DyNAMiC Workbench: an integrated development environment for dynamic DNA nanotechnology

Grun, Casey
Werfel, Justin
Zhang, David Yu
Yin, Peng
Journal Title
Journal ISSN
Volume Title
The Royal Society

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.

Journal article

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.

Forms part of
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.
Citable link to this page