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dc.contributor.authorGrun, Casey
Werfel, Justin
Zhang, David Yu
Yin, Peng
dc.date.accessioned 2016-01-19T19:19:42Z
dc.date.available 2016-01-19T19:19:42Z
dc.date.issued 2015
dc.identifier.citation Grun, Casey, Werfel, Justin, Zhang, David Yu, et al.. "DyNAMiC Workbench: an integrated development environment for dynamic DNA nanotechnology." Journal of the Royal Society Interface, 12, (2015) The Royal Society: 20150580. http://dx.doi.org/10.1098/rsif.2015.0580.
dc.identifier.urihttps://hdl.handle.net/1911/87879
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.
dc.language.iso eng
dc.publisher The Royal Society
dc.rights Published 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.
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.title DyNAMiC Workbench: an integrated development environment for dynamic DNA nanotechnology
dc.type Journal article
dc.contributor.funder Office of Naval Research
dc.contributor.funder National Institutes of Health
dc.contributor.funder National Science Foundation
dc.contributor.funder Wyss Institute
dc.citation.journalTitle Journal of the Royal Society Interface
dc.subject.keywordDNA nanotechnology
molecular programming
self-assembly
software
sequence design
integrated development environment
dc.citation.volumeNumber 12
dc.type.dcmi Text
dc.identifier.doihttp://dx.doi.org/10.1098/rsif.2015.0580
dc.identifier.grantID N000141110914 (Office of Naval Research)
dc.identifier.grantID N000141010827 (Office of Naval Research)
dc.identifier.grantID N000141310593 (Office of Naval Research)
dc.identifier.grantID N000141410610 (Office of Naval Research)
dc.identifier.grantID 1DP2OD007292 (National Institutes of Health)
dc.identifier.grantID CCF1054898 (National Science Foundation)
dc.identifier.grantID CCF1317291 (National Science Foundation)
dc.identifier.grantID CCF1162459 (National Science Foundation)
dc.type.publication publisher version
dc.citation.firstpage 20150580


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