WO2002081490A8 - Computer-directed assembly of a polynucleotide encoding a target polypeptide - Google Patents

Computer-directed assembly of a polynucleotide encoding a target polypeptide

Info

Publication number
WO2002081490A8
WO2002081490A8 PCT/US2002/001649 US0201649W WO02081490A8 WO 2002081490 A8 WO2002081490 A8 WO 2002081490A8 US 0201649 W US0201649 W US 0201649W WO 02081490 A8 WO02081490 A8 WO 02081490A8
Authority
WO
WIPO (PCT)
Prior art keywords
computer
target polypeptide
target
polynucleotide encoding
polynucleotide
Prior art date
Application number
PCT/US2002/001649
Other languages
French (fr)
Other versions
WO2002081490A2 (en
WO2002081490A3 (en
Inventor
Glen A Evans
Original Assignee
Egea Biosciences Inc
Glen A Evans
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Egea Biosciences Inc, Glen A Evans filed Critical Egea Biosciences Inc
Priority to KR1020037009589A priority Critical patent/KR100860291B1/en
Priority to DE60227361T priority patent/DE60227361D1/en
Priority to MXPA03006344A priority patent/MXPA03006344A/en
Priority to CA002433463A priority patent/CA2433463A1/en
Priority to DK02739079T priority patent/DK1385950T3/en
Priority to EP02739079A priority patent/EP1385950B1/en
Priority to JP2002579476A priority patent/JP2004533228A/en
Priority to US10/250,894 priority patent/US20040241650A1/en
Publication of WO2002081490A2 publication Critical patent/WO2002081490A2/en
Publication of WO2002081490A3 publication Critical patent/WO2002081490A3/en
Publication of WO2002081490A8 publication Critical patent/WO2002081490A8/en

Links

Classifications

    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K1/00—General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/66—General methods for inserting a gene into a vector to form a recombinant vector using cleavage and ligation; Use of non-functional linkers or adaptors, e.g. linkers containing the sequence for a restriction endonuclease
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/20—Sequence assembly
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583—Features relative to the processes being carried out
    • B01J2219/00603—Making arrays on substantially continuous surfaces
    • B01J2219/00659—Two-dimensional arrays
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/0068—Means for controlling the apparatus of the process
    • B01J2219/00686—Automatic
    • B01J2219/00689—Automatic using computers
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/0068—Means for controlling the apparatus of the process
    • B01J2219/00695—Synthesis control routines, e.g. using computer programs
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/0068—Means for controlling the apparatus of the process
    • B01J2219/007—Simulation or vitual synthesis
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00718—Type of compounds synthesised
    • B01J2219/0072—Organic compounds
    • B01J2219/00722—Nucleotides
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07B—GENERAL METHODS OF ORGANIC CHEMISTRY; APPARATUS THEREFOR
    • C07B2200/00—Indexing scheme relating to specific properties of organic compounds
    • C07B2200/11—Compounds covalently bound to a solid support
    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B40/00—Libraries per se, e.g. arrays, mixtures
    • C40B40/04—Libraries containing only organic compounds
    • C40B40/06—Libraries containing nucleotides or polynucleotides, or derivatives thereof

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • Physics & Mathematics (AREA)
  • Organic Chemistry (AREA)
  • General Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • General Engineering & Computer Science (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Biomedical Technology (AREA)
  • Molecular Biology (AREA)
  • Biochemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Analytical Chemistry (AREA)
  • Plant Pathology (AREA)
  • Theoretical Computer Science (AREA)
  • Microbiology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Medical Informatics (AREA)
  • Evolutionary Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Medicinal Chemistry (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Peptides Or Proteins (AREA)
  • Medicines That Contain Protein Lipid Enzymes And Other Medicines (AREA)
  • Preparation Of Compounds By Using Micro-Organisms (AREA)
  • Medicines Containing Antibodies Or Antigens For Use As Internal Diagnostic Agents (AREA)
  • Pharmaceuticals Containing Other Organic And Inorganic Compounds (AREA)

Abstract

The present invention outlines a novel approach to utilizing the results of genomic sequence information by computer-directed polynucleotide assembly based upon information available in databases such as the human genome database. Specifically, the present invention may be used to select, synthesize and assemble a novel, synthetic target polynucleotide sequence encoding a target polypeptide. The target polynucleotide may encode a target polypeptide that exhibits enhanced or altered biological activity as compared to a model polypeptide encoded by a natural (wild-type) or model polynucleotide sequence.
PCT/US2002/001649 2001-01-19 2002-01-18 Computer-directed assembly of a polynucleotide encoding a target polypeptide WO2002081490A2 (en)

