U.S. patents available from 1976 to present.
U.S. patent applications available from 2005 to present.

Methods for determining properties that affect an expression property value of polynucleotides in an expression system

Patent 7561973 Issued on July 14, 2009. Estimated Expiration Date: Icon_subject July 31, 2028. Estimated Expiration Date is calculated based on simple USPTO term provisions. It does not account for terminal disclaimers, term adjustments, failure to pay maintenance fees, or other factors which might affect the term of a patent.

Patent References

Method for expression of bovine growth hormone
Patent #: 5254463
Issued on: 10/19/1993
Inventor: de Boer, et al.

Synthetic plant genes
Patent #: 5500365
Issued on: 03/19/1996
Inventor: Fischhoff, et al.

Synthetic DNA sequences having enhanced expression in monocotyledonous plants and method for preparation thereof
Patent #: 5689052
Issued on: 11/18/1997
Inventor: Brown, et al.

Overexpression of mammalian and viral proteins
Patent #: 5786464
Issued on: 07/28/1998
Inventor: Seed

High level expression of proteins
Patent #: 5795737
Issued on: 08/18/1998
Inventor: Seed, et al.

Method of eliminating inhibitory/ instability regions of mRNA
Patent #: 5965726
Issued on: 10/12/1999
Inventor: Pavlakis, et al.

High level expression of proteins
Patent #: 6114148
Issued on: 09/05/2000
Inventor: Seed, et al.

Method of eliminating inhibitory/instability regions of mRNA
Patent #: 6291664
Issued on: 09/18/2001
Inventor: Pavlakis, et al.

Method of eliminating inhibitory/instability regions of mRNA
Patent #: 6414132
Issued on: 07/02/2002
Inventor: Pavlakis, et al.

Highly expressible genes
Patent #: 6733994
Issued on: 05/11/2004
Inventor: Weiner, et al.

More ...

Inventors

Assignee

Application

No. 12184240 filed on 07/31/2008

US Classes:

702/19Biological or biochemical

Examiners

Primary: Zhou, Shubo (Joe)

Attorney, Agent or Firm

Foreign Patent References

  • WO 2005/013090 WO 02/01/2005
  • WO 2008/075911 WO 06/01/2008

International Classes

G01N 33/48
C12Q 1/00
C12Q 1/48
C12Q 1/68
C07H 21/02
C07H 21/04
C12Q 1/08

Abstract

A method of determining a property that affects expression of polynucleotides in an expression system. A plurality of polynucleotides, each encoding a polypeptide sequence, is constructed. An amino acid is encoded a plurality of times in both a first and second polynucleotide in the plurality. The amino acid is encodable by a plurality of synonymous codons including a first codon. The first codon is in the first polynucleotide at a first frequency relative to other synonymous codons, and is in the second polynucleotide at a second frequency relative to other synonymous codons. The first and second frequencies are different. Each polynucleotide is individually expressed in the expression system to measure an expression property value of the polynucleotides, thereby determining a property that affects expression of polynucleotides. The property is an effect that a frequency of use of one or more codons has on expression of polynucleotides in the expression system.

