESEARCH FOUNDATIONInventors: Stephen J. BENKOVIC, Frank Salinas
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Patent number: 8759000Abstract: 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: GrantFiled: December 20, 2012Date of Patent: June 24, 2014Assignee: The Penn State Research FoundationInventors: Stephen J Benkovic, Frank Salinas
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Patent number: 8722917Abstract: 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: GrantFiled: January 23, 2012Date of Patent: May 13, 2014Assignee: 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
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Patent number: 8673561Abstract: 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: GrantFiled: December 20, 2012Date of Patent: March 18, 2014Assignee: The Penn State Research FoundationInventors: Stephen J Benkovic, Frank Salinas
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Patent number: 8637267Abstract: 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: GrantFiled: April 28, 2008Date of Patent: January 28, 2014Assignee: The Penn State Research FoundationInventors: Kenneth C. Keiler, Stephen J. Benkovic
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Patent number: 8637243Abstract: 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: GrantFiled: December 20, 2012Date of Patent: January 28, 2014Assignee: The Penn State Research FoundationInventors: Stephen J Benkovic, Frank Salinas
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Publication number: 20130330776Abstract: 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: ApplicationFiled: December 20, 2012Publication date: December 12, 2013Applicant: THE PENN STATE RESEARCH FOUNDATIONInventors: Stephen J BENKOVIC, Frank SALINAS
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Publication number: 20130330775Abstract: 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: ApplicationFiled: December 20, 2012Publication date: December 12, 2013Applicant: THE PENN STATE RESEARCH FOUNDATIONInventors: Stephen J BENKOVIC, Frank SALINAS
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Publication number: 20130323792Abstract: 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: ApplicationFiled: December 20, 2012Publication date: December 5, 2013Applicant: THE PENN STATE RESEARCH FOUNDATIONInventors: Stephen J BENKOVIC, Frank SALINAS
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Publication number: 20130137145Abstract: 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: ApplicationFiled: December 20, 2012Publication date: May 30, 2013Inventors: Stephen J Benkovic, Frank Salinas
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Publication number: 20130064783Abstract: 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: ApplicationFiled: September 7, 2012Publication date: March 14, 2013Applicant: 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
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Publication number: 20130059803Abstract: 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: ApplicationFiled: September 7, 2012Publication date: March 7, 2013Applicant: 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
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Publication number: 20130059802Abstract: 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: ApplicationFiled: September 7, 2012Publication date: March 7, 2013Applicant: 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
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Patent number: 8389216Abstract: 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: GrantFiled: May 24, 2010Date of Patent: March 5, 2013Assignee: The Penn State Research FoundationInventors: Stephen J. Benkovic, Frank Salinas
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Patent number: 8361718Abstract: 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: GrantFiled: May 24, 2010Date of Patent: January 29, 2013Assignee: The Penn State Research FoundationInventors: Stephen J. Benkovic, Frank Salinas