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WO2007123742A3 - Methods and compositions for increasing the fidelity of multiplex nucleic acid assembly - Google Patents

Methods and compositions for increasing the fidelity of multiplex nucleic acid assembly Download PDF

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Publication number
WO2007123742A3
WO2007123742A3 PCT/US2007/007988 US2007007988W WO2007123742A3 WO 2007123742 A3 WO2007123742 A3 WO 2007123742A3 US 2007007988 W US2007007988 W US 2007007988W WO 2007123742 A3 WO2007123742 A3 WO 2007123742A3
Authority
WO
WIPO (PCT)
Prior art keywords
fidelity
nucleic acid
compositions
increasing
acid assembly
Prior art date
Application number
PCT/US2007/007988
Other languages
French (fr)
Other versions
WO2007123742A2 (en
Inventor
Brian M Baynes
Kenneth G Nesmith
Gerald Thomas Marsischky
Jennifer A Camacho
Original Assignee
Codon Devices Inc
Brian M Baynes
Kenneth G Nesmith
Gerald Thomas Marsischky
Jennifer A Camacho
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 Codon Devices Inc, Brian M Baynes, Kenneth G Nesmith, Gerald Thomas Marsischky, Jennifer A Camacho filed Critical Codon Devices Inc
Publication of WO2007123742A2 publication Critical patent/WO2007123742A2/en
Publication of WO2007123742A3 publication Critical patent/WO2007123742A3/en

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Classifications

    • 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
    • C12N15/64—General methods for preparing the vector, for introducing it into the cell or for selecting the vector-containing host
    • 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
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/686—Polymerase chain reaction [PCR]

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  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Chemical & Material Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Organic Chemistry (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • General Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • Biomedical Technology (AREA)
  • Molecular Biology (AREA)
  • Microbiology (AREA)
  • Biophysics (AREA)
  • Physics & Mathematics (AREA)
  • Biochemistry (AREA)
  • General Health & Medical Sciences (AREA)
  • Plant Pathology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Cell Biology (AREA)
  • Analytical Chemistry (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Immunology (AREA)
  • Preparation Of Compounds By Using Micro-Organisms (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)

Abstract

Certain aspects of the present invention provide methods for increasing the fidelity of nucleic acid assembly reactions. Fidelity-optimized conditions may be used in certain embodiments. Nucleic acid binding proteins and/or recombinases (e.g., heat stable variants) may be used in some embodiments. A RecA protein (e.g., a heat stable RecA) may be included in some assembly reactions. Aspects of the invention also provide related kits, compositions, devices, and systems to increase the fidelity of multiplex nucleic acid assembly reaction.
PCT/US2007/007988 2006-03-31 2007-03-30 Methods and compositions for increasing the fidelity of multiplex nucleic acid assembly WO2007123742A2 (en)

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US78844006P 2006-03-31 2006-03-31
US78829306P 2006-03-31 2006-03-31
US60/788,293 2006-03-31
US60/788,440 2006-03-31

Publications (2)

Publication Number Publication Date
WO2007123742A2 WO2007123742A2 (en) 2007-11-01
WO2007123742A3 true WO2007123742A3 (en) 2008-02-28

Family

ID=38535591

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2007/007988 WO2007123742A2 (en) 2006-03-31 2007-03-30 Methods and compositions for increasing the fidelity of multiplex nucleic acid assembly

Country Status (1)

Country Link
WO (1) WO2007123742A2 (en)

Cited By (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9023601B2 (en) 2002-09-12 2015-05-05 Gen9, Inc. Microarray synthesis and assembly of gene-length polynucleotides
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
US11845054B2 (en) 2010-11-12 2023-12-19 Gen9, Inc. Methods and devices for nucleic acids synthesis

