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.

Compiler-aided systematic construction of large-scale DNA strand displacement circuits using unpurified components

“…Software tools have been developed for designing and analysing DNA strand displacement systems, capable of generating nucleic acid sequences from well-defined structures and molecular interactions 2 3 , calculating the thermodynamic 2 4 5 and kinetic 6 properties of designed molecules, and evaluating if the behaviours of the molecular systems agree with the higher-level designs 3 7 8 9 10 11 . There also exist a few molecular compilers that can translate abstract functions such as a logic function to DNA strand displacement implementations without requiring an understanding of the molecular level details 12 13 . However, there has been little independent experimental validation of these compilers, most of which were developed in parallel with or after experimental findings 12 14 .…”

Domain-Specific Programming Languages for Computational Nucleic Acid Systems

“…Rectangular nodes represent complexes, joined by circular nodes representing reactions between intermediates. Reprinted with permission from ref , Copyright 2015, The Royal Society.…”

“…Another highly integrated toolkit is the DyNAMiC Workbench, 34 which provides a wide range of design tools in a webbased format. The DyNAMiC Workbench uses the port-based, "nodal" design abstraction, as shown in Figure 6, to provide a high-level specification framework for intended circuit behavior.…”

Molecular communication relays for dynamic cross-regulation of self-sorting fibrillar self-assemblies

“…The behavior of DSD circuits is programmable in a straightforward manner because of the Watson-Crick base pairing of DNA and can be predicted using thermodynamic and kinetic models (12,15,16). Several programs (14,(17)(18)(19)(20), such as Visual DSD (21)(22)(23), have been developed for this purpose. The information processing of DSD circuits complements both biological and chemical systems for a wide range of applications (24,25).…”