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WO2003054232A3 - Methods for removal of double-stranded oligonucleotides containing sequence errors using mismatch recognition proteins - Google Patents

Methods for removal of double-stranded oligonucleotides containing sequence errors using mismatch recognition proteins Download PDF

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Publication number
WO2003054232A3
WO2003054232A3 PCT/US2002/040138 US0240138W WO03054232A3 WO 2003054232 A3 WO2003054232 A3 WO 2003054232A3 US 0240138 W US0240138 W US 0240138W WO 03054232 A3 WO03054232 A3 WO 03054232A3
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WO
WIPO (PCT)
Prior art keywords
methods
duplexes
oligonucleotide
oligonucleotides
double
Prior art date
Legal status (The legal status 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 status listed.)
Ceased
Application number
PCT/US2002/040138
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French (fr)
Other versions
WO2003054232A2 (en
Inventor
John C Tabone
John T Mulligan
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Blue Heron Biotechnology Inc
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Blue Heron Biotechnology Inc
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Filing date
Publication date
Application filed by Blue Heron Biotechnology Inc filed Critical Blue Heron Biotechnology Inc
Priority to AU2002357249A priority Critical patent/AU2002357249A1/en
Publication of WO2003054232A2 publication Critical patent/WO2003054232A2/en
Publication of WO2003054232A3 publication Critical patent/WO2003054232A3/en
Anticipated expiration legal-status Critical
Ceased legal-status Critical Current

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    • 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

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  • Chemical & Material Sciences (AREA)
  • Organic Chemistry (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Microbiology (AREA)
  • Biochemistry (AREA)
  • Physics & Mathematics (AREA)
  • Molecular Biology (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Analytical Chemistry (AREA)
  • Immunology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Saccharide Compounds (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

In embodiments of the present invention, methods are provided for removing double-stranded oligonucleotide (e.g., DNA) molecules containing one or more sequence errors, generated during nucleic acid synthesis, from a population of correct oligonucleotide duplexes. In one embodiment, the oligonucleotides are generated enzymatically. Heteroduplex (containing mismatched bases) oligonucleotides may be created by denaturing and reannealing the population of duplexes. The reannealed oligonucleotide duplexes are contacted with a mismatch recognition protein that interacts with (e.g., binds and/or cleaves) the duplexes containing a base pair mismatch. The oligonucleotide heteroduplexes that have interacted with such a protein are separated, simultaneously with contacting or sequentially in a separate step, from homoduplexes. These methods are also used in another embodiment to remove heteroduplex oligonucleotides (e.g., DNA) that are formed directly from chemical nucleic acid synthesis.
PCT/US2002/040138 2001-12-13 2002-12-12 Methods for removal of double-stranded oligonucleotides containing sequence errors using mismatch recognition proteins Ceased WO2003054232A2 (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
AU2002357249A AU2002357249A1 (en) 2001-12-13 2002-12-12 Methods for removal of double-stranded oligonucleotides containing sequence errors using mismatch recognition proteins

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US34140901P 2001-12-13 2001-12-13
US60/341,409 2001-12-13

Publications (2)

Publication Number Publication Date
WO2003054232A2 WO2003054232A2 (en) 2003-07-03
WO2003054232A3 true WO2003054232A3 (en) 2003-12-11

Family

ID=23337431

Family Applications (1)

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PCT/US2002/040138 Ceased WO2003054232A2 (en) 2001-12-13 2002-12-12 Methods for removal of double-stranded oligonucleotides containing sequence errors using mismatch recognition proteins

Country Status (2)

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AU (1) AU2002357249A1 (en)
WO (1) WO2003054232A2 (en)

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US7323320B2 (en) 2002-09-12 2008-01-29 Combimatrix Corporation Microarray synthesis and assembly of gene-length polynucleotides
US9217144B2 (en) 2010-01-07 2015-12-22 Gen9, Inc. Assembly of high fidelity polynucleotides
US9216414B2 (en) 2009-11-25 2015-12-22 Gen9, Inc. Microfluidic devices and methods for gene synthesis
US11845054B2 (en) 2010-11-12 2023-12-19 Gen9, Inc. Methods and devices for nucleic acids synthesis

