Stephen J Benkovic, 87500 E Marylyn Ave UNIT K171, State College, PA 16801

6413751, Jul 2, 2002

Jul 19, 1999

09/269137

Stephen J. Benkovic - State College PA
Anthony Berdis - Shaker Heights OH
Irene Lee - Shaker Heights OH
Lucy Shapiro - Stanford CA
Rachel Wright - Menlo Park CA
Craig Stephens - Mountain View CA
Lyn Sue Kahng - Mountain View CA

The Board of Trustees of the Leland Stanford Jr. University - Stanford CA
The Penn State Research Foundation - University Park PA

C12N 910

435193, 536 232

The present invention relates to the isolation and sequencing of a novel class of methyltransferase genes, including the methyltransferase gene from and The invention further comprises efficient methods of assaying methyltransferase activity.

6929915, Aug 16, 2005

Apr 19, 2002

10/125973

Stephen J. Benkovic - State College PA, US
Frank Salinas - Wheaton IL, US

The Penn State Research Foundation - University Park PA

C12Q001/68
C12P019/34
C07H021/02
C07H021/04

435 6, 435 911, 435 912, 435 915, 536 231, 536 243

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.

7332308, Feb 19, 2008

Nov 15, 2000

09/718465

Stephen J. Benkovic - State College PA, US
Marc Ostermeier - Baltimore MD, US
Stefan Lutz - State College PA, US
Andrew E. Nixon - Quincy MA, US

The Penn State Research Foundation - University Park PA

C12N 15/64
C12N 5/10
C12Q 1/68
C07H 21/02

435 9142, 435 6, 435410, 435DIG 47, 536 231

A series of methods that utilize the incremental truncation of nucleic acids are described to create a plurality of modified nucleic acids and hybrid polypeptides. A plurality of substantially all possible single base-pair deletions of a given nucleic acid sequence is created. A method of making shuffled incremental truncated nucleic acids, which is independent of nucleic acid sequence homology, is also described. These methods can be used in protein engineering, protein folding, protein evolution, and the chemical synthesis of novel hybrid proteins and polypeptides.

7354756, Apr 8, 2008

Dec 18, 1999

09/868469

Stephen J. Benkovic - State College PA, US
Charles P. Scott - Narberth PA, US

The Penn State Research Foundation - University Park PA

C12N 1/20
C12N 9/14
C12N 15/00
C12P 21/06
C07H 21/04

4352523, 435 691, 435183, 435195, 4353201, 536 232

Methods of producing cyclic peptides and splicing intermediates of peptides in a looped conformation are disclosed. The methods utilize the trans-splicing ability of split inteins to catalyze cyclization of peptides from a precursor peptide having a target peptide interposed between two portions of a split intein. The interaction of the two portions of the split intein creates a catalytically-active intein and also forces the target peptide into a loop configuration that stabilizes the ester isomer of the amino acid at the junction between one of the intein portions and the target peptide. A heteroatom from the other intein portion then reacts with the ester to form a cyclic ester intermediate. The active intein catalyzes the formation of an aminosuccinimide that liberates a cyclized form of the target peptide, which spontaneously rearranges to form the thermodynamically favored backbone cyclic peptide product. Also disclosed are nucleic acid molecules, polypeptides, methods for making cyclic peptides, methods of making libraries, and methods of screening peptides.

7390806, Jun 24, 2008

Jun 14, 2004

10/867465

Ving Lee - Los Altos CA, US
Stephen J. Benkovic - State College PA, US
Stephen J. Baker - Mountain View CA, US
Kirk R. Maples - San Jose CA, US
Tsutomu Akama - Sunnyvale CA, US
Yong-Kang Zhang - San Jose CA, US
Rajeshwar Singh - Edmonton, CA
Vittorio A. Sauro - Edmonton, CA
Chetan Pandit - Edmonton, CA
Zhuoyi Su - Edmonton, CA
Zhixiang Yang - Edmonton, CA

Anacor Pharmaceuticals, Inc. - Palo Alto CA

C07D 484/04
C07D 215/02
C07D 215/20
C07D 239/70
C07D 253/08
A61K 31/47
A61P 31/04
A61P 31/10

514242, 514248, 544 69, 546 13

The structure and preparation of antibiotics incorporating borinic acid complexes are disclosed, especially hydroxyquinoline, imidazole and picolinic acid derivatives, along with compositions of these antibiotics and methods of using the antibiotics and compositions as bactericidal and fungicidal agents as well as therapeutic agents for the treatment of diseases caused by bacteria and fungi.

7405304, Jul 29, 2008

Jan 9, 2003

10/501755

Ali Tavassoli - State College PA, US
Stephen J. Benkovic - State College PA, US

The Penn State Research Foundation - University Park PA

C07D 231/00

548110, 514 64

The present invention provides methods for preparing complexed diaryl boronic acids from alkyl diarylborinates.

7465836, Dec 16, 2008

Jun 15, 2004

10/868268

Ving Lee - Los Altos CA, US
Jacob J. Plattner - Berkeley CA, US
Stephen J. Benkovic - State College PA, US
Stephen J. Baker - Mountain View CA, US
Kirk R. Maples - San Jose CA, US
Tsutomu Akama - Sunnyvale CA, US
Yong-Kang Zhang - San Jose CA, US
Rajeshwar Singh - Edmonton, CA
Vittorio A. Sauro - Edmonton, CA

Anacor Pharmaceuticals, Inc. - Palo Alto CA

C07F 9/02

568 8

Compositions and methods of use of borole derivatives, including benzoxaboroles, benzazaboroles and benzthiaboroles, as therapeutic agents for treatment of diseases caused by bacteria or viruses are disclosed, as well as methods for synthesis of said agents and compositions thereof.

7723031, May 25, 2010

Aug 15, 2005

11/204125

Stephen J. Benkovic - State College PA, US
Frank Salinas - Wheaton IL, US

ThePenn State Research Foundation - University Park PA

C12Q 1/68
C12P 19/34
C07H 21/02
C07H 21/04

435 6, 435 912, 536 231, 536 243

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.