oxDNA: coarse-grained simulations of nucleic acids madesimple
Erik Poppleton, Michael Matthies, Debesh Mandal, Flavio Romano, Petr Šulc, Lorenzo Rovigatti
Abstract
The fields of DNA and RNA nanotechnology have progressed from pioneering, proof-of-principle \nexperiments to fully-fledged applications in material science, biology and medicine. These \napplications exploit the intrinsic programmability of nucleic acids to generate nano- and \neven micro-scale structures with tailored properties. However, the design of the DNA/RNA \nsequences that self-assemble into a desired structure is not