In vivo incorporation of unnatural amino acids

Schultz, Peter; Wang, Lei; Anderson, John Christopher; Chin, Jason William; Liu, David R.; Magliery, Thomas J.; Meggers, Eric L.; Mehl, Ryan A.; Pastrnak, Miro; Santoro, Steven William; Zhang, Zhiwen

Title: In vivo incorporation of unnatural amino acids

Abstract

The invention provides methods and compositions for in vivo incorporation of unnatural amino acids. Also provided are compositions including proteins with unnatural amino acids.

Inventors:: Schultz, Peter; Wang, Lei; Anderson, John Christopher; Chin, Jason William; Liu, David R.; Magliery, Thomas J.; Meggers, Eric L.; Mehl, Ryan A.; Pastrnak, Miro; Santoro, Steven William; Zhang, Zhiwen

Issue Date:: 2006-05-16

Research Org.:: Scripps Research Institute, San Diego, CA (United States)

Sponsoring Org.:: USDOE

OSTI Identifier:: 1175742

Patent Number(s):: 7045337

Application Number:: 10/126,927

Assignee:: Scripps Research Institute; Regents of the University of California

Patent Classifications (CPCs):: A - HUMAN NECESSITIES A61 - MEDICAL OR VETERINARY SCIENCE A61P - SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS

C - CHEMISTRY C07 - ORGANIC CHEMISTRY C07K - PEPTIDES

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A - HUMAN NECESSITIES A61 - MEDICAL OR VETERINARY SCIENCE A61P - SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
A61P43/00 - Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
A61P7/00 - Drugs for disorders of the blood or the extracellular fluid

C - CHEMISTRY C07 - ORGANIC CHEMISTRY C07K - PEPTIDES
C07K14/00 - Peptides having more than 20 amino acids
C07K14/505 - Erythropoietin [EPO]

C - CHEMISTRY C12 - BIOCHEMISTRY C12N - MICROORGANISMS OR ENZYMES
C12N15/67 - General methods for enhancing the expression
C12N9/93 - {Ligases

C - CHEMISTRY C12 - BIOCHEMISTRY C12P - FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE {
C12P13/00 - Preparation of nitrogen-containing organic compounds
C12P13/005 - {Amino acids other than alpha- or beta amino acids, e.g. gamma amino acids}
C12P13/04 - Alpha- or beta- amino acids {
C12P13/22 - Tryptophan
C12P19/26 - Preparation of nitrogen-containing carbohydrates
C12P21/00 - Preparation of peptides or proteins
C12P21/02 - having a known sequence of two or more amino acids, e.g. glutathione

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DOE Contract Number:: AC03-76SF00098

Resource Type:: Patent

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES

Citation Formats


                    Schultz, Peter, Wang, Lei, Anderson, John Christopher, Chin, Jason William, Liu, David R., Magliery, Thomas J., Meggers, Eric L., Mehl, Ryan A., Pastrnak, Miro, Santoro, Steven William, and Zhang, Zhiwen. In vivo incorporation of unnatural amino acids.  United States: N. p., 2006. 
        Web.

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                    Schultz, Peter, Wang, Lei, Anderson, John Christopher, Chin, Jason William, Liu, David R., Magliery, Thomas J., Meggers, Eric L., Mehl, Ryan A., Pastrnak, Miro, Santoro, Steven William, & Zhang, Zhiwen. In vivo incorporation of unnatural amino acids.  United States.

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                    Schultz, Peter, Wang, Lei, Anderson, John Christopher, Chin, Jason William, Liu, David R., Magliery, Thomas J., Meggers, Eric L., Mehl, Ryan A., Pastrnak, Miro, Santoro, Steven William, and Zhang, Zhiwen. Tue .  
        "In vivo incorporation of unnatural amino acids".  United States.  https://www.osti.gov/servlets/purl/1175742.