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US7932025B2 (en) 2002-12-10 2011-04-26 Massachusetts Institute Of Technology Methods for high fidelity production of long nucleic acid molecules with error control
US7879580B2 (en) 2002-12-10 2011-02-01 Massachusetts Institute Of Technology Methods for high fidelity production of long nucleic acid molecules
EP1613776A1 (en) * 2003-04-02 2006-01-11 Blue Heron Biotechnology, Inc. Error reduction in automated gene synthesis
ES2534744T3 (en) 2004-04-22 2015-04-28 Grifols Therapeutics Inc. Recombinantly modified plasmin
AU2005279931B2 (en) * 2004-08-27 2011-02-10 Wisconsin Alumni Research Foundation Method of error reduction in nucleic acid populations
WO2008027558A2 (en) 2006-08-31 2008-03-06 Codon Devices, Inc. Iterative nucleic acid assembly using activation of vector-encoded traits
CA2707266C (en) 2007-11-29 2013-12-31 Talecris Biotherapeutics, Inc. Recombinantly modified plasmin
EP2297317A4 (en) 2008-06-04 2011-12-07 Talecris Biotherapeutics Inc Composition, method and kit for preparing plasmin
WO2010025310A2 (en) 2008-08-27 2010-03-04 Westend Asset Clearinghouse Company, Llc Methods and devices for high fidelity polynucleotide synthesis
US8999679B2 (en) 2008-12-18 2015-04-07 Iti Scotland Limited Method for assembly of polynucleic acid sequences
PT2403865E (en) 2009-03-03 2015-11-18 Grifols Therapeutics Inc Methods for preparing plasminogen
WO2011056872A2 (en) 2009-11-03 2011-05-12 Gen9, Inc. Methods and microfluidic devices for the manipulation of droplets in high fidelity polynucleotide assembly
MX2012005527A (en) 2009-11-13 2012-08-08 Grifols Therapeutics Inc Von willebrand factor (vwf)-containing preparations, and methods, kits, and uses related thereto.
EP3597771A1 (en) 2009-11-25 2020-01-22 Gen9, Inc. Methods and apparatuses for chip-based dna error reduction
GB2481425A (en) 2010-06-23 2011-12-28 Iti Scotland Ltd Method and device for assembling polynucleic acid sequences
EP2637780B1 (en) 2010-11-12 2022-02-09 Gen9, Inc. Protein arrays and methods of using and making the same
US9752176B2 (en) 2011-06-15 2017-09-05 Ginkgo Bioworks, Inc. Methods for preparative in vitro cloning
EP3954770A1 (en) 2011-08-26 2022-02-16 Gen9, Inc. Compositions and methods for high fidelity assembly of nucleic acids
AU2012340501A1 (en) 2011-12-19 2013-07-11 Grifols, S.A. Compositions, methods, and kits for preparing sialylated recombinant proteins
US8691960B2 (en) 2012-02-29 2014-04-08 Duke University Oxidoreductases for enantioselective reactions
US9150853B2 (en) 2012-03-21 2015-10-06 Gen9, Inc. Methods for screening proteins using DNA encoded chemical libraries as templates for enzyme catalysis
WO2013163263A2 (en) 2012-04-24 2013-10-31 Gen9, Inc. Methods for sorting nucleic acids and multiplexed preparative in vitro cloning
LT2864531T (en) 2012-06-25 2019-03-12 Gen9, Inc. Methods for nucleic acid assembly and high throughput sequencing
EP4610368A3 (en) 2013-08-05 2025-11-05 Twist Bioscience Corporation De novo synthesized gene libraries
WO2016126987A1 (en) 2015-02-04 2016-08-11 Twist Bioscience Corporation Compositions and methods for synthetic gene assembly
WO2016126882A1 (en) 2015-02-04 2016-08-11 Twist Bioscience Corporation Methods and devices for de novo oligonucleic acid assembly
WO2016172377A1 (en) 2015-04-21 2016-10-27 Twist Bioscience Corporation Devices and methods for oligonucleic acid library synthesis
JP6982362B2 (en) 2015-09-18 2021-12-17 ツイスト バイオサイエンス コーポレーション Oligonucleic acid mutant library and its synthesis
KR20250053972A (en) 2015-09-22 2025-04-22 트위스트 바이오사이언스 코포레이션 Flexible substrates for nucleic acid synthesis
WO2017095958A1 (en) 2015-12-01 2017-06-08 Twist Bioscience Corporation Functionalized surfaces and preparation thereof
CN109996876A (en) 2016-08-22 2019-07-09 特韦斯特生物科学公司 The nucleic acid library of de novo formation
US10417457B2 (en) 2016-09-21 2019-09-17 Twist Bioscience Corporation Nucleic acid based data storage
JP7169975B2 (en) 2016-12-16 2022-11-11 ツイスト バイオサイエンス コーポレーション Immune synapse mutant library and its synthesis
EP3586255B1 (en) 2017-02-22 2025-01-15 Twist Bioscience Corporation Nucleic acid based data storage
EP3595674A4 (en) 2017-03-15 2020-12-16 Twist Bioscience Corporation VARIANT LIBRARIES OF THE IMMUNOLOGICAL SYNAPSE AND SYNTHESIS THEREOF
AU2018284227B2 (en) 2017-06-12 2024-05-02 Twist Bioscience Corporation Methods for seamless nucleic acid assembly
WO2018231864A1 (en) 2017-06-12 2018-12-20 Twist Bioscience Corporation Methods for seamless nucleic acid assembly
JP2020536504A (en) 2017-09-11 2020-12-17 ツイスト バイオサイエンス コーポレーション GPCR-coupled protein and its synthesis
US10894242B2 (en) 2017-10-20 2021-01-19 Twist Bioscience Corporation Heated nanowells for polynucleotide synthesis
CN120485344A (en) 2018-01-04 2025-08-15 特韦斯特生物科学公司 DNA-based digital information storage
JP2021526366A (en) 2018-05-18 2021-10-07 ツイスト バイオサイエンス コーポレーション Polynucleotides, Reagents, and Methods for Nucleic Acid Hybridization
WO2020139871A1 (en) 2018-12-26 2020-07-02 Twist Bioscience Corporation Highly accurate de novo polynucleotide synthesis
SG11202109322TA (en) 2019-02-26 2021-09-29 Twist Bioscience Corp Variant nucleic acid libraries for glp1 receptor
WO2020176680A1 (en) 2019-02-26 2020-09-03 Twist Bioscience Corporation Variant nucleic acid libraries for antibody optimization
CN109825431A (en) * 2019-03-18 2019-05-31 中国人民解放军军事科学院军事医学研究院 Oligonucleotide In Situ Assembler
CA3144644A1 (en) 2019-06-21 2020-12-24 Twist Bioscience Corporation Barcode-based nucleic acid sequence assembly
CA3155630A1 (en) 2019-09-23 2021-04-01 Twist Bioscience Corporation Variant nucleic acid libraries for single domain antibodies
AU2020356471A1 (en) 2019-09-23 2022-04-21 Twist Bioscience Corporation Variant nucleic acid libraries for CRTH2
CN115820625A (en) * 2022-12-05 2023-03-21 中国科学技术大学 Method, device and preparation method and kit for removing mismatched DNA

