DNA-library assembly programmed by on-demand nano-liter droplets from a custom microfluidic chip

Nanoscale synthetic biology can benefit from programmable nanoliter-scale processing of DNA in microfluidic chips if they are interfaced effectively to biochemical arrays such as microwell plates. Whereas active microvalve chips require complex fabrication and operation, we show here how a passive a...

Full description

Saved in:
Bibliographic Details
Published in:Biomicrofluidics 2015-07, Vol.9 (4), p.044103-044103
Main Authors: Tangen, Uwe, Minero, Gabriel Antonio S, Sharma, Abhishek, Wagler, Patrick F, Cohen, Rafael, Raz, Ofir, Marx, Tzipy, Ben-Yehezkel, Tuval, McCaskill, John S
Format: Article
Language:English
Subjects:
Assembly
Chip formation
Combinatorial analysis
Deoxyribonucleic acid
DNA
Droplets
Electrophoresis
Gene sequencing
Plates (structural members)
Plugs
Reaction control
Regular
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
cited_by cdi_FETCH-LOGICAL-c403t-17ec61c33d5e83d90be548b0afd77a3143d4004254290bbbc01b632cd5e157c23
cites cdi_FETCH-LOGICAL-c403t-17ec61c33d5e83d90be548b0afd77a3143d4004254290bbbc01b632cd5e157c23
container_end_page 044103
container_issue 4
container_start_page 044103
container_title Biomicrofluidics
container_volume 9
creator Tangen, Uwe
Minero, Gabriel Antonio S
Sharma, Abhishek
Wagler, Patrick F
Cohen, Rafael
Raz, Ofir
Marx, Tzipy
Ben-Yehezkel, Tuval
McCaskill, John S
description Nanoscale synthetic biology can benefit from programmable nanoliter-scale processing of DNA in microfluidic chips if they are interfaced effectively to biochemical arrays such as microwell plates. Whereas active microvalve chips require complex fabrication and operation, we show here how a passive and readily fabricated microchip can be employed for customizable nanoliter scale pipetting and reaction control involving DNA. This recently developed passive microfluidic device, supporting nanoliter scale combinatorial droplet generation and mixing, is here used to generate a DNA test library with one member per droplet exported to addressed locations on microwell plates. Standard DNA assembly techniques, such as Gibson assembly, compatible with isothermal on-chip operation, are employed and checked using off-chip PCR and assembly PCR. The control of output droplet sequences and mixing performance was verified using dyes and fluorescently labeled DNA solutions, both on-chip and in external capillary channels. Gel electrophoresis of products and DNA sequencing were employed to further verify controlled combination and functional enzymatic assembly. The scalability of the results to larger DNA libraries is also addressed by combinatorial input expansion using sequential injection plugs from a multiwell plate. Hence, the paper establishes a proof of principle of the production of functional combinatorial mixtures at the nanoliter scale for one sequence per well DNA libraries.
doi_str_mv 10.1063/1.4926616
format article
fullrecord <record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_4499045</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>1700334634</sourcerecordid><originalsourceid>FETCH-LOGICAL-c403t-17ec61c33d5e83d90be548b0afd77a3143d4004254290bbbc01b632cd5e157c23</originalsourceid><addsrcrecordid>eNpdkUtLxDAUhYMoOo4u_AMScKOLjrlJ2k43wjA-QXSj65hXNdI2NWmF-fdGHEVd3QP343DuPQgdAJkBKdgpzHhFiwKKDTSBitEMSD7f_KV30G6Mr4TkUFK6jXZoQSlANZ-gp_O7RdY4FWRYYRmjbVWzwn3wz0G2rTVYrbDvMmNb2Rncyc4nerABm-D7xg4R18G3WGI9xiGJ1ung62Z0xmmsX1y_h7Zq2US7v55T9Hh58bC8zm7vr26Wi9tMc8KGDEqrC9CMmdzOmamIsjmfKyJrU5aSAWeGE8JpzmnaKaUJqIJRnXDIS03ZFJ19-fajSrm17YYgG9EH16bThJdO_N107kU8-3fBeVURnieD47VB8G-jjYNoXdS2aWRn_RgFlIQwxgvGE3r0D331Y-jSeYIC5QA58CpRJ19U-kiMwdY_YYCIz94EiHVviT38nf6H_C6KfQD4Z5K6</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2124115149</pqid></control><display><type>article</type><title>DNA-library assembly programmed by on-demand nano-liter droplets from a custom microfluidic chip</title><source>American Institute of Physics:Jisc Collections:Transitional Journals Agreement 2021-23 (Reading list)</source><source>PubMed Central</source><creator>Tangen, Uwe ; Minero, Gabriel Antonio S ; Sharma, Abhishek ; Wagler, Patrick F ; Cohen, Rafael ; Raz, Ofir ; Marx, Tzipy ; Ben-Yehezkel, Tuval ; McCaskill, John S</creator><creatorcontrib>Tangen, Uwe ; Minero, Gabriel Antonio S ; Sharma, Abhishek ; Wagler, Patrick F ; Cohen, Rafael ; Raz, Ofir ; Marx, Tzipy ; Ben-Yehezkel, Tuval ; McCaskill, John S</creatorcontrib><description>Nanoscale synthetic biology can benefit from programmable nanoliter-scale processing of DNA in microfluidic chips if they are interfaced effectively to biochemical arrays such as microwell plates. Whereas active microvalve chips require complex fabrication and operation, we show here how a passive and readily fabricated microchip can be employed for customizable nanoliter scale pipetting and reaction control involving DNA. This recently developed passive microfluidic device, supporting nanoliter scale combinatorial droplet generation and mixing, is here used to generate a DNA test library with one member per droplet exported to addressed locations on microwell plates. Standard DNA assembly techniques, such as Gibson assembly, compatible with isothermal on-chip operation, are employed and checked using off-chip PCR and assembly PCR. The control of output droplet sequences and mixing performance was verified using dyes and fluorescently labeled DNA solutions, both on-chip and in external capillary channels. Gel electrophoresis of products and DNA sequencing were employed to further verify controlled combination and functional enzymatic assembly. The scalability of the results to larger DNA libraries is also addressed by combinatorial input expansion using sequential injection plugs from a multiwell plate. Hence, the paper establishes a proof of principle of the production of functional combinatorial mixtures at the nanoliter scale for one sequence per well DNA libraries.</description><identifier>ISSN: 1932-1058</identifier><identifier>EISSN: 1932-1058</identifier><identifier>DOI: 10.1063/1.4926616</identifier><identifier>PMID: 26221198</identifier><language>eng</language><publisher>United States: American Institute of Physics</publisher><subject>Assembly ; Chip formation ; Combinatorial analysis ; Deoxyribonucleic acid ; DNA ; Droplets ; Electrophoresis ; Gene sequencing ; Plates (structural members) ; Plugs ; Reaction control ; Regular</subject><ispartof>Biomicrofluidics, 2015-07, Vol.9 (4), p.044103-044103</ispartof><rights>2015 AIP Publishing LLC.</rights><rights>Copyright © 2015 AIP Publishing LLC 2015 AIP Publishing LLC</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c403t-17ec61c33d5e83d90be548b0afd77a3143d4004254290bbbc01b632cd5e157c23</citedby><cites>FETCH-LOGICAL-c403t-17ec61c33d5e83d90be548b0afd77a3143d4004254290bbbc01b632cd5e157c23</cites><orcidid>0000-0002-2123-4768 ; 0000-0002-3408-7357</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4499045/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4499045/$$EHTML$$P50$$Gpubmedcentral$$H</linktohtml><link.rule.ids>230,315,733,786,790,891,27957,27958,53827,53829</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26221198$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Tangen, Uwe</creatorcontrib><creatorcontrib>Minero, Gabriel Antonio S</creatorcontrib><creatorcontrib>Sharma, Abhishek</creatorcontrib><creatorcontrib>Wagler, Patrick F</creatorcontrib><creatorcontrib>Cohen, Rafael</creatorcontrib><creatorcontrib>Raz, Ofir</creatorcontrib><creatorcontrib>Marx, Tzipy</creatorcontrib><creatorcontrib>Ben-Yehezkel, Tuval</creatorcontrib><creatorcontrib>McCaskill, John S</creatorcontrib><title>DNA-library assembly programmed by on-demand nano-liter droplets from a custom microfluidic chip</title><title>Biomicrofluidics</title><addtitle>Biomicrofluidics</addtitle><description>Nanoscale synthetic biology can benefit from programmable nanoliter-scale processing of DNA in microfluidic chips if they are interfaced effectively to biochemical arrays such as microwell plates. Whereas active microvalve chips require complex fabrication and operation, we show here how a passive and readily fabricated microchip can be employed for customizable nanoliter scale pipetting and reaction control involving DNA. This