David J Liu

US Patent:

7070928, Jul 4, 2006

Filed:

Mar 19, 2002

Appl. No.:

10/101030

Inventors:

David R. Liu - Lexington MA, US
Zev Gartner - Somerville MA, US
Matthew W. Kanan - Cambridge MA, US

Assignee:

President and Fellows of Harvard College - Cambridge MA

International Classification:

C12Q 1/68

US Classification:

435 6

Abstract:

Nature evolves biological molecules such as proteins through iterated rounds of diversification, selection, and amplification. The present invention provides methods, compositions, and systems for synthesizing, selecting, amplifying, and evolving non-natural molecules based on nucleic acid templates. The sequence of a nucleic acid template is used to direct the synthesis of non-natural molecules such as unnatural polymers and small molecules. Using this method combinatorial libraries of these molecules can be prepared and screened. Upon selection of a molecule, its encoding nucleic acid template may be amplified and/or evolved to yield the same molecule or related molecules for re-screening. The inventive methods and compositions of the present invention allow for the amplification and evolution of non-natural molecules in a manner analogous to the amplification of natural biopolymer such as polynucleotides and protein.

US Patent:

7192739, Mar 20, 2007

Filed:

Mar 30, 2005

Appl. No.:

11/093808

Inventors:

David R. Liu - Lexington MA, US
Allen R. Buskirk - Provo UT, US

Assignee:

President and Fellows of Harvard College - Cambridge MA

International Classification:

C12P 21/06
C12P 21/04

US Classification:

435 691, 435 697

Abstract:

Ligand-dependent inteins allow for modulation of a protein's activity in vivo. Upon binding of the ligand to the ligand-dependent intein inserted into the protein of interest, the hybrid protein undergoes protein splicing removing the intein. The activity of the spliced protein is then restored. A 4-hydroxytamoxifen-dependent intein based on the RecA intein is prepared and demonstrated in a variety of exteins contexts. The invention provides a system for engineering other ligand-dependent inteins and using them, including the ligand-dependent inteins themselves, hybrid proteins with the inserted ligand-dependent inteins, polynucleotides encoding inteins and hybrid proteins, and engineered cells. Kits with the materials and reagents necessary for preparing and using ligand-dependent inteins are also included.

US Patent:

7223545, May 29, 2007

Filed:

Sep 24, 2004

Appl. No.:

10/949163

Inventors:

David R. Liu - Lexington MA, US
Zev J. Gartner - Somerville MA, US
Matthew W. Kanan - Cambridge MA, US

Assignee:

President and Fellows of Harvard College - Cambridge MA

International Classification:

C12Q 1/68
C12P 19/34
C07H 21/02
C07H 21/04
C07K 1/00

US Classification:

435 6, 435 911, 435 912, 536 231, 536 243, 536 2431, 536 2432, 536 2433, 530350

Abstract:

Nature evolves biological molecules such as proteins through iterated rounds of diversification, selection, and amplification. The present invention provides methods, compositions, and systems for synthesizing, selecting, amplifying, and evolving non-natural molecules based on nucleic acid templates. The sequence of a nucleic acid template is used to direct the synthesis of non-natural molecules such as unnatural polymers and small molecules. Using this method combinatorial libraries of these molecules can be prepared and screened. Upon selection of a molecule, its encoding nucleic acid template may be amplified and/or evolved to yield the same molecule or related molecules for re-screening. The inventive methods and compositions of the present invention allow for the amplification and evolution of non-natural molecules in a manner analogous to the amplification of natural biopolymer such as polynucleotides and protein.

US Patent:

7442160, Oct 28, 2008

Filed:

May 31, 2005

Appl. No.:

11/141542

Inventors:

David R. Liu - Lexington MA, US
Zev J. Gartner - Somerville MA, US
Matthew W. Kanan - Cambridge MA, US

Assignee:

President and Fellows of Harvard College - Cambridge MA

International Classification:

C40B 30/04
C40B 10/00
C40B 30/08
C40B 40/00
C40B 50/10
C40B 70/00
C12Q 1/68
C07H 21/02

US Classification:

506 9, 506 1, 506 11, 506 13, 506 28, 506 41, 435 6, 435 912, 536 231

Abstract:

