Loop assembly: a simple and open system for recursive fabrication of DNA circuits
• High-efficiency methods for DNA assembly have enabled the routine assembly of synthetic DNAs of increased size and complexity. However, these techniques require customization, elaborate vector sets or serial manipulations for the different stages of assembly. • We have developed Loop assembly base...
Gespeichert in:
| Veröffentlicht in: | The New phytologist 2019-04, Vol.222 (1), p.628-640 |
|---|---|
| Hauptverfasser: | , , , , , , , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | 640 |
|---|---|
| container_issue | 1 |
| container_start_page | 628 |
| container_title | The New phytologist |
| container_volume | 222 |
| creator | Pollak, Bernardo Cerda, Ariel Delmans, Mihails Álamos, Simón Moyano, Tomás West, Anthony Gutiérrez, Rodrigo A. Patron, Nicola J. Federici, Fernán Haseloff, Jim |
| description | • High-efficiency methods for DNA assembly have enabled the routine assembly of synthetic DNAs of increased size and complexity. However, these techniques require customization, elaborate vector sets or serial manipulations for the different stages of assembly.
• We have developed Loop assembly based on a recursive approach to DNA fabrication. The system makes use of two Type IIS restriction endonucleases and corresponding vector sets for efficient and parallel assembly of large DNA circuits. Standardized level 0 parts can be assembled into circuits containing 1, 4, 16 or more genes by looping between the two vector sets.
• The vectors also contain modular sites for hybrid assembly using sequence overlap methods. - Loop assembly enables efficient and versatile DNA fabrication for plant transformation. We show the construction of plasmids up to 16 genes and 38 kb with high efficiency (> 80%). We have characterized Loop assembly on over 200 different DNA constructs and validated the fidelity of the method by high-throughput Illumina plasmid sequencing.
• Our method provides a simple generalized solution for DNA construction with standardized parts. The cloning system is provided under an OpenMTA license for unrestricted sharing and open access. |
| doi_str_mv | 10.1111/nph.15625 |
| format | Article |
| fullrecord | <record><control><sourceid>jstor_proqu</sourceid><recordid>TN_cdi_proquest_miscellaneous_2179232655</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><jstor_id>26629272</jstor_id><sourcerecordid>26629272</sourcerecordid><originalsourceid>FETCH-LOGICAL-c4765-32e4b4c2ecaa852e78d0df998e985b95063da4c9b1725b4206d62010498d92d23</originalsourceid><addsrcrecordid>eNp10E1LAzEQBuAgiq21B3-AInjRw7bJ5GOToxS1QlEPCt5CdpNiy26zJl2k_97otj0IzmUuz7wML0JnBI9ImvGq-RgRLoAfoD5hQmWS0PwQ9TEGmQkm3nvoJMYlxlgldYx6FHMgBKs-Gs68by5NjK4uqs0pOpqbKrrhdg_Q2_3d62SazZ4fHie3s6xkueAZBccKVoIrjZEcXC4ttnOlpFOSF4pjQa1hpSpIDrxggIUVgAlmSloFFugAXXe5TfCfrYtrXS9i6arKrJxvowaSK6AgOE_06g9d-jas0ndJSSEoAyaSuulUGXyMwc11Exa1CRtNsP7pSKeO9G9HyV5sE9uidnYvd6UkMO7A16Jym_-T9NPLdBd53l0s49qH_QUIAQpyoN_m93Wj</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2186634246</pqid></control><display><type>article</type><title>Loop assembly: a simple and open system for recursive fabrication of DNA circuits</title><source>MEDLINE</source><source>Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals</source><source>Access via Wiley Online Library</source><source>Wiley Online Library (Open Access Collection)</source><source>JSTOR</source><creator>Pollak, Bernardo ; Cerda, Ariel ; Delmans, Mihails ; Álamos, Simón ; Moyano, Tomás ; West, Anthony ; Gutiérrez, Rodrigo A. ; Patron, Nicola J. ; Federici, Fernán ; Haseloff, Jim</creator><creatorcontrib>Pollak, Bernardo ; Cerda, Ariel ; Delmans, Mihails ; Álamos, Simón ; Moyano, Tomás ; West, Anthony ; Gutiérrez, Rodrigo A. ; Patron, Nicola J. ; Federici, Fernán ; Haseloff, Jim</creatorcontrib><description>• High-efficiency methods for DNA assembly have enabled the routine assembly of synthetic DNAs of increased size and complexity. However, these techniques require customization, elaborate vector sets or serial manipulations for the different stages of assembly.
• We have developed Loop assembly based on a recursive approach to DNA fabrication. The system makes use of two Type IIS restriction endonucleases and corresponding vector sets for efficient and parallel assembly of large DNA circuits. Standardized level 0 parts can be assembled into circuits containing 1, 4, 16 or more genes by looping between the two vector sets.