recently developed passive microfluidic device, supporting nanoliter scale combinatorial droplet generation and mixing, is here used to generate a DNA test library with one member per droplet exported to addressed locations on microwell plates. Standard DNA assembly techniques, such as Gibson assembly, compatible with isothermal on-chip operation, are employed and checked using off-chip PCR and assembly PCR. The control of output droplet sequences and mixing performance was verified using dyes and fluorescently labeled DNA solutions, both on-chip and in external capillary channels. Gel electrophoresis of products and DNA sequencing were employed to further verify controlled combination and functional enzymatic assembly. The scalability of the results to larger DNA libraries is also addressed by combinatorial input expansion using sequential injection plugs from a multiwell plate. Hence, the paper establishes a proof of principle of the production of functional combinatorial mixtures at the nanoliter scale for one sequence per well DNA libraries.</description><subject>Assembly</subject><subject>Chip formation</subject><subject>Combinatorial analysis</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>Droplets</subject><subject>Electrophoresis</subject><subject>Gene sequencing</subject><subject>Plates (structural members)</subject><subject>Plugs</subject><subject>Reaction control</subject><subject>Regular</subject><issn>1932-1058</issn><issn>1932-1058</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><recordid>eNpdkUtLxDAUhYMoOo4u_AMScKOLjrlJ2k43wjA-QXSj65hXNdI2NWmF-fdGHEVd3QP343DuPQgdAJkBKdgpzHhFiwKKDTSBitEMSD7f_KV30G6Mr4TkUFK6jXZoQSlANZ-gp_O7RdY4FWRYYRmjbVWzwn3wz0G2rTVYrbDvMmNb2Rncyc4nerABm-D7xg4R18G3WGI9xiGJ1ung62Z0xmmsX1y_h7Zq2US7v55T9Hh58bC8zm7vr26Wi9tMc8KGDEqrC9CMmdzOmamIsjmfKyJrU5aSAWeGE8JpzmnaKaUJqIJRnXDIS03ZFJ19-fajSrm17YYgG9EH16bThJdO_N107kU8-3fBeVURnieD47VB8G-jjYNoXdS2aWRn_RgFlIQwxgvGE3r0D331Y-jSeYIC5QA58CpRJ19U-kiMwdY_YYCIz94EiHVviT38nf6H_C6KfQD4Z5K6</recordid><startdate>20150701</startdate><enddate>20150701</enddate><creator>Tangen, Uwe</creator><creator>Minero, Gabriel Antonio S</creator><creator>Sharma, Abhishek</creator><creator>Wagler, Patrick F</creator><creator>Cohen, Rafael</creator><creator>Raz, Ofir</creator><creator>Marx, Tzipy</creator><creator>Ben-Yehezkel, Tuval</creator><creator>McCaskill, John S</creator><general>American Institute of Physics</general><general>AIP Publishing LLC</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>8FD</scope><scope>H8D</scope><scope>L7M</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-2123-4768</orcidid><orcidid>https://orcid.org/0000-0002-3408-7357</orcidid></search><sort><creationdate>20150701</creationdate><title>DNA-library assembly programmed by on-demand nano-liter droplets from a custom microfluidic chip</title><author>Tangen, Uwe ; Minero, Gabriel Antonio S ; Sharma, Abhishek ; Wagler, Patrick F ; Cohen, Rafael ; Raz, Ofir ; Marx, Tzipy ; Ben-Yehezkel, Tuval ; McCaskill, John S</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c403t-17ec61c33d5e83d90be548b0afd77a3143d4004254290bbbc01b632cd5e157c23</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>Assembly</topic><topic>Chip formation</topic><topic>Combinatorial analysis</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>Droplets</topic><topic>Electrophoresis</topic><topic>Gene sequencing</topic><topic>Plates (structural members)</topic><topic>Plugs</topic><topic>Reaction control</topic><topic>Regular</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Tangen, Uwe</creatorcontrib><creatorcontrib>Minero, Gabriel Antonio S</creatorcontrib><creatorcontrib>Sharma, Abhishek</creatorcontrib><creatorcontrib>Wagler, Patrick F</creatorcontrib><creatorcontrib>Cohen, Rafael</creatorcontrib><creatorcontrib>Raz, Ofir</creatorcontrib><creatorcontrib>Marx, Tzipy</creatorcontrib><creatorcontrib>Ben-Yehezkel, Tuval</creatorcontrib><creatorcontrib>McCaskill, John S</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>Technology Research Database</collection><collection>Aerospace Database</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Biomicrofluidics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Tangen, Uwe</au><au>Minero, Gabriel