title: DyNAMiC Workbench: an integrated development environment for dynamic DNA nanotechnology.
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.
authors.affiliation: Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA casey.grun@wyss.harvard.edu.
authors.forename: Casey
authors.identifier: http://orcid.org/0000-0002-4563-6358
authors.initials: C
authors.lastname: Grun
authors.affiliation: Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
authors.forename: Justin
authors.initials: J
authors.lastname: Werfel
authors.affiliation: Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
authors.forename: David Yu
authors.initials: DY
authors.lastname: Zhang
authors.affiliation: Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA Department of Systems Biology, Harvard Medical School, Boston, MA, USA py@hms.harvard.edu.
authors.forename: Peng
authors.initials: P
authors.lastname: Yin
mesh_terms: D001331:Automation; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D030541:Databases, Genetic; D020407:Internet; D007700:Kinetics; D015394:Molecular Structure; D036103:Nanotechnology / Q000379:methods*; D009690:Nucleic Acid Conformation; D009711:Nucleotides / Q000737:chemistry; D011381:Programming Languages; D012984:Software; D013269:Stochastic Processes; D013816:Thermodynamics; D014584:User-Computer Interface
chemical_list: D009711:Nucleotides; D004247:DNA
keywords: DNA nanotechnology; integrated development environment; molecular programming; self-assembly; sequence design; software