• The vectors also contain modular sites for hybrid assembly using sequence overlap methods. - Loop assembly enables efficient and versatile DNA fabrication for plant transformation. We show the construction of plasmids up to 16 genes and 38 kb with high efficiency (> 80%). We have characterized Loop assembly on over 200 different DNA constructs and validated the fidelity of the method by high-throughput Illumina plasmid sequencing.
• Our method provides a simple generalized solution for DNA construction with standardized parts. The cloning system is provided under an OpenMTA license for unrestricted sharing and open access.</description><identifier>ISSN: 0028-646X</identifier><identifier>EISSN: 1469-8137</identifier><identifier>DOI: 10.1111/nph.15625</identifier><identifier>PMID: 30521109</identifier><language>eng</language><publisher>England: Wiley</publisher><subject>Assembly ; Automation ; Circuits ; Cloning ; common syntax ; Construction ; Deoxyribonucleic acid ; DNA ; DNA sequencing ; DNA, Plant - genetics ; Fabrication ; Genes ; Genetic transformation ; Genetic Vectors - genetics ; Loop assembly ; LoopDesigner ; Marchantia - genetics ; Methods ; Nucleotide sequence ; Open systems ; OpenMTA ; Plasmids ; Plasmids - genetics ; Promoter Regions, Genetic - genetics ; recursive assembly ; Recursive methods ; Reproducibility of Results ; standardized DNA assembly ; Type IIS ; unique nucleotide sequences (UNSs) ; Vectors</subject><ispartof>The New phytologist, 2019-04, Vol.222 (1), p.628-640</ispartof><rights>2018 The Authors © 2018 New Phytologist Trust</rights><rights>2018 The Authors. © 2018 New Phytologist Trust</rights><rights>2018 The Authors. New Phytologist © 2018 New Phytologist Trust.</rights><rights>Copyright © 2019 New Phytologist Trust</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4765-32e4b4c2ecaa852e78d0df998e985b95063da4c9b1725b4206d62010498d92d23</citedby><cites>FETCH-LOGICAL-c4765-32e4b4c2ecaa852e78d0df998e985b95063da4c9b1725b4206d62010498d92d23</cites><orcidid>0000-0003-2329-7401 ; 0000-0003-4793-8058 ; 0000-0001-9200-5383 ; 0000-0002-8389-1851</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.jstor.org/stable/pdf/26629272$$EPDF$$P50$$Gjstor$$H</linktopdf><linktohtml>$$Uhttps://www.jstor.org/stable/26629272$$EHTML$$P50$$Gjstor$$H</linktohtml><link.rule.ids>315,782,786,805,1419,1435,27933,27934,45583,45584,46418,46842,58026,58259</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/30521109$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Pollak, Bernardo</creatorcontrib><creatorcontrib>Cerda, Ariel</creatorcontrib><creatorcontrib>Delmans, Mihails</creatorcontrib><creatorcontrib>Álamos, Simón</creatorcontrib><creatorcontrib>Moyano, Tomás</creatorcontrib><creatorcontrib>West, Anthony</creatorcontrib><creatorcontrib>Gutiérrez, Rodrigo A.</creatorcontrib><creatorcontrib>Patron, Nicola J.</creatorcontrib><creatorcontrib>Federici, Fernán</creatorcontrib><creatorcontrib>Haseloff, Jim</creatorcontrib><title>Loop assembly: a simple and open system for recursive fabrication of DNA circuits</title><title>The New phytologist</title><addtitle>New Phytol</addtitle><description>• High-efficiency methods for DNA assembly have enabled the routine assembly of synthetic DNAs of increased size and complexity. However, these techniques require customization, elaborate vector sets or serial manipulations for the different stages of assembly.
• We have developed Loop assembly based on a recursive approach to DNA fabrication. The system makes use of two Type IIS restriction endonucleases and corresponding vector sets for efficient and parallel assembly of large DNA circuits. Standardized level 0 parts can be assembled into circuits containing 1, 4, 16 or more genes by looping between the two vector sets.
• The vectors also contain modular sites for hybrid assembly using sequence overlap methods. - Loop assembly enables efficient and versatile DNA fabrication for plant transformation. We show the construction of plasmids up to 16 genes and 38 kb with high efficiency (> 80%). We have characterized Loop assembly on over 200 different DNA constructs and validated the fidelity of the method by high-throughput Illumina plasmid sequencing.