Other References

  • Office Action dated Jan. 26, 2009 for U.S. Appl. No. 12/184,234.
  • Zhao et al., 2008, “Gene Codon Composition Determines Differentiation-Dependent Expression of a Viral Capsid Gene in Keratinocytes In vitro and In Vivo,” Molecular and Cellular Biology 25, pp. 8643-8655.
  • Zeeberg, 2008, “Shannon Information Theoretic Computation of Synonymous Codon Usage Biases in Coding Regions of Human and Mouse Genomes,” Cold Spring Harbor of Laboratory Press 12, pp. 944-955, www.genome.org/cgi/doi/10.1101/gr.213402 last accessed Jul. 31, 2008.
  • Williams et al., 1988, “Design synthesis and expression of a human interleukin-2 gene incorporating the codon usage bias found in highly expressed Escherichia coli genes,” Nucleic Acids Research, 16:10453-10465.
  • Villalobos et al., 2006, “Gene Designer: a synthetic biology tool for constructing artificial DNA segments,” BMC Bioinformatics 7:285 doi:10.1186/1471-2105-7-285.
  • Upton et al., 2002, “A Dictionary of Statistics,” Oxford University Press, pp. 138-139.
  • Upton et al., 2002, “A Dictionary of Statistics,” Oxford University Press, pp. 83-84.
  • Terpe, K., 2003, “Overview of tag protein fusions: from molecular and biochemical fundamentals to commercial systems,” Appl. Microbiol Biotechnol. 60:523-533.
  • Smith et al., 2001, “Synonymous Codon Bias is not Caused by Mutation Bias in G+C Rich Genes in Humans,” Mol. Biol. Evol. 18, pp. 982-986.
  • Shields et al., 1987, “Synonymous codon usage in Bacillus subtilis refelects both translational selection and mutational biases,” Nucleic Acids Research 15, pp. 8023-8040.
  • Sharp et al., 1987, “The codon adaptation index—a measure of directional synonymous codon usage bias, and its potential applications,” Nucleic Acids Research, 15:1281-1295.
  • Perlak et al., 1991, “Modification of the coding sequence enhances plant expression of insect control protein genes,” Proc. Natl. Acad. Sci. USA, 88:3324-3328.
  • Narum et al., 2001, “Codon Optimization of Gene Fragments Encoding Plasmodium falciparum Merzoite Proteins Enhances DNA Vaccine Protein Expression and Immunogenicity in Mice,” Infection and Immunity 69, pp. 7250-7253.
  • McLachlan et al., 1984, “A method for measuring the non-random bias of a codon usage table,” Nucleic Acids Research 12, pp. 9567-9575.
  • Makoff et al., 1989, “Expression of tetanus toxin fragment C in E.coli: high level expression by removing rare codons,” Nucleic Acids Research, 17:10191-10202.
  • Ko et al., 2005, “Optimization of Codon Usage Enhances the Immunogenicity of a DNA Vaccine Encoding Mycobacterial Antigen Ag85B,” Infection and Immunity 73, pp. 5666-5674.
  • Gustafsson et al., 2004, “Codon bias and heterologous protein expression,” Trends in Biotechnology, 22:346-353.
  • Gribskov et al., 1984, “The Codon Preference Plot: Graphic Analysis of Protein Coding Sequences and Prediction of Gene Expression,” Nucleic Acids Research 12, pp. 539-549.
  • Duret et al., 2000, “Determinants of Substitution Rates in Mammalian Rates in Mammalian Genes: Expression Pattern Affects Selection Intensity but not Mutation Rate,” Biol. Biol. Evol. 17, pp. 68-74.
  • Angellotti et al., 2007, “CodonO: codon usage bias analysis within and across genomes,” Nucleic Acids Research 35, Web Server Issue doi:10.1093/nar/gkm392, W132-W136.
  • U.S. Appl. No. 12/184,230, filed Jul. 31, 2008, Welch and Gustafsson.
  • U.S. Appl. No. 12/184,233, filed Jul. 31, 2008, Welch and Gustafsson.
  • U.S. Appl. No. 12/184,234, filed Jul. 31, 2008, Welch and Gustafsson.
  • Vervoort et al., 2000, “Optimizing heterologous expression in Dictyostelium: importance of 5' codon adaptation,” Nucleic Acids Res., 28 pp. 2069-2074.
  • Hu et al., 1996, “Specific Replacement of Consecutive AGG Codons Results in High-Level Expression of Human Cardiac Troponin T in Escherichia coli,” Protein Expression and Purification 7 pp. 289-293.
  • Carton et al., 2007, “Codon engineering for improved antibody expression in mammalian cells,” Protein Expression and Purification 55, pp. 279-286.
  • Grote et al., 2005, “JCat: a novel tool to adapt codon usage of a target gene to its potential expression host”, Nucleic Acids Research, 33, Web Server issue doi: 10.1093/nar/gki376, W526-W531.
  • Angellotti et al., 2007, “CodonO: codon usage bias analysis within and across genomes”, Nucleic Acids Research, 35, Web Server issue doi: 10.1093/nar/gkm392, W132-W136.
  • Duret et al., Proc. Natl. Acad. Sci. USA, vol. 96, pp. 4482-4487, 1999.
  • Fuglsang, A., Gene, vol. 320, pp. 185-190, 2003.
  • Fuglsang, A., Antonie van Leeuwenhoek, vol. 86, pp. 135-147, 2004.
  • Park et al., Protein Expression and Purification, vol. 24, pp. 470-480, 2002.
PatentsPlus Images
Enhanced PDF formats
loading...
PatentsPlus: add to cart
PatentsPlus: add to cartSearch-enhanced full patent PDF image
$9.95more info
PatentsPlus: add to cart
PatentsPlus: add to cartIntelligent turbocharged patent PDFs with marked up images
$16.95more info
 
Sign InRegister
Username  
Password   
forgot password?