DyNAMiC Workbench: an integrated development environment for dynamic DNA nanotechnology

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DyNAMiC Workbench: an integrated development environment for dynamic DNA nanotechnology

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Title: DyNAMiC Workbench: an integrated development environment for dynamic DNA nanotechnology
Author: Grun, Casey; Werfel, Justin; Zhang, David Yu; Yin, Peng

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Citation: Grun, Casey, Justin Werfel, David Yu Zhang, and Peng Yin. 2015. “DyNAMiC Workbench: an integrated development environment for dynamic DNA nanotechnology.” Journal of the Royal Society Interface 12 (111): 20150580. doi:10.1098/rsif.2015.0580. http://dx.doi.org/10.1098/rsif.2015.0580.
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Abstract: Dynamic 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.
Published Version: doi:10.1098/rsif.2015.0580
Other Sources: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4614494/pdf/
Terms of Use: This article is made available under the terms and conditions applicable to Other Posted Material, as set forth at http://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of-use#LAA
Citable link to this page: http://nrs.harvard.edu/urn-3:HUL.InstRepos:23845237
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