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@article{osti_1175742,

  title        = {In vivo incorporation of unnatural amino acids},

  author       = {Schultz, Peter and Wang, Lei and Anderson, John Christopher and Chin, Jason William and Liu, David R. and Magliery, Thomas J. and Meggers, Eric L. and Mehl, Ryan A. and Pastrnak, Miro and Santoro, Steven William and Zhang, Zhiwen},

  abstractNote = {The invention provides methods and compositions for in vivo incorporation of unnatural amino acids. Also provided are compositions including proteins with unnatural amino acids.},

  doi          = {},

  journal      = {},
number       = ,

  volume       = ,

  place        = {United States},

  year         = {2006},

  month        = {5}

}

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Patent:

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Pastrnak, M.
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Expanding the genetic code: selection of efficient suppressors of four-base codons and identification of “shifty” four-base codons with a library approach in Escherichia coli
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A Mutant Escherichia coli Tyrosyl-tRNA Synthetase Utilizes the Unnatural Amino Acid Azatyrosine More Efficiently than Tyrosine
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Kowal, A.
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Furter, Rolf
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Title: In vivo incorporation of unnatural amino acids

Abstract

Citation Formats

Twenty-first aminoacyl-tRNA synthetase-suppressor tRNA pairs for possible use in site-specific incorporation of amino acid analogues into proteins in eukaryotes and in eubacteria journal, January 2001

Bio–incorporation of telluromethionine into buried residues of dihydrofolate reductase journal, May 1994

An unnatural base pair for incorporating amino acid analogs into proteins journal, February 2002

Site-specific incorporation of novel backbone structures into proteins journal, January 1992

An engineered Escherichia coli tyrosyl-tRNA synthetase for site-specific incorporation of an unnatural amino acid into proteins in eukaryotic translation and its application in a wheat germ cell-free system journal, July 2002

In vitro protein engineering using synthetic tRNAAla with different anticodons journal, August 1993

An efficient system for the evolution of aminoacyl-tRNA synthetase specificity journal, September 2002

Modification of the amino acid specificity of tyrosyl-tRNA synthetase by protein engineering journal, March 1993

Flash Decaging of Tyrosine Sidechains in an Ion Channel journal, April 1998

Synthesis of 4-substituted prolines as conformationally constrained amino acid analogs journal, April 1989

Probing the Structure and Function of the Tachykinin Neurokinin-2 Receptor through Biosynthetic Incorporation of Fluorescent Amino Acids at Specific Sites journal, August 1996

Mutational Analysis of Invariant Valine B12 in Insulin: Implications for Receptor Binding journal, November 2000

Relaxing the substrate specificity of an aminoacyl-tRNA synthetase allows in vitro and in vivo synthesis of proteins containing unnatural amino acids journal, May 1995

A set of plasmids constitutively producing different RNA levels in Escherichia coli journal, July 1999

Efforts toward Expansion of the Genetic Alphabet: Replication of DNA with Three Base Pairs journal, August 2001

Photocrosslinking of the signal sequence of nascent preprolactin to the 54-kilodalton polypeptide of the signal recognition particle. journal, November 1986

Adding l-3-(2-Naphthyl)alanine to the Genetic Code of E. coli journal, March 2002

Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): a vehicle for direct determination of three-dimensional structure. journal, May 1990

Evolutionary relationship between Halobacterium cutirubrum and eukaryotes determined by use of aminoacyl-tRNA synthetases as phylogenetic probes journal, March 1980

[15] Biosynthetic method for introducing unnatural amino acids site-specifically into proteins book, January 1991

Human Tyrosyl-tRNA Synthetase Shares Amino Acid Sequence Homology with a Putative Cytokine journal, May 1997

Rational Design of an Unnatural Base Pair with Increased Kinetic Selectivity journal, September 2000

Unnatural amino acids as probes of protein structure and function journal, December 2000

TRNA2Gln Su+2 mutants that increase amber suppression. journal, January 1981

Progress toward the evolution of an organism with an expanded genetic code journal, April 1999

