Is SGD a Bayesian sampler? Well, almost
(2020)
Reconfigurable T鈥恓unction DNA origami
Angewandte Chemie Wiley (2020) ange.202006281
Characterising DNA T-motifs by Simulation and Experiment
(2020)
Design of hidden thermodynamic driving for non-equilibrium systems via mismatch elimination during DNA strand displacement
Nature Communications Springer Nature 11 (2020) 2562
Abstract:
Recent years have seen great advances in the development of synthetic self-assembling molecular systems. Designing out-of-equilibrium architectures, however, requires a more subtle control over the thermodynamics and kinetics of reactions. We propose a mechanism for enhancing the thermodynamic drive of DNA strand-displacement reactions whilst barely perturbing forward reaction rates: the introduction of mismatches within the initial duplex. Through a combination of experiment and simulation, we demonstrate that displacement rates are strongly sensitive to mismatch location and can be tuned by rational design. By placing mismatches away from duplex ends, the thermodynamic drive for a strand-displacement reaction can be varied without significantly affecting the forward reaction rate. This hidden thermodynamic driving motif is ideal for the engineering of non-equilibrium systems that rely on catalytic control and must be robust to leak reactions.The oxDNA coarse-grained model as a tool to simulate DNA origami
arXiv (2020)