Priority Applications (8)

Application Number Priority Date Filing Date Title
KR1020037009589A KR100860291B1 (en) 2001-01-19 2002-01-18 Computer-directed assembly of a polynucleotide encoding a target polypeptide
DE60227361T DE60227361D1 (en) 2001-01-19 2002-01-18 COMPUTER MEDIATED ASSEMBLY OF POLYNUCLEOTIDES ENCODING A TARGETED POLYPEPTIDE
MXPA03006344A MXPA03006344A (en) 2001-01-19 2002-01-18 Computer-directed assembly of a polynucleotide encoding a target polypeptide.
CA002433463A CA2433463A1 (en) 2001-01-19 2002-01-18 Computer-directed assembly of a polynucleotide encoding a target polypeptide
DK02739079T DK1385950T3 (en) 2001-01-19 2002-01-18 Computer controlled assembly of a polynucleotide encoding a target polypeptide
EP02739079A EP1385950B1 (en) 2001-01-19 2002-01-18 Computer-directed assembly of a polynucleotide encoding a target polypeptide
JP2002579476A JP2004533228A (en) 2001-01-19 2002-01-18 Computer-based assembly of a polynucleotide encoding a target polypeptide
US10/250,894 US20040241650A1 (en) 2001-01-19 2002-01-18 Computer-directed assembly of a polynucleotide encoding a target polypeptide

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US26269301P 2001-01-19 2001-01-19
US60/262,693 2001-01-19

Publications (3)

Publication Number Publication Date
WO2002081490A2 WO2002081490A2 (en) 2002-10-17
WO2002081490A3 WO2002081490A3 (en) 2003-11-27
WO2002081490A8 true WO2002081490A8 (en) 2004-05-21

Family

ID=22998593

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2002/001649 WO2002081490A2 (en) 2001-01-19 2002-01-18 Computer-directed assembly of a polynucleotide encoding a target polypeptide

Country Status (13)

Country Link
US (9) US20030138782A1 (en)
EP (1) EP1385950B1 (en)
JP (1) JP2004533228A (en)
KR (1) KR100860291B1 (en)
AT (1) ATE399857T1 (en)
AU (1) AU2008201007A1 (en)
CA (1) CA2433463A1 (en)
DE (1) DE60227361D1 (en)
DK (1) DK1385950T3 (en)
ES (1) ES2309175T3 (en)
MX (1) MXPA03006344A (en)
PT (1) PT1385950E (en)
WO (1) WO2002081490A2 (en)

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US9023601B2 (en) 2002-09-12 2015-05-05 Gen9, Inc. Microarray synthesis and assembly of gene-length polynucleotides
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US9132394B2 (en) 2008-09-23 2015-09-15 Bio-Rad Laboratories, Inc. System for detection of spaced droplets
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US9216414B2 (en) 2009-11-25 2015-12-22 Gen9, Inc. Microfluidic devices and methods for gene synthesis
US9217144B2 (en) 2010-01-07 2015-12-22 Gen9, Inc. Assembly of high fidelity polynucleotides
US9222128B2 (en) 2011-03-18 2015-12-29 Bio-Rad Laboratories, Inc. Multiplexed digital assays with combinatorial use of signals
US9347059B2 (en) 2011-04-25 2016-05-24 Bio-Rad Laboratories, Inc. Methods and compositions for nucleic acid analysis
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US20050221340A1 (en) 2005-10-06
ES2309175T3 (en) 2008-12-16
US20050244841A1 (en) 2005-11-03
MXPA03006344A (en) 2004-12-03
DE60227361D1 (en) 2008-08-14
US20050118628A1 (en) 2005-06-02
WO2002081490A2 (en) 2002-10-17
EP1385950A2 (en) 2004-02-04
US20050053997A1 (en) 2005-03-10
KR100860291B1 (en) 2008-09-25
DK1385950T3 (en) 2008-11-03
KR20030077582A (en) 2003-10-01
PT1385950E (en) 2008-08-12
US20070054277A1 (en) 2007-03-08
WO2002081490A3 (en) 2003-11-27
US20060154283A1 (en) 2006-07-13
US20040241650A1 (en) 2004-12-02
JP2004533228A (en) 2004-11-04
US20030138782A1 (en) 2003-07-24
ATE399857T1 (en) 2008-07-15
US20050191648A1 (en) 2005-09-01
CA2433463A1 (en) 2002-10-17

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