WO2015021080A3 - De novo synthesized gene libraries - Google Patents

De novo synthesized gene libraries Download PDF

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Publication number
WO2015021080A3
WO2015021080A3 PCT/US2014/049834 US2014049834W WO2015021080A3 WO 2015021080 A3 WO2015021080 A3 WO 2015021080A3 US 2014049834 W US2014049834 W US 2014049834W WO 2015021080 A3 WO2015021080 A3 WO 2015021080A3
Authority
WO
WIPO (PCT)
Prior art keywords
nucleic acids
novo synthesized
quality
gene libraries
large libraries
Prior art date
Application number
PCT/US2014/049834
Other languages
French (fr)
Other versions
WO2015021080A2 (en
Inventor
William Banyai
Bill James PECK
Andres Fernandez
Siyuan CHEN
Pierre Indermuhle
Original Assignee
Twist Bioscience Corporation
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
Family has litigation
First worldwide family litigation filed litigation Critical https://patents.darts-ip.com/?family=52428204&utm_source=google_patent&utm_medium=platform_link&utm_campaign=public_patent_search&patent=WO2015021080(A3) "Global patent litigation dataset” by Darts-ip is licensed under a Creative Commons Attribution 4.0 International License.
Priority to EP14834665.3A priority Critical patent/EP3030682B1/en
Priority to KR1020167005273A priority patent/KR102122632B1/en
Priority to EA201690081A priority patent/EA034459B1/en
Priority to CA2918258A priority patent/CA2918258A1/en
Priority to KR1020217025517A priority patent/KR102351838B1/en
Priority to DK14834665.3T priority patent/DK3030682T3/en
Priority to KR1020227000941A priority patent/KR102423377B1/en
Priority to GB1502580.2A priority patent/GB2533173A/en
Priority to CN201480054963.8A priority patent/CN105637097A/en
Application filed by Twist Bioscience Corporation filed Critical Twist Bioscience Corporation
Priority to KR1020207007228A priority patent/KR102160389B1/en
Priority to EP23166418.6A priority patent/EP4242321A3/en
Priority to KR1020207026902A priority patent/KR102207770B1/en
Priority to PL14834665T priority patent/PL3030682T3/en
Priority to SG11201600853UA priority patent/SG11201600853UA/en
Priority to EP20169965.9A priority patent/EP3722442B1/en
Priority to JP2016533384A priority patent/JP6656733B2/en
Priority to KR1020217001198A priority patent/KR102291045B1/en
Priority to ES14834665T priority patent/ES2815099T3/en
Publication of WO2015021080A2 publication Critical patent/WO2015021080A2/en
Publication of WO2015021080A3 publication Critical patent/WO2015021080A3/en
Priority to US14/885,962 priority patent/US9833761B2/en
Priority to US14/885,965 priority patent/US10272410B2/en
Priority to US14/885,963 priority patent/US9403141B2/en
Priority to US15/187,721 priority patent/US9555388B2/en
Priority to US15/245,054 priority patent/US9889423B2/en
Priority to US15/377,547 priority patent/US10384188B2/en
Priority to US16/409,608 priority patent/US10583415B2/en
Priority to US16/535,779 priority patent/US10773232B2/en
Priority to US16/535,777 priority patent/US11185837B2/en
Priority to US16/737,401 priority patent/US11452980B2/en
Priority to US17/818,656 priority patent/US20230086062A1/en

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    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
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    • B01J19/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J19/0046—Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • 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
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    • 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
    • C12N15/1096—Processes for the isolation, preparation or purification of DNA or RNA cDNA Synthesis; Subtracted cDNA library construction, e.g. RT, RT-PCR
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    • 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
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    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/74—Vectors or expression systems specially adapted for prokaryotic hosts other than E. coli, e.g. Lactobacillus, Micromonospora
    • 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
    • C12Q1/6806—Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
    • 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
    • C40B40/08—Libraries containing RNA or DNA which encodes proteins, e.g. gene libraries
    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B50/00—Methods of creating libraries, e.g. combinatorial synthesis
    • C40B50/14—Solid phase synthesis, i.e. wherein one or more library building blocks are bound to a solid support during library creation; Particular methods of cleavage from the solid support
    • C40B50/18—Solid phase synthesis, i.e. wherein one or more library building blocks are bound to a solid support during library creation; Particular methods of cleavage from the solid support using a particular method of attachment to the solid support
    • B—PERFORMING OPERATIONS; TRANSPORTING
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    • B01J2219/00378—Piezo-electric or ink jet dispensers
    • B—PERFORMING OPERATIONS; TRANSPORTING
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    • B01J2219/00277—Apparatus
    • B01J2219/00497—Features relating to the solid phase supports
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
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    • B01J2219/00583—Features relative to the processes being carried out
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    • 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
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    • B—PERFORMING OPERATIONS; TRANSPORTING
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    • B01J2219/00619—Delimitation of the attachment areas by chemical means using hydrophilic or hydrophobic regions
    • B—PERFORMING OPERATIONS; TRANSPORTING
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    • B01J2219/00603—Making arrays on substantially continuous surfaces
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    • B01J2219/00623—Immobilisation or binding
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    • B01J2219/00632—Introduction of reactive groups to the surface
    • B01J2219/00637—Introduction of reactive groups to the surface by coating it with another layer
    • B—PERFORMING OPERATIONS; TRANSPORTING
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    • B01J2219/00718—Type of compounds synthesised
    • B01J2219/0072—Organic compounds
    • B01J2219/00722—Nucleotides
    • C—CHEMISTRY; METALLURGY
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    • 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
    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B40/00—Libraries per se, e.g. arrays, mixtures
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    • 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
    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B50/00—Methods of creating libraries, e.g. combinatorial synthesis
    • C40B50/14—Solid phase synthesis, i.e. wherein one or more library building blocks are bound to a solid support during library creation; Particular methods of cleavage from the solid support

Abstract

De novo synthesized large libraries of nucleic acids are provided herein with low error rates. Further, devices for the manufacturing of high-quality building blocks, such as oligonucleotides, are described herein. Longer nucleic acids can be synthesized in parallel using microfluidic assemblies. Further, methods herein allow for the fast construction of large libraries of long, high-quality genes. Devices for the manufacturing of large libraries of long and high-quality nucleic acids are further described herein.
PCT/US2014/049834 2013-08-05 2014-08-05 De novo synthesized gene libraries WO2015021080A2 (en)

Priority Applications (29)

Application Number Priority Date Filing Date Title
SG11201600853UA SG11201600853UA (en) 2013-08-05 2014-08-05 De novo synthesized gene libraries
EP20169965.9A EP3722442B1 (en) 2013-08-05 2014-08-05 De novo synthesized gene libraries
EA201690081A EA034459B1 (en) 2013-08-05 2014-08-05 De novo synthesized gene libraries
CA2918258A CA2918258A1 (en) 2013-08-05 2014-08-05 De novo synthesized gene libraries
KR1020217025517A KR102351838B1 (en) 2013-08-05 2014-08-05 De novo synthesized gene libraries
DK14834665.3T DK3030682T3 (en) 2013-08-05 2014-08-05 DE NOVO SYNTHESIZED GENE LIBRARIES
JP2016533384A JP6656733B2 (en) 2013-08-05 2014-08-05 Newly synthesized gene library
GB1502580.2A GB2533173A (en) 2013-08-05 2014-08-05 De Novo synthesized gene libraries
CN201480054963.8A CN105637097A (en) 2013-08-05 2014-08-05 De novo synthesized gene libraries
KR1020167005273A KR102122632B1 (en) 2013-08-05 2014-08-05 De novo synthesized gene libraries
KR1020207007228A KR102160389B1 (en) 2013-08-05 2014-08-05 De novo synthesized gene libraries
EP23166418.6A EP4242321A3 (en) 2013-08-05 2014-08-05 De novo synthesized gene libraries
KR1020207026902A KR102207770B1 (en) 2013-08-05 2014-08-05 De novo synthesized gene libraries
PL14834665T PL3030682T3 (en) 2013-08-05 2014-08-05 De novo synthesized gene libraries
ES14834665T ES2815099T3 (en) 2013-08-05 2014-08-05 De novo synthesized libraries
EP14834665.3A EP3030682B1 (en) 2013-08-05 2014-08-05 De novo synthesized gene libraries
KR1020227000941A KR102423377B1 (en) 2013-08-05 2014-08-05 De novo synthesized gene libraries
KR1020217001198A KR102291045B1 (en) 2013-08-05 2014-08-05 De novo synthesized gene libraries
US14/885,963 US9403141B2 (en) 2013-08-05 2015-10-16 De novo synthesized gene libraries
US14/885,965 US10272410B2 (en) 2013-08-05 2015-10-16 De novo synthesized gene libraries
US14/885,962 US9833761B2 (en) 2013-08-05 2015-10-16 De novo synthesized gene libraries
US15/187,721 US9555388B2 (en) 2013-08-05 2016-06-20 De novo synthesized gene libraries
US15/245,054 US9889423B2 (en) 2013-08-05 2016-08-23 De novo synthesized gene libraries
US15/377,547 US10384188B2 (en) 2013-08-05 2016-12-13 De novo synthesized gene libraries
US16/409,608 US10583415B2 (en) 2013-08-05 2019-05-10 De novo synthesized gene libraries
US16/535,779 US10773232B2 (en) 2013-08-05 2019-08-08 De novo synthesized gene libraries
US16/535,777 US11185837B2 (en) 2013-08-05 2019-08-08 De novo synthesized gene libraries
US16/737,401 US11452980B2 (en) 2013-08-05 2020-01-08 De novo synthesized gene libraries
US17/818,656 US20230086062A1 (en) 2013-08-05 2022-08-09 De novo synthesized gene libraries

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US201361862445P 2013-08-05 2013-08-05
US201361862457P 2013-08-05 2013-08-05
US61/862,445 2013-08-05
US61/862,457 2013-08-05

Related Child Applications (3)

Application Number Title Priority Date Filing Date
US14/885,965 Continuation US10272410B2 (en) 2013-08-05 2015-10-16 De novo synthesized gene libraries
US14/885,963 Continuation US9403141B2 (en) 2013-08-05 2015-10-16 De novo synthesized gene libraries
US14/885,962 Continuation US9833761B2 (en) 2013-08-05 2015-10-16 De novo synthesized gene libraries

Publications (2)

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