Antonio S</au><au>Sharma, Abhishek</au><au>Wagler, Patrick F</au><au>Cohen, Rafael</au><au>Raz, Ofir</au><au>Marx, Tzipy</au><au>Ben-Yehezkel, Tuval</au><au>McCaskill, John S</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>DNA-library assembly programmed by on-demand nano-liter droplets from a custom microfluidic chip</atitle><jtitle>Biomicrofluidics</jtitle><addtitle>Biomicrofluidics</addtitle><date>2015-07-01</date><risdate>2015</risdate><volume>9</volume><issue>4</issue><spage>044103</spage><epage>044103</epage><pages>044103-044103</pages><issn>1932-1058</issn><eissn>1932-1058</eissn><notes>ObjectType-Article-1</notes><notes>SourceType-Scholarly Journals-1</notes><notes>ObjectType-Feature-2</notes><notes>content type line 23</notes><notes>Author to whom correspondence should be addressed. Electronic mail: john.mccaskill@rub.de</notes><abstract>Nanoscale synthetic biology can benefit from programmable nanoliter-scale processing of DNA in microfluidic chips if they are interfaced effectively to biochemical arrays such as microwell plates. Whereas active microvalve chips require complex fabrication and operation, we show here how a passive and readily fabricated microchip can be employed for customizable nanoliter scale pipetting and reaction control involving DNA. This recently developed passive microfluidic device, supporting nanoliter scale combinatorial droplet generation and mixing, is here used to generate a DNA test library with one member per droplet exported to addressed locations on microwell plates. Standard DNA assembly techniques, such as Gibson assembly, compatible with isothermal on-chip operation, are employed and checked using off-chip PCR and assembly PCR. The control of output droplet sequences and mixing performance was verified using dyes and fluorescently labeled DNA solutions, both on-chip and in external capillary channels. Gel electrophoresis of products and DNA sequencing were employed to further verify controlled combination and functional enzymatic assembly. The scalability of the results to larger DNA libraries is also addressed by combinatorial input expansion using sequential injection plugs from a multiwell plate. Hence, the paper establishes a proof of principle of the production of functional combinatorial mixtures at the nanoliter scale for one sequence per well DNA libraries.</abstract><cop>United States</cop><pub>American Institute of Physics</pub><pmid>26221198</pmid><doi>10.1063/1.4926616</doi><tpages>1</tpages><orcidid>https://orcid.org/0000-0002-2123-4768</orcidid><orcidid>https://orcid.org/0000-0002-3408-7357</orcidid><oa>free_for_read</oa></addata></record>
fulltext fulltext
identifier ISSN: 1932-1058
ispartof Biomicrofluidics, 2015-07, Vol.9 (4), p.044103-044103
issn 1932-1058
1932-1058
language eng
recordid cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_4499045
source American Institute of Physics:Jisc Collections:Transitional Journals Agreement 2021-23 (Reading list); PubMed Central
subjects Assembly
Chip formation
Combinatorial analysis
Deoxyribonucleic acid
DNA
Droplets
Electrophoresis
Gene sequencing
Plates (structural members)
Plugs
Reaction control
Regular
title DNA-library assembly programmed by on-demand nano-liter droplets from a custom microfluidic chip
url http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-09-21T06%3A47%3A25IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_pubme&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=DNA-library%20assembly%20programmed%20by%20on-demand%20nano-liter%20droplets%20from%20a%20custom%20microfluidic%20chip&rft.jtitle=Biomicrofluidics&rft.au=Tangen,%20Uwe&rft.date=2015-07-01&rft.volume=9&rft.issue=4&rft.spage=044103&rft.epage=044103&rft.pages=044103-044103&rft.issn=1932-1058&rft.eissn=1932-1058&rft_id=info:doi/10.1063/1.4926616&rft_dat=%3Cproquest_pubme%3E1700334634%3C/proquest_pubme%3E%3Cgrp_id%3Ecdi_FETCH-LOGICAL-c403t-17ec61c33d5e83d90be548b0afd77a3143d4004254290bbbc01b632cd5e157c23%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_pqid=2124115149&rft_id=info:pmid/26221198&rfr_iscdi=true