Enzymatic incorporation of a new base pair into DNA and RNA extends the genetic alphabet journal, January 1990

Construction of Escherichia coli amber suppressor tRNA genes: II. Synthesis of additional tRNA genes and improvement of suppressor efficiency journal, June 1990

Editing of errors in selection of amino acids for protein synthesis. journal, January 1992

Genetic code in evolution: switching species-specific aminoacylation with a peptide transplant journal, January 1998

An Engineered Tetrahymena tRNA Gln for in Vivo Incorporation of Unnatural Amino Acids into Proteins by Nonsense Suppression journal, September 1996

Incorporation of Trifluoromethionine into a Phage Lysozyme: Implications and a New Marker for Use in Protein 19 F NMR † journal, March 1997

2 .ANG. Resolution Structure of DppA, a Periplasmic Dipeptide Transport/Chemosensory Receptor journal, December 1995

Enzyme-generated intracellular fluorescence for single-cell reporter gene analysis utilizing Escherichia coli-glucuronidase journal, August 1996

Differences in Backbone Structure between Angiotensin II Agonists and Type I Antagonists journal, November 1995

Engineering a tRNA and aminoacyl-tRNA synthetase for the site-specific incorporation of unnatural amino acids into proteins in vivo journal, September 1997

Protein Engineering by In Vivo Incorporation of Non-Natural Amino Acids: Control of Incorporation of Methionine Analogues by Methionyl-tRNA Synthetase journal, November 2000

Enlarging the Amino Acid Set of Escherichia coli by Infiltration of the Valine Coding Pathway journal, April 2001

Site-Directed Mutagenesis with an Expanded Genetic Code journal, June 1995

A synthetic IgG-binding domain based on staphylococcal protein A journal, January 1987

Co-Expression of Yeast Amber Suppressor tRNATyr and Tyrosyl-tRNA Synthetase in Escherichia coli: Possibility to Expand the Genetic Code journal, December 1998

Barnase and barstar: Expression of its cloned inhibitor permits expression of a cloned ribonuclease journal, August 1988

Substrate Specificity Is Determined by Amino Acid Binding Pocket Size in Escherichia coli Phenylalanyl-tRNA Synthetase journal, June 1994

Biosynthetic site-specific incorporation of a non-natural amino acid into a polypeptide journal, September 1989

Residue-specific bioincorporation of non-natural, biologically active amino acids into proteins as possible drug carriers: Structure and stability of the per-thiaproline mutant of annexin V journal, January 1998

Complete Genome Sequence of the Methanogenic Archaeon, Methanococcus jannaschii journal, August 1996

New Photolabeling and Crosslinking Methods journal, June 1993

Universal rules and idiosyncratic features in tRNA identity journal, November 1998

Structure of T7 RNA polymerase complexed to the transcriptional inhibitor T7 lysozyme journal, July 1998

Absolute configuration of the enantiomers of 7-chloro-4-[[4-(diethylamino)-1-methylbutyl]amino]quinoline (chloroquine) journal, March 1988

Site-Specific Protein Modification Using a Ketone Handle journal, January 1996

Nicotinic receptor binding site probed with unnatural amino acid incorporation in intact cells journal, April 1995

Probing Protein Structure and Function with an Expanded Genetic Code journal, March 1995

Highly Precise Shape Mimicry by a Difluorotoluene Deoxynucleoside, a Replication-Competent Substitute for Thymidine journal, January 1997

Site-specific incorporation of biotinylated amino acids to identify surface-exposed residues in integral membrane proteins journal, October 1997

A general approach for the generation of orthogonal tRNAs journal, September 2001

Structure of tyrosyl-tRNA synthetase refined at 2.3 Å resolution: Interaction of the enzyme with the tyrosyl adenylate intermediate journal, July 1989

Major Anticodon-binding Region Missing from an Archaebacterial tRNA Synthetase journal, December 1999

A Novel Copper-Mediated DNA Base Pair journal, November 2000

Backbone Mutations in Transmembrane Domains of a Ligand-Gated Ion Channel journal, January 1999

