We introduce a coarse-grained model of DNA that captures the thermodynamic and mechanical changes associated with duplex formation. Despite this, the model's representation of DNA as a chain of rigid nucleotides is simple enough to allow access to large length- and time-scales in simulations. As a consequence, the model is appropriate for investigating the kinetic and thermodynamic factors that underpin the burgeoning field of DNA nanotechnology.We first outline the model and its parameterization, before demonstrating its applicability in understanding the behavior of self-assembling DNA. In particular, we show that the model gives a remarkably accurate representation of toehold-mediated strand-displacement, thereby explaining the dependence of displacement rate on toehold length. We will also consider the model's predictions for the operation of DNA 'walkers', discuss non-trivial mechanisms for DNA duplex formation and highlight the role of sequence-dependent interaction strengths in a number of processes.

Coarse-grained modeling of DNA and DNA nanotechnology

244th National Meeting (2012)

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