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WO1997021837A1 (en) * 1995-12-15 1997-06-19 Amersham Life Science, Inc. Methods for the detection and removal of mutant sequences that arise during enzymatic amplification using mismatch repair systems
WO1999022029A1 (en) * 1997-10-28 1999-05-06 The Regents Of The University Of California Dna base mismatch detection using flow cytometry
WO1999036575A1 (en) * 1998-01-15 1999-07-22 Valigene Corporation Multiplex vgid
WO2000024939A1 (en) * 1998-10-27 2000-05-04 Affymetrix, Inc. Complexity management and analysis of genomic dna
US6120992A (en) * 1993-11-04 2000-09-19 Valigene Corporation Use of immobilized mismatch binding protein for detection of mutations and polymorphisms, and allele identification in a diseased human

Patent Citations (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1993022457A1 (en) * 1992-04-24 1993-11-11 Massachusetts Institute Of Technology Screening for genetic variation
US6120992A (en) * 1993-11-04 2000-09-19 Valigene Corporation Use of immobilized mismatch binding protein for detection of mutations and polymorphisms, and allele identification in a diseased human
WO1997021837A1 (en) * 1995-12-15 1997-06-19 Amersham Life Science, Inc. Methods for the detection and removal of mutant sequences that arise during enzymatic amplification using mismatch repair systems
WO1999022029A1 (en) * 1997-10-28 1999-05-06 The Regents Of The University Of California Dna base mismatch detection using flow cytometry
WO1999036575A1 (en) * 1998-01-15 1999-07-22 Valigene Corporation Multiplex vgid
WO2000024939A1 (en) * 1998-10-27 2000-05-04 Affymetrix, Inc. Complexity management and analysis of genomic dna

Cited By (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7323320B2 (en) 2002-09-12 2008-01-29 Combimatrix Corporation 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

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Publication number Publication date
AU2002357249A1 (en) 2003-07-09
WO2003054232A2 (en) 2003-07-03

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