Strategies for in vitro and in vivo translation with non-natural amino acids journal, December 1996

A New Functional Suppressor tRNA/Aminoacyl−tRNA Synthetase Pair for the in Vivo Incorporation of Unnatural Amino Acids into Proteins journal, May 2000

Efforts toward Expansion of the Genetic Alphabet: DNA Polymerase Recognition of a Highly Stable, Self-Pairing Hydrophobic Base journal, December 1999

Quisqualic acid analogs: synthesis of .beta.-heterocyclic 2-aminopropanoic acid derivatives and their activity at a novel quisqualate-sensitized site journal, November 1992

Noninvasive Tracing of Recombinant Proteins with “Fluorophenylalanine-Fingers” journal, August 2000

Libraries of hybrid proteins from distantly related sequences journal, May 2001

5′–3′ Exonucleases in phosphorothioate-based oligonucleotide-directed mutagenesis journal, January 1988

Compilation of tRNA sequences and sequences of tRNA genes journal, January 1998

Glycine tRNA mutants with normal anticodon loop size cause -1 frameshifting. journal, October 1989

A general method for site-specific incorporation of unnatural amino acids into proteins journal, April 1989

Bioincorporation of telluromethionine into proteins: a promising new approach for X-ray structure analysis of proteins journal, July 1997

Production and fluorescence-activated cell sorting of Escherichia coli expressing a functional antibody fragment on the external surface. journal, November 1993

Efficient introduction of alkene functionality into proteins in vivo journal, May 1998

Enzymatic incorporation of a new base pair into DNA and RNA journal, October 1989

Unprotected Peptides as Building Blocks for the Synthesis of Peptide Dendrimers with Oxime, Hydrazone, and Thiazolidine Linkages journal, April 1995

Major tyrosine identity determinants in Methanococcus jannaschii and Saccharomyces cerevisiae tRNA Tyr are conserved but expressed differently : tRNA identity for journal, February 2001

C EREAL C HROMOSOME S TRUCTURE , E VOLUTION, AND P AIRING journal, June 2000

Fluorinated Coiled-Coil Proteins Prepared In Vivo Display Enhanced Thermal and Chemical Stability journal, April 2001

Twenty-first aminoacyl-tRNA synthetase-suppressor tRNA pairs for possible use in site-specific incorporation of amino acid analogues into proteins in eukaryotes and in eubacteria
journal, January 2001

Bio–incorporation of telluromethionine into buried residues of dihydrofolate reductase
journal, May 1994

An unnatural base pair for incorporating amino acid analogs into proteins
journal, February 2002

Site-specific incorporation of novel backbone structures into proteins
journal, January 1992

An engineered Escherichia coli tyrosyl-tRNA synthetase for site-specific incorporation of an unnatural amino acid into proteins in eukaryotic translation and its application in a wheat germ cell-free system
journal, July 2002

In vitro protein engineering using synthetic tRNAAla with different anticodons
journal, August 1993

An efficient system for the evolution of aminoacyl-tRNA synthetase specificity
journal, September 2002

Modification of the amino acid specificity of tyrosyl-tRNA synthetase by protein engineering
journal, March 1993

Flash Decaging of Tyrosine Sidechains in an Ion Channel
journal, April 1998

Synthesis of 4-substituted prolines as conformationally constrained amino acid analogs
journal, April 1989

Probing the Structure and Function of the Tachykinin Neurokinin-2 Receptor through Biosynthetic Incorporation of Fluorescent Amino Acids at Specific Sites
journal, August 1996

Mutational Analysis of Invariant Valine B12 in Insulin: Implications for Receptor Binding
journal, November 2000

Relaxing the substrate specificity of an aminoacyl-tRNA synthetase allows in vitro and in vivo synthesis of proteins containing unnatural amino acids
journal, May 1995

A set of plasmids constitutively producing different RNA levels in Escherichia coli
journal, July 1999