Nature evolves biological molecules such as proteins through iterated rounds of diversification, selection, and amplification. The present invention provides methods, compositions, and systems for synthesizing, selecting, amplifying, and evolving non-natural molecules based on nucleic acid templates. The sequence of a nucleic acid template is used to direct the synthesis of non-natural molecules such as unnatural polymers and small molecules. Using this method combinatorial libraries of these molecules can be prepared and screened. Upon selection of a molecule, its encoding nucleic acid template may be amplified and/or evolved to yield the same molecule or related molecules for re-screening. The inventive methods and compositions of the present invention allow for the amplification and evolution of non-natural molecules in a manner analogous to the amplification of natural biopolymer such as polynucleotides and protein.

US Patent:

7476500, Jan 13, 2009

Filed:

Mar 19, 2002

Appl. No.:

10/102056

Inventors:

David R. Liu - Lexington MA, US
Zev Gartner - Somerville MA, US
Daniel M. Rosenbaum - Cambridge MA, US
Mathias Gruen - Jena, DE
Jeffrey Doyon - Allston MA, US

Assignee:

President and Fellows of Harvard College - Cambridge MA

International Classification:

C12Q 1/68
C12N 9/22

US Classification:

435 6, 435199

Abstract:

The present invention provides in vivo systems in which activity of a biological cleavage enzyme, such as a site-specific recombinase, a homing endonuclease, or an intein, is linked to cell viability and therefore can be selected. The invention further provides methods of making cells in which the activity of a biological cleavage enzyme is linked to viability, as well as methods of identifying new biological cleavage enzymes, including enzymes having altered site specificity, using such cells.

US Patent:

7476734, Jan 13, 2009

Filed:

Dec 6, 2005

Appl. No.:

11/295155

Inventors:

David R. Liu - Lexington MA, US

Assignee:

Helicos Biosciences Corporation - Cambridge MA

International Classification:

C07H 19/04
C07H 19/20

US Classification:

536 2621, 536 221, 536 253, 536 2532, 536 261, 536 262

Abstract:

The invention provides nucleotide analogs for use in sequencing nucleic acid molecules.

US Patent:

7491494, Feb 17, 2009

Filed:

Aug 19, 2003

Appl. No.:

10/643752

Inventors:

David R. Liu - Lexington MA, US
Zev J. Gartner - Somerville MA, US
Christopher T. Calderone - Cambridge MA, US

Assignee:

President and Fellows of Harvard College - Cambridge MA

International Classification:

C12Q 1/68

US Classification:

435 6, 435 912, 506 1, 506 16, 506 9

Abstract:

Nature evolves biological molecules such as proteins through iterated rounds of diversification, selection, and amplification. The power of Nature and the flexibility of organic synthesis are combined in nucleic acid-templated synthesis. The present invention provides a variety of template architectures for performing nucleic acid-templated synthesis, methods for increasing the selectivity of nucleic acid-templated reactions, methods for performing stereoselective nucleic acid-templated reactions, methods of selecting for reaction products resulting from nucleic acid-templated synthesis, and methods of identifying new chemical reactions based on nucleic acid-templated synthesis.

US Patent:

7541450, Jun 2, 2009

Filed:

Mar 19, 2007

Appl. No.:

11/688073

Inventors:

David R. Liu - Lexington MA, US
Allen R. Buskirk - Provo UT, US

Assignee:

President and Fellows of Harvard College - Cambridge MA

International Classification:

C07H 21/02
C12P 21/06
C12P 21/04

US Classification:

536 231, 435 691, 435 697

Abstract:

Ligand-dependent inteins allow for modulation of a protein's activity in vivo. Upon binding of the ligand to the ligand-dependent intein inserted into the protein of interest, the hybrid protein undergoes protein splicing removing the intein. The activity of the spliced protein is then restored. A 4-hydroxytamoxifen-dependent intein based on the RecA intein is prepared and demonstrated in a variety of exteins contexts. The invention provides a system for engineering other ligand-dependent inteins and using them, including the ligand-dependent inteins themselves, hybrid proteins with the inserted ligand-dependent inteins, polynucleotides encoding inteins and hybrid proteins, and engineered cells. Kits with the materials and reagents necessary for preparing and using ligand-dependent inteins are also included.