DNA walker circuits: computational potential, design, and verification
Natural Computing Springer Nature 14:2 (2015) 195-211
Automated design and verification of localized DNA computation circuits
DNA 2015: DNA Computing and Molecular Programming Springer International Publishing Switzerland 9211 (2015) 168-180
Abstract:
Simple computations can be performed using the interactions between single-stranded molecules of DNA. These interactions are typically toehold-mediated strand displacement reactions in a well-mixed solution. We demonstrate that a DNA circuit with tethered reactants is a distributed system and show how it can be described as a stochastic Petri net. The system can be verified by mapping the Petri net onto a continuous time Markov chain, which can also be used to find an optimal design for the circuit. This theoretical machinery can be applied to create software that automatically designs a DNA circuit, linking an abstract propositional formula to a physical DNA computation system that is capable of evaluating it.Folding pathways: DNA origami as a model system
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS 44 (2015) S67-S67
Programmable energy landscapes for kinetic control of DNA strand displacement.
Nature communications 5 (2014) 5324-5324
Abstract:
DNA is used to construct synthetic systems that sense, actuate, move and compute. The operation of many dynamic DNA devices depends on toehold-mediated strand displacement, by which one DNA strand displaces another from a duplex. Kinetic control of strand displacement is particularly important in autonomous molecular machinery and molecular computation, in which non-equilibrium systems are controlled through rates of competing processes. Here, we introduce a new method based on the creation of mismatched base pairs as kinetic barriers to strand displacement. Reaction rate constants can be tuned across three orders of magnitude by altering the position of such a defect without significantly changing the stabilities of reactants or products. By modelling reaction free-energy landscapes, we explore the mechanistic basis of this control mechanism. We also demonstrate that oxDNA, a coarse-grained model of DNA, is capable of accurately predicting and explaining the impact of mismatches on displacement kinetics.Transport and self-organization across different length scales powered by motor proteins and programmed by DNA
Nature Nanotechnology 9:1 (2014) 44-47