Visual DSD: a design and analysis tool for DNA strand displacement systems

Abstract

Summary: The Visual DSD (DNA Strand Displacement) tool allows rapid prototyping and analysis of computational devices implemented using DNA strand displacement, in a convenient web-based graphical interface. It is an implementation of the DSD programming language and compiler described by Lakin et al. (2011) with additional features such as support for polymers of unbounded length. It also supports stochastic and deterministic simulation, construction of continuous-time Markov chains and various export formats which allow models to be analysed using third-party tools.Availability: Visual DSD is available as a web-based Silverlight application for most major browsers on Windows and Mac OS X at http://research.microsoft.com/dna. It can be installed locally for offline use. Command-line versions for Windows, Mac OS X and Linux are also available from the web page.Contact: aphillip@microsoft.comSupplementary Information:Supplementary data are available at Bioinformatics online.

Implementing Nonlinear Feedback Controllers Using DNA Strand Displacement Reactions

“…A DSD Fig. 2: Examples of DNA strand displacement reactions illustrated using the software package Visual DSD [25] : the DNA strands are bonded by Watson-Crick base pairing, denoted by * and the basic steps involved are (a) binding of toehold 1 to 1*, (b) branch migration wherein the strand 1-2 partially displaces strand 2-3, and (c) complete separation of strand 2-3 [26].…”

“…When implemented as elementary DNA reactions, for example by using the software package Visual DSD [25], these reactions can be used to construct a nonlinear QSM feedback controller. Consider the following set of idealized CRNs, where the signal X 1 is the input of the system and the signal A is the output, …”

“…The CRNs (2) are approximations of elementary DNA reactions which can be realized using Visual DSD software, [25], as illustrated in Figs. 5, 6 and 9.…”

Biologically inspired design of feedback control systems implemented using DNA strand displacement reactions

“…adenine-thymine and guaninecytosine), the selection of appropriate DNA sequences allows precise control over the dynamics of the implemented DNA reactions, thus facilitating a precise molecular programming of the desired function, operator or circuit. Sophisticated CAD tools are also now becoming available to facilitate the design of synthetic circuits using this approach [5]. Examples of complex biomolecular circuits successfully designed and implemented through this approach include predator-prey dynamics [6], oscillators [7], and both linear and nonlinear feedback controllers [3], [8], [9].…”

Plasmid-derived DNA Strand Displacement Gates for Implementing Chemical Reaction Networks

“…DNA strand displacement cascades have been used to create digital and analog molecular circuits [4][5][6][7] , switchable nanostructures [8][9][10] , autonomous molecular motors [11][12][13][14][15] , and non-covalent catalytic amplifiers 13,[16][17][18][19][20][21] . Moreover, DNA devices using strand displacement reactions can be simulated and designed for diverse applications using computer-assisted design software [22][23][24] .…”