Efforts toward Expansion of the Genetic Alphabet: Replication of DNA with Three Base Pairs
journal, August 2001

Photocrosslinking of the signal sequence of nascent preprolactin to the 54-kilodalton polypeptide of the signal recognition particle.
journal, November 1986

Adding l-3-(2-Naphthyl)alanine to the Genetic Code of E. coli
journal, March 2002

Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): a vehicle for direct determination of three-dimensional structure.
journal, May 1990

Evolutionary relationship between Halobacterium cutirubrum and eukaryotes determined by use of aminoacyl-tRNA synthetases as phylogenetic probes
journal, March 1980

[15] Biosynthetic method for introducing unnatural amino acids site-specifically into proteins
book, January 1991

Human Tyrosyl-tRNA Synthetase Shares Amino Acid Sequence Homology with a Putative Cytokine
journal, May 1997

Rational Design of an Unnatural Base Pair with Increased Kinetic Selectivity
journal, September 2000

Unnatural amino acids as probes of protein structure and function
journal, December 2000

TRNA2Gln Su+2 mutants that increase amber suppression.
journal, January 1981

Progress toward the evolution of an organism with an expanded genetic code
journal, April 1999

Enzymatic incorporation of a new base pair into DNA and RNA extends the genetic alphabet
journal, January 1990

Construction of Escherichia coli amber suppressor tRNA genes: II. Synthesis of additional tRNA genes and improvement of suppressor efficiency
journal, June 1990

Editing of errors in selection of amino acids for protein synthesis.
journal, January 1992

Genetic code in evolution: switching species-specific aminoacylation with a peptide transplant
journal, January 1998

An Engineered Tetrahymena tRNA ^Gln for in Vivo Incorporation of Unnatural Amino Acids into Proteins by Nonsense Suppression
journal, September 1996

Incorporation of Trifluoromethionine into a Phage Lysozyme: Implications and a New Marker for Use in Protein ¹⁹ F NMR ^†
journal, March 1997

2 .ANG. Resolution Structure of DppA, a Periplasmic Dipeptide Transport/Chemosensory Receptor
journal, December 1995

Enzyme-generated intracellular fluorescence for single-cell reporter gene analysis utilizing Escherichia coli-glucuronidase
journal, August 1996

Differences in Backbone Structure between Angiotensin II Agonists and Type I Antagonists
journal, November 1995

Engineering a tRNA and aminoacyl-tRNA synthetase for the site-specific incorporation of unnatural amino acids into proteins in vivo
journal, September 1997

Protein Engineering by In Vivo Incorporation of Non-Natural Amino Acids: Control of Incorporation of Methionine Analogues by Methionyl-tRNA Synthetase
journal, November 2000

Enlarging the Amino Acid Set of Escherichia coli by Infiltration of the Valine Coding Pathway
journal, April 2001

Site-Directed Mutagenesis with an Expanded Genetic Code
journal, June 1995

A synthetic IgG-binding domain based on staphylococcal protein A
journal, January 1987

Co-Expression of Yeast Amber Suppressor tRNATyr and Tyrosyl-tRNA Synthetase in Escherichia coli: Possibility to Expand the Genetic Code
journal, December 1998

Barnase and barstar: Expression of its cloned inhibitor permits expression of a cloned ribonuclease
journal, August 1988

Substrate Specificity Is Determined by Amino Acid Binding Pocket Size in Escherichia coli Phenylalanyl-tRNA Synthetase
journal, June 1994

Biosynthetic site-specific incorporation of a non-natural amino acid into a polypeptide
journal, September 1989

Residue-specific bioincorporation of non-natural, biologically active amino acids into proteins as possible drug carriers: Structure and stability of the per-thiaproline mutant of annexin V
journal, January 1998

Complete Genome Sequence of the Methanogenic Archaeon, Methanococcus jannaschii
journal, August 1996

New Photolabeling and Crosslinking Methods
journal, June 1993

Universal rules and idiosyncratic features in tRNA identity
journal, November 1998

