DyNAMiC Workbench: an integrated development environment for dynamic DNA nanotechnology

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dc.citation.firstpage20150580en_US
dc.citation.journalTitleJournal of the Royal Society Interfaceen_US
dc.citation.volumeNumber12en_US
dc.contributor.authorGrun, Caseyen_US
dc.contributor.authorWerfel, Justinen_US
dc.contributor.authorZhang, David Yuen_US
dc.contributor.authorYin, Pengen_US
dc.date.accessioned2016-01-19T19:19:42Zen_US
dc.date.available2016-01-19T19:19:42Zen_US
dc.date.issued2015en_US
dc.description.abstractDynamic DNA nanotechnology provides a promising avenue for implementing sophisticated assembly processes, mechanical behaviours, sensing and computation at the nanoscale. However, design of these systems is complex and error-prone, because the need to control the kinetic pathway of a system greatly increases the number of design constraints and possible failure modes for the system. Previous tools have automated some parts of the design workflow, but an integrated solution is lacking. Here, we present software implementing a three ‘tier’ design process: a high-level visual programming language is used to describe systems, a molecular compiler builds a DNA implementation and nucleotide sequences are generated and optimized. Additionally, our software includes tools for analysing and ‘debugging’ the designs in silico, and for importing/exporting designs to other commonly used software systems. The software we present is built on many existing pieces of software, but is integrated into a single package—accessible using a Web-based interface at http://molecular-systems.net/workbench. We hope that the deep integration between tools and the flexibility of this design process will lead to better experimental results, fewer experimental design iterations and the development of more complex DNA nanosystems.en_US
dc.identifier.citationGrun, Casey, Werfel, Justin, Zhang, David Yu, et al.. "DyNAMiC Workbench: an integrated development environment for dynamic DNA nanotechnology." <i>Journal of the Royal Society Interface,</i> 12, (2015) The Royal Society: 20150580. http://dx.doi.org/10.1098/rsif.2015.0580.en_US
dc.identifier.doihttp://dx.doi.org/10.1098/rsif.2015.0580en_US
dc.identifier.urihttps://hdl.handle.net/1911/87879en_US
dc.language.isoengen_US
dc.publisherThe Royal Societyen_US
dc.rightsPublished by the Royal Society under the terms of the Creative Commons Attribution License, which permits unrestricted use, provided the original author and source are credited.en_US
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en_US
dc.subject.keywordDNA nanotechnologyen_US
dc.subject.keywordmolecular programmingen_US
dc.subject.keywordself-assemblyen_US
dc.subject.keywordsoftwareen_US
dc.subject.keywordsequence designen_US
dc.subject.keywordintegrated development environmenten_US
dc.titleDyNAMiC Workbench: an integrated development environment for dynamic DNA nanotechnologyen_US
dc.typeJournal articleen_US
dc.type.dcmiTexten_US
dc.type.publicationpublisher versionen_US
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