• Our method provides a simple generalized solution for DNA construction with standardized parts. The cloning system is provided under an OpenMTA license for unrestricted sharing and open access.</description><subject>Assembly</subject><subject>Automation</subject><subject>Circuits</subject><subject>Cloning</subject><subject>common syntax</subject><subject>Construction</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA sequencing</subject><subject>DNA, Plant - genetics</subject><subject>Fabrication</subject><subject>Genes</subject><subject>Genetic transformation</subject><subject>Genetic Vectors - genetics</subject><subject>Loop assembly</subject><subject>LoopDesigner</subject><subject>Marchantia - genetics</subject><subject>Methods</subject><subject>Nucleotide sequence</subject><subject>Open systems</subject><subject>OpenMTA</subject><subject>Plasmids</subject><subject>Plasmids - genetics</subject><subject>Promoter Regions, Genetic - genetics</subject><subject>recursive assembly</subject><subject>Recursive methods</subject><subject>Reproducibility of Results</subject><subject>standardized DNA assembly</subject><subject>Type IIS</subject><subject>unique nucleotide sequences (UNSs)</subject><subject>Vectors</subject><issn>0028-646X</issn><issn>1469-8137</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2019</creationdate><recordtype>article</recordtype><sourceid>24P</sourceid><sourceid>WIN</sourceid><sourceid>EIF</sourceid><recordid>eNp10E1LAzEQBuAgiq21B3-AInjRw7bJ5GOToxS1QlEPCt5CdpNiy26zJl2k_97otj0IzmUuz7wML0JnBI9ImvGq-RgRLoAfoD5hQmWS0PwQ9TEGmQkm3nvoJMYlxlgldYx6FHMgBKs-Gs68by5NjK4uqs0pOpqbKrrhdg_Q2_3d62SazZ4fHie3s6xkueAZBccKVoIrjZEcXC4ttnOlpFOSF4pjQa1hpSpIDrxggIUVgAlmSloFFugAXXe5TfCfrYtrXS9i6arKrJxvowaSK6AgOE_06g9d-jas0ndJSSEoAyaSuulUGXyMwc11Exa1CRtNsP7pSKeO9G9HyV5sE9uidnYvd6UkMO7A16Jym_-T9NPLdBd53l0s49qH_QUIAQpyoN_m93Wj</recordid><startdate>201904</startdate><enddate>201904</enddate><creator>Pollak, Bernardo</creator><creator>Cerda, Ariel</creator><creator>Delmans, Mihails</creator><creator>Álamos, Simón</creator><creator>Moyano, Tomás</creator><creator>West, Anthony</creator><creator>Gutiérrez, Rodrigo A.</creator><creator>Patron, Nicola J.</creator><creator>Federici, Fernán</creator><creator>Haseloff, Jim</creator><general>Wiley</general><general>Wiley Subscription Services, Inc</general><scope>24P</scope><scope>WIN</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QO</scope><scope>7SN</scope><scope>8FD</scope><scope>C1K</scope><scope>F1W</scope><scope>FR3</scope><scope>H95</scope><scope>L.G</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0003-2329-7401</orcidid><orcidid>https://orcid.org/0000-0003-4793-8058</orcidid><orcidid>https://orcid.org/0000-0001-9200-5383</orcidid><orcidid>https://orcid.org/0000-0002-8389-1851</orcidid></search><sort><creationdate>201904</creationdate><title>Loop assembly</title><author>Pollak, Bernardo ; Cerda, Ariel ; Delmans, Mihails ; Álamos, Simón ; Moyano, Tomás ; West, Anthony ; Gutiérrez, Rodrigo A. ; Patron, Nicola J. ; Federici, Fernán ; Haseloff, Jim</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4765-32e4b4c2ecaa852e78d0df998e985b95063da4c9b1725b4206d62010498d92d23</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><topic>Assembly</topic><topic>Automation</topic><topic>Circuits</topic><topic>Cloning</topic><topic>common syntax</topic><topic>Construction</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA sequencing</topic><topic>DNA, Plant - genetics</topic><topic>Fabrication</topic><topic>Genes</topic><topic>Genetic transformation</topic><topic>Genetic Vectors - genetics</topic><topic>Loop assembly</topic><topic>LoopDesigner</topic><topic>Marchantia - genetics</topic><topic>Methods</topic><topic>Nucleotide sequence</topic><topic>Open systems</topic><topic>OpenMTA</topic><topic>Plasmids</topic><topic>Plasmids - genetics</topic><topic>Promoter Regions, Genetic - genetics</topic><topic>recursive assembly</topic><topic>Recursive methods</topic><topic>Reproducibility of Results</topic><topic>standardized DNA assembly</topic><topic>Type IIS</topic><topic>unique nucleotide sequences (UNSs)</topic><topic>Vectors</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Pollak, Bernardo</creatorcontrib><creatorcontrib>Cerda, Ariel</creatorcontrib><creatorcontrib>Delmans, Mihails</creatorcontrib><creatorcontrib>Álamos, Simón</creatorcontrib><creatorcontrib>Moyano, Tomás</creatorcontrib><creatorcontrib>West, Anthony</creatorcontrib><creatorcontrib>Gutiérrez, Rodrigo A.</creatorcontrib><creatorcontrib>Patron, Nicola J.