Families Citing this family (12)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US8053191B2 (en) 2006-08-31 2011-11-08 Westend Asset Clearinghouse Company, Llc Iterative nucleic acid assembly using activation of vector-encoded traits
US8999679B2 (en) 2008-12-18 2015-04-07 Iti Scotland Limited Method for assembly of polynucleic acid sequences
US10207240B2 (en) 2009-11-03 2019-02-19 Gen9, Inc. Methods and microfluidic devices for the manipulation of droplets in high fidelity polynucleotide assembly
GB2481425A (en) 2010-06-23 2011-12-28 Iti Scotland Ltd Method and device for assembling polynucleic acid sequences
WO2012064975A1 (en) 2010-11-12 2012-05-18 Gen9, Inc. Protein arrays and methods of using and making the same
US20130059296A1 (en) 2011-08-26 2013-03-07 Gen9, Inc. Compositions and Methods For High Fidelity Assembly of Nucleic Acids
US9150853B2 (en) 2012-03-21 2015-10-06 Gen9, Inc. Methods for screening proteins using DNA encoded chemical libraries as templates for enzyme catalysis
EP4001427A1 (en) 2012-04-24 2022-05-25 Gen9, Inc. Methods for sorting nucleic acids and multiplexed preparative in vitro cloning
AU2013280661A1 (en) 2012-06-25 2015-01-22 Gen9, Inc. Methods for nucleic acid assembly and high throughput sequencing
DK3828277T3 (en) 2013-03-13 2023-09-04 Gen9 Inc COMPOSITIONS, METHODS AND APPARATUS FOR THE SYNTHESIS OF OLIGONUCLEOTIDES
EP3362577B1 (en) 2015-10-16 2024-07-03 Qiagen Sciences, LLC Methods and kits for highly multiplex single primer extension
GB2566986A (en) 2017-09-29 2019-04-03 Evonetix Ltd Error detection during hybridisation of target double-stranded nucleic acid

Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2002101004A2 (en) * 2001-06-08 2002-12-19 Shanghai Mendel Dna Center Co., Ltd Low-temperature cycle extension of dna with high priming specificity
US20040241655A1 (en) * 2003-05-29 2004-12-02 Yuchi Hwang Conditional touchdown multiplex polymerase chain reaction
WO2006044956A1 (en) * 2004-10-18 2006-04-27 Codon Devices, Inc. Methods for assembly of high fidelity synthetic polynucleotides

Patent Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2002101004A2 (en) * 2001-06-08 2002-12-19 Shanghai Mendel Dna Center Co., Ltd Low-temperature cycle extension of dna with high priming specificity
US20040241655A1 (en) * 2003-05-29 2004-12-02 Yuchi Hwang Conditional touchdown multiplex polymerase chain reaction
WO2006044956A1 (en) * 2004-10-18 2006-04-27 Codon Devices, Inc. Methods for assembly of high fidelity synthetic polynucleotides

Non-Patent Citations (5)

* Cited by examiner, † Cited by third party
Title
HENEGARIU O ET AL: "MULTIPLEX PCR: CRITICAL PARAMETERS AND STEP-BY-STEP PROTOCOL", BIOTECHNIQUES, INFORMA LIFE SCIENCES PUBLISHING, WESTBOROUGH, MA, US, vol. 23, no. 3, September 1997 (1997-09-01), pages 504 - 511, XP000703350, ISSN: 0736-6205 *
SHIGEMORI YASUSHI ET AL: "Multiplex PCR: use of heat-stable Thermus thermophilus RecA protein to minimize non-specific PCR products", NUCLEIC ACIDS RESEARCH, vol. 33, no. 14, 2005, XP002454038, ISSN: 0305-1048 *
STEMMER W P C ET AL: "Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides", GENE, ELSEVIER, AMSTERDAM, NL, vol. 164, no. 1, 1995, pages 49 - 53, XP004041916, ISSN: 0378-1119 *
TIAN J ET AL: "Accurate multiplex gene synthesis from programmable DNA microchips", NATURE, NATURE PUBLISHING GROUP, LONDON, GB, vol. 432, no. 7020, 23 December 2004 (2004-12-23), pages 1050 - 1054, XP002371017, ISSN: 0028-0836 *
XIONG AI-SHENG ET AL: "A simple, rapid, high-fidelity and cost-effective PCR-based two-step DNA synthesis method for long gene sequences", NUCLEIC ACIDS RESEARCH, vol. 32, no. 12, July 2004 (2004-07-01), XP002454037, ISSN: 0305-1048 *

Cited By (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9023601B2 (en) 2002-09-12 2015-05-05 Gen9, Inc. Microarray synthesis and assembly of gene-length polynucleotides
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
US11845054B2 (en) 2010-11-12 2023-12-19 Gen9, Inc. Methods and devices for nucleic acids synthesis

Also Published As

Publication number Publication date
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