Structure of T7 RNA polymerase complexed to the transcriptional inhibitor T7 lysozyme
journal, July 1998

Absolute configuration of the enantiomers of 7-chloro-4-[[4-(diethylamino)-1-methylbutyl]amino]quinoline (chloroquine)
journal, March 1988

Site-Specific Protein Modification Using a Ketone Handle
journal, January 1996

Nicotinic receptor binding site probed with unnatural amino acid incorporation in intact cells
journal, April 1995

Probing Protein Structure and Function with an Expanded Genetic Code
journal, March 1995

Highly Precise Shape Mimicry by a Difluorotoluene Deoxynucleoside, a Replication-Competent Substitute for Thymidine
journal, January 1997

Site-specific incorporation of biotinylated amino acids to identify surface-exposed residues in integral membrane proteins
journal, October 1997

A general approach for the generation of orthogonal tRNAs
journal, September 2001

Structure of tyrosyl-tRNA synthetase refined at 2.3 Å resolution: Interaction of the enzyme with the tyrosyl adenylate intermediate
journal, July 1989

Major Anticodon-binding Region Missing from an Archaebacterial tRNA Synthetase
journal, December 1999

A Novel Copper-Mediated DNA Base Pair
journal, November 2000

Backbone Mutations in Transmembrane Domains of a Ligand-Gated Ion Channel
journal, January 1999

Strategies for in vitro and in vivo translation with non-natural amino acids
journal, December 1996

A New Functional Suppressor tRNA/Aminoacyl−tRNA Synthetase Pair for the in Vivo Incorporation of Unnatural Amino Acids into Proteins
journal, May 2000

Efforts toward Expansion of the Genetic Alphabet: DNA Polymerase Recognition of a Highly Stable, Self-Pairing Hydrophobic Base
journal, December 1999

Quisqualic acid analogs: synthesis of .beta.-heterocyclic 2-aminopropanoic acid derivatives and their activity at a novel quisqualate-sensitized site
journal, November 1992

Noninvasive Tracing of Recombinant Proteins with “Fluorophenylalanine-Fingers”
journal, August 2000

Libraries of hybrid proteins from distantly related sequences
journal, May 2001

5′–3′ Exonucleases in phosphorothioate-based oligonucleotide-directed mutagenesis
journal, January 1988

Compilation of tRNA sequences and sequences of tRNA genes
journal, January 1998

Glycine tRNA mutants with normal anticodon loop size cause -1 frameshifting.
journal, October 1989

A general method for site-specific incorporation of unnatural amino acids into proteins
journal, April 1989

Bioincorporation of telluromethionine into proteins: a promising new approach for X-ray structure analysis of proteins
journal, July 1997

Production and fluorescence-activated cell sorting of Escherichia coli expressing a functional antibody fragment on the external surface.
journal, November 1993

Efficient introduction of alkene functionality into proteins in vivo
journal, May 1998

Enzymatic incorporation of a new base pair into DNA and RNA
journal, October 1989

Unprotected Peptides as Building Blocks for the Synthesis of Peptide Dendrimers with Oxime, Hydrazone, and Thiazolidine Linkages
journal, April 1995

Major tyrosine identity determinants in Methanococcus jannaschii and Saccharomyces cerevisiae tRNA ^Tyr are conserved but expressed differently : tRNA identity for
journal, February 2001

C EREAL C HROMOSOME S TRUCTURE , E VOLUTION, AND P AIRING
journal, June 2000

Fluorinated Coiled-Coil Proteins Prepared In Vivo Display Enhanced Thermal and Chemical Stability
journal, April 2001

693. A new synthesis of glutamine and of γ-dipeptides of glutamic acid from phthalylated intermediates
journal, January 1949

Toward the experimental codon reassignment in vivo : protein building with an expanded amino acid repertoire
journal, January 1999

Exploring the Limits of Codon and Anticodon Size
journal, February 2002