</creatorcontrib><creatorcontrib>Federici, Fernán</creatorcontrib><creatorcontrib>Haseloff, Jim</creatorcontrib><collection>Wiley Online Library Open Access</collection><collection>Wiley Online Library (Open Access Collection)</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Biotechnology Research Abstracts</collection><collection>Ecology Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ASFA: Aquatic Sciences and Fisheries Abstracts</collection><collection>Engineering Research Database</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) 1: Biological Sciences & Living Resources</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) Professional</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>The New phytologist</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Pollak, Bernardo</au><au>Cerda, Ariel</au><au>Delmans, Mihails</au><au>Álamos, Simón</au><au>Moyano, Tomás</au><au>West, Anthony</au><au>Gutiérrez, Rodrigo A.</au><au>Patron, Nicola J.</au><au>Federici, Fernán</au><au>Haseloff, Jim</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Loop assembly: a simple and open system for recursive fabrication of DNA circuits</atitle><jtitle>The New phytologist</jtitle><addtitle>New Phytol</addtitle><date>2019-04</date><risdate>2019</risdate><volume>222</volume><issue>1</issue><spage>628</spage><epage>640</epage><pages>628-640</pages><issn>0028-646X</issn><eissn>1469-8137</eissn><abstract>• High-efficiency methods for DNA assembly have enabled the routine assembly of synthetic DNAs of increased size and complexity. However, these techniques require customization, elaborate vector sets or serial manipulations for the different stages of assembly.
• We have developed Loop assembly based on a recursive approach to DNA fabrication. The system makes use of two Type IIS restriction endonucleases and corresponding vector sets for efficient and parallel assembly of large DNA circuits. Standardized level 0 parts can be assembled into circuits containing 1, 4, 16 or more genes by looping between the two vector sets.
• The vectors also contain modular sites for hybrid assembly using sequence overlap methods. - Loop assembly enables efficient and versatile DNA fabrication for plant transformation. We show the construction of plasmids up to 16 genes and 38 kb with high efficiency (> 80%). We have characterized Loop assembly on over 200 different DNA constructs and validated the fidelity of the method by high-throughput Illumina plasmid sequencing.
• Our method provides a simple generalized solution for DNA construction with standardized parts. The cloning system is provided under an OpenMTA license for unrestricted sharing and open access.</abstract><cop>England</cop><pub>Wiley</pub><pmid>30521109</pmid><doi>10.1111/nph.15625</doi><tpages>13</tpages><orcidid>https://orcid.org/0000-0003-2329-7401</orcidid><orcidid>https://orcid.org/0000-0003-4793-8058</orcidid><orcidid>https://orcid.org/0000-0001-9200-5383</orcidid><orcidid>https://orcid.org/0000-0002-8389-1851</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0028-646X |
| ispartof | The New phytologist, 2019-04, Vol.222 (1), p.628-640 |
| issn | 0028-646X 1469-8137 |
| language | eng |
| recordid | cdi_proquest_miscellaneous_2179232655 |
| source | MEDLINE; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Access via Wiley Online Library; Wiley Online Library (Open Access Collection); JSTOR |
| subjects | Assembly Automation Circuits Cloning common syntax Construction Deoxyribonucleic acid DNA DNA sequencing DNA, Plant - genetics Fabrication Genes Genetic transformation Genetic Vectors - genetics Loop assembly LoopDesigner Marchantia - genetics Methods Nucleotide sequence Open systems OpenMTA Plasmids Plasmids - genetics Promoter Regions, Genetic - genetics recursive assembly Recursive methods Reproducibility of Results standardized DNA assembly Type IIS unique nucleotide sequences (UNSs) Vectors |
| title | Loop assembly: a simple and open system for recursive fabrication of DNA circuits |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-03T03%3A16%3A06IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-jstor_proqu&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Loop%20assembly:%20a%20simple%20and%20open%20system%20for%20recursive%20fabrication%20of%20DNA%20circuits&rft.jtitle=The%20New%20phytologist&rft.au=Pollak,%20Bernardo&rft.date=2019-04&rft.volume=222&rft.issue=1&rft.spage=628&rft.epage=640&rft.pages=628-640&rft.issn=0028-646X&rft.eissn=1469-8137&rft_id=info:doi/10.1111/nph.15625&rft_dat=%3Cjstor_proqu%3E26629272%3C/jstor_proqu%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2186634246&rft_id=info:pmid/30521109&rft_jstor_id=26629272&rfr_iscdi=true |