CA2744153C - Compositions and methods for the assembly of polynucleotides - Google Patents

Compositions and methods for the assembly of polynucleotides Download PDF

Info

Publication number
CA2744153C
CA2744153C CA2744153A CA2744153A CA2744153C CA 2744153 C CA2744153 C CA 2744153C CA 2744153 A CA2744153 A CA 2744153A CA 2744153 A CA2744153 A CA 2744153A CA 2744153 C CA2744153 C CA 2744153C
Authority
CA
Canada
Prior art keywords
nucleic acid
annealable linker
linker sequence
sequence
acid molecules
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.)
Active
Application number
CA2744153A
Other languages
English (en)
French (fr)
Other versions
CA2744153A1 (en
Inventor
Zach Serber
Raymond Lowe
Jeffrey A. Ubersax
Sunil S. Chandran
Erik Jedediah Dean
Darren M. Platt
Kenneth Toshiki Takeoka
Original Assignee
Amyris Inc
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 Amyris Inc filed Critical Amyris Inc
Publication of CA2744153A1 publication Critical patent/CA2744153A1/en
Application granted granted Critical
Publication of CA2744153C publication Critical patent/CA2744153C/en
Active legal-status Critical Current
Anticipated expiration legal-status Critical

Links

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
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1093—General methods of preparing gene libraries, not provided for in other subgroups
    • 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
    • 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
    • C12N15/63—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
    • 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
    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B50/00—Methods of creating libraries, e.g. combinatorial synthesis
    • C40B50/06—Biochemical methods, e.g. using enzymes or whole viable microorganisms

Landscapes

  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Chemical & Material Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Organic Chemistry (AREA)
  • General Engineering & Computer Science (AREA)
  • Biomedical Technology (AREA)
  • Biotechnology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Wood Science & Technology (AREA)
  • Zoology (AREA)
  • Molecular Biology (AREA)
  • Biochemistry (AREA)
  • Microbiology (AREA)
  • Biophysics (AREA)
  • Plant Pathology (AREA)
  • General Health & Medical Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • General Chemical & Material Sciences (AREA)
  • Medicinal Chemistry (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Cell Biology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)
  • Enzymes And Modification Thereof (AREA)
CA2744153A 2008-11-19 2009-11-19 Compositions and methods for the assembly of polynucleotides Active CA2744153C (en)

Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
US11610908P 2008-11-19 2008-11-19
US61/116,109 2008-11-19
US16223009P 2009-03-20 2009-03-20
US61/162,230 2009-03-20
PCT/US2009/065048 WO2010059763A1 (en) 2008-11-19 2009-11-19 Compositions and methods for the assembly of polynucleotides

Publications (2)

Publication Number Publication Date
CA2744153A1 CA2744153A1 (en) 2010-05-27
CA2744153C true CA2744153C (en) 2020-07-07

Family

ID=41698076

Family Applications (1)

Application Number Title Priority Date Filing Date
CA2744153A Active CA2744153C (en) 2008-11-19 2009-11-19 Compositions and methods for the assembly of polynucleotides

Country Status (12)

Country Link
US (3) US8221982B2 (enExample)
EP (1) EP2358875B1 (enExample)
JP (1) JP2012509084A (enExample)
KR (1) KR101794298B1 (enExample)
CN (1) CN102282255B (enExample)
AU (1) AU2009316660B2 (enExample)
BR (1) BRPI0922187B1 (enExample)
CA (1) CA2744153C (enExample)
MX (1) MX2011005195A (enExample)
SG (1) SG171760A1 (enExample)
WO (1) WO2010059763A1 (enExample)
ZA (1) ZA201103637B (enExample)

Families Citing this family (61)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP2358875B1 (en) * 2008-11-19 2015-08-12 Amyris, Inc. Compositions and methods for the assembly of polynucleotides
US7919605B1 (en) 2010-08-30 2011-04-05 Amyris, Inc. Nucleic acids, compositions and methods for the excision of target nucleic acids
CA2834375C (en) 2011-04-27 2020-07-14 Amyris, Inc. Methods for genomic modification
ES2628847T3 (es) 2011-11-09 2017-08-04 Amyris, Inc. Producción de isoprenoides derivados de acetil-coenzima a
US8332160B1 (en) 2011-11-17 2012-12-11 Amyris Biotechnologies, Inc. Systems and methods for engineering nucleic acid constructs using scoring techniques
WO2013106868A1 (en) * 2012-01-13 2013-07-18 Chromatin, Inc. Engineering plants with rate limiting farnesene metabolic genes
WO2013144257A1 (en) * 2012-03-27 2013-10-03 Dsm Ip Assets B.V. Cloning method
CA2877962C (en) * 2012-06-29 2018-06-05 Massachusetts Institute Of Technology Massively parallel combinatorial genetics
US9976162B2 (en) 2012-12-10 2018-05-22 Agilent Technologies, Inc. Pairing code directed assembly
BR112015023089A2 (pt) 2013-03-15 2017-11-21 Amyris Inc célula hospedeira, método para produzir um isoprenoide, e método para aumentar a produção de acetil-coa ou um composto derivado de acetil-coa
DK2986635T3 (en) 2013-04-18 2019-01-28 Fond Telethon EFFECTIVE DELIVERY OF BIG GENES THROUGH DUAL-AAV VECTORS
US9476065B2 (en) 2013-12-19 2016-10-25 Amyris, Inc. Methods for genomic integration
US10287627B2 (en) 2014-02-08 2019-05-14 The Regents Of The University Of Colorado, A Body Corporate Multiplexed linking PCR
WO2015184016A2 (en) * 2014-05-27 2015-12-03 The Broad Institute, Inc. High-thoughput assembly of genetic elements
WO2016077457A1 (en) 2014-11-11 2016-05-19 Clara Foods Co. Methods and compositions for egg white protein production
US20180127804A1 (en) 2014-12-05 2018-05-10 Amyris, Inc. High-throughput sequencing of polynucleotides
CA2979120A1 (en) * 2015-03-03 2016-09-09 Fondazione Telethon Multiple aav vector system for expressing genes over 5 kilobases, comprising at least one degradation signal and uses thereof
WO2016201142A1 (en) 2015-06-09 2016-12-15 Life Technologies Corporation Methods, systems, compositions, kits, apparatus and computer-readable media for molecular tagging
US10793851B2 (en) 2015-08-04 2020-10-06 The Regents Of The University Of Colorado, A Body Corporate Multiplexed binary assembly and quantitative tracking of bacterial populations
EP3368673B1 (en) 2015-10-29 2020-07-29 Amyris, Inc. Compositions and methods for production of myrcene
CN106811459B (zh) * 2015-11-27 2019-09-27 清华大学 一种利用短链引物阻遏提高dna克隆及组装效率的方法
US9988624B2 (en) 2015-12-07 2018-06-05 Zymergen Inc. Microbial strain improvement by a HTP genomic engineering platform
JP6821598B2 (ja) 2015-12-07 2021-01-27 ザイマージェン インコーポレイテッド Ｃｏｒｙｎｅｂａｃｔｅｒｉｕｍ ｇｌｕｔａｍｉｃｕｍ由来のプロモーター
US11293033B2 (en) 2016-05-18 2022-04-05 Amyris, Inc. Compositions and methods for genomic integration of nucleic acids into exogenous landing pads
EP3478833A4 (en) 2016-06-30 2019-10-02 Zymergen, Inc. METHOD FOR PRODUCING A BACTERIAL HEMOGLOBIN LIBRARY AND ITS USE
US10544411B2 (en) 2016-06-30 2020-01-28 Zymergen Inc. Methods for generating a glucose permease library and uses thereof
GB201621589D0 (en) * 2016-12-19 2017-02-01 Univ Gent And Katholieke Univ Leuven K U Leuven R&D Polynucleotide shuffling method
WO2018140652A1 (en) 2017-01-25 2018-08-02 Amyris, Inc. Co-production of a sesquiterpene and a carotenoid
MX2019015505A (es) 2017-06-30 2020-07-28 Inscripta Inc Metodos, modulos, instrumentos y sistemas de procesamiento de celulas automatizados.
US10738327B2 (en) 2017-08-28 2020-08-11 Inscripta, Inc. Electroporation cuvettes for automation
WO2019055495A1 (en) 2017-09-18 2019-03-21 Amyris, Inc. METHODS FOR GENETICALLY MODIFYING KLUYVEROMYCES HOST CELLS
WO2019055481A1 (en) 2017-09-18 2019-03-21 Amyris, Inc. METHODS OF GENOMIC INTEGRATION IN PICHIA AND OTHER HOST CELLS
US11685934B2 (en) 2017-09-18 2023-06-27 Amyris, Inc. Methods for genomic integration for Kluyveromyces host cells
WO2019055535A1 (en) 2017-09-18 2019-03-21 Amyris, Inc. METHODS OF GENOMIC INTEGRATION FOR HOST CELLS COMPRISING HANSENULA AND ARXULA
EP3688167A4 (en) * 2017-09-29 2021-07-14 Victoria Link Limited SYSTEM FOR MODULAR DNA ARRANGEMENT
US10435713B2 (en) 2017-09-30 2019-10-08 Inscripta, Inc. Flow through electroporation instrumentation
US10443031B1 (en) 2018-03-29 2019-10-15 Inscripta, Inc. Methods for controlling the growth of prokaryotic and eukaryotic cells
WO2019200004A1 (en) 2018-04-13 2019-10-17 Inscripta, Inc. Automated cell processing instruments comprising reagent cartridges
EP3782057B1 (en) * 2018-04-17 2025-06-25 Nanjing GenScript Biotech Co., Ltd. Dna construct design system
US10858761B2 (en) 2018-04-24 2020-12-08 Inscripta, Inc. Nucleic acid-guided editing of exogenous polynucleotides in heterologous cells
US10557216B2 (en) 2018-04-24 2020-02-11 Inscripta, Inc. Automated instrumentation for production of T-cell receptor peptide libraries
US10508273B2 (en) 2018-04-24 2019-12-17 Inscripta, Inc. Methods for identifying selective binding pairs
US11142740B2 (en) 2018-08-14 2021-10-12 Inscripta, Inc. Detection of nuclease edited sequences in automated modules and instruments
US10532324B1 (en) 2018-08-14 2020-01-14 Inscripta, Inc. Instruments, modules, and methods for improved detection of edited sequences in live cells
IL292273B2 (en) 2018-08-14 2023-10-01 Inscripta Inc Devices, modules and methods for improved detection of edited sequences in living cells
CA3108892A1 (en) 2018-08-30 2020-04-23 Inscripta, Inc. Improved detection of nuclease edited sequences in automated modules and instruments
EP3874037A4 (en) * 2018-10-31 2021-12-15 Zymergen, Inc. DETERMINIST MULTIPLEXED SET OF DNA LIBRARIES
CN118957766A (zh) * 2019-04-01 2024-11-15 国立大学法人神户大学 嵌合质粒文库的构建方法
CN114008070A (zh) 2019-06-21 2022-02-01 因思科瑞普特公司 导致大肠杆菌赖氨酸产量增加的全基因组合理设计的突变
US10927385B2 (en) 2019-06-25 2021-02-23 Inscripta, Inc. Increased nucleic-acid guided cell editing in yeast
FI13395Y1 (fi) 2019-07-11 2023-06-06 Clara Foods Co Koostumuksia, jotka käsittävät rekombinanttia ovomukoidiproteiinia
US12096784B2 (en) 2019-07-11 2024-09-24 Clara Foods Co. Protein compositions and consumable products thereof
US10927360B1 (en) 2019-08-07 2021-02-23 Clara Foods Co. Compositions comprising digestive enzymes
US10689669B1 (en) 2020-01-11 2020-06-23 Inscripta, Inc. Automated multi-module cell processing methods, instruments, and systems
JP7473953B2 (ja) * 2020-03-24 2024-04-24 国立大学法人 東京大学 連結ｄｎａの製造方法及びそれに用いるためのベクターの組み合わせ
WO2021211972A1 (en) * 2020-04-16 2021-10-21 Zymergen Inc. Circular-permuted nucleic acids for homology-directed editing
US20210332388A1 (en) 2020-04-24 2021-10-28 Inscripta, Inc. Compositions, methods, modules and instruments for automated nucleic acid-guided nuclease editing in mammalian cells
US11787841B2 (en) 2020-05-19 2023-10-17 Inscripta, Inc. Rationally-designed mutations to the thrA gene for enhanced lysine production in E. coli
CN112813103A (zh) * 2021-01-28 2021-05-18 云舟生物科技（广州）有限公司 一种标准品载体及其在测定重组腺相关病毒滴度中的应用
CN113943666B (zh) * 2021-11-11 2023-08-22 广西壮族自治区农业科学院 一种酿酒酵母工程菌及其应用
CN115261377B (zh) * 2021-12-27 2024-11-19 天津大学 一种dna串联重复单元的拆分组装方法

Family Cites Families (16)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5057419A (en) * 1988-09-22 1991-10-15 Rutgers University Genetically engineered plasmid and organisms for the production of specialized oils
US5976846A (en) * 1996-01-13 1999-11-02 Passmore; Steven E. Method for multifragment in vivo cloning and mutation mapping
AU9577998A (en) * 1997-09-29 1999-04-23 City Of Hope Efficient linking of nucleic acid segments
EP1196554B1 (en) * 1999-03-18 2009-02-25 Complete Genomics AS Methods of cloning and producing fragment chains with readable information content
CA2317865A1 (en) * 2000-03-07 2001-09-07 University Of Guelph Dna joining method
US6916632B2 (en) * 2000-08-21 2005-07-12 Invitrogen Corporation Methods and reagents for molecular cloning
US20030087254A1 (en) * 2001-04-05 2003-05-08 Simon Delagrave Methods for the preparation of polynucleotide libraries and identification of library members having desired characteristics
US20020165175A1 (en) * 2001-04-17 2002-11-07 Xiaowu Liang Fast and enzymeless cloning of nucleic acid fragments
CN1263860C (zh) * 2002-09-30 2006-07-12 华南农业大学 多基因载体的构建方法与应用
US20080050808A1 (en) * 2002-10-09 2008-02-28 Reed Thomas D DNA modular cloning vector plasmids and methods for their use
DK1915446T3 (en) * 2005-08-11 2017-09-11 Synthetic Genomics Inc IN VITRO RECOMBINATION PROCEDURE
WO2007032837A2 (en) * 2005-08-11 2007-03-22 The J. Craig Venter Institute Method for in vitro recombination
WO2008045380A2 (en) * 2006-10-04 2008-04-17 Codon Devices, Inc. Nucleic acid libraries and their design and assembly
US20100291633A1 (en) * 2007-09-03 2010-11-18 Thorsten Selmer Method of cloning at least one nucleic acid molecule of interest using type iis restriction endonucleases, and corresponding cloning vectors, kits and system using type iis restriction endonucleases
US9593329B2 (en) * 2007-10-08 2017-03-14 Synthetic Genomics, Inc. Assembly of large nucleic acids
EP2358875B1 (en) * 2008-11-19 2015-08-12 Amyris, Inc. Compositions and methods for the assembly of polynucleotides

Also Published As

Publication number Publication date
US20120245056A1 (en) 2012-09-27
SG171760A1 (en) 2011-07-28
EP2358875A1 (en) 2011-08-24
US20100124768A1 (en) 2010-05-20
EP2358875B1 (en) 2015-08-12
CN102282255A (zh) 2011-12-14
CA2744153A1 (en) 2010-05-27
WO2010059763A1 (en) 2010-05-27
US8110360B2 (en) 2012-02-07
KR20110102351A (ko) 2011-09-16
CN102282255B (zh) 2014-05-07
ZA201103637B (en) 2012-08-29
BRPI0922187A2 (pt) 2018-10-23
AU2009316660B2 (en) 2015-01-29
BRPI0922187B1 (pt) 2021-05-04
US20100136633A1 (en) 2010-06-03
US8221982B2 (en) 2012-07-17
AU2009316660A1 (en) 2011-07-07
US8546136B2 (en) 2013-10-01
JP2012509084A (ja) 2012-04-19
MX2011005195A (es) 2011-09-01
KR101794298B1 (ko) 2017-11-20

Similar Documents

Publication Publication Date Title
US8546136B2 (en) Compositions and methods for the assembly of polynucleotides
US8332160B1 (en) Systems and methods for engineering nucleic acid constructs using scoring techniques
CA2715586C (en) Methods for in vitro joining and combinatorial assembly of nucleic acid molecules
EP2580332B1 (en) System and method of modular cloning
KR102488128B1 (ko) 게놈의 큰 단편 직접 클로닝 및 dna 다중-분자 어셈블리를 위한 새로운 기술
EP4219731A2 (en) Compositions and methods for genomic integration of nucleic acids into exogenous landing pads
EP2255001B1 (en) Method of nucleic acid recombination
US20260109973A1 (en) High-throughput combinatorial genetic modification system and optimized cas9 enzyme variants
US20220170072A1 (en) Programmable dna-guided artificial restriction enzymes
US20050090010A1 (en) Cloning vectors and method for molecular cloning
JP2004528801A (ja) 増加的切断短縮化核酸及びその製造方法
EP1838851B1 (en) Polypeptide mutagenesis method
EP4715055A1 (en) Method for high efficiency bacterial in vivo or in vitro cloning
EP1546395A2 (en) Methods and nucleic acid vectors for rapid expression and screening of cdna clones
EP4301854A1 (en) In vivo dna assembly and analysis
CN117677694A (zh) 体内dna组装和分析
CA2689273A1 (en) Means and methods for cloning nucleic acid sequences

Legal Events

Date Code Title Description
EEER Examination request

Effective date: 20140811

W00 Other event occurred

Free format text: ST27 STATUS EVENT CODE: A-4-4-W10-W00-W100 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: LETTER SENT

Effective date: 20251020

H13 Ip right lapsed

Free format text: ST27 STATUS EVENT CODE: N-4-6-H10-H13-H100 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: MAINTENANCE FEE AND LATE FEE NOT PAID BY DEADLINE OF NOTICE

Effective date: 20260202

W00 Other event occurred

Free format text: ST27 STATUS EVENT CODE: N-6-6-W10-W00-W100 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: LETTER SENT

Effective date: 20260203