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    DyNAMiC Workbench: an integrated development environment for dynamic DNA nanotechnology

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    Author
    Grun, Casey; Werfel, Justin; Zhang, David Yu; Yin, Peng
    Date
    2015
    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.
    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.
    Published Version
    http://dx.doi.org/10.1098/rsif.2015.0580
    Keyword
    DNA nanotechnology; molecular programming; self-assembly; software; sequence design; More... integrated development environment Less...
    Type
    Journal article
    Publisher
    The Royal Society
    Citable link to this page
    https://hdl.handle.net/1911/87879
    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.
    Link to License
    http://creativecommons.org/licenses/by/4.0/
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    • Bioengineering Publications [632]
    • Faculty Publications [4988]

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    Home | FAQ | Contact Us | Privacy Notice | Accessibility Statement
    Managed by the Digital Scholarship Services at Fondren Library, Rice University
    Physical Address: 6100 Main Street, Houston, Texas 77005
    Mailing Address: MS-44, P.O.BOX 1892, Houston, Texas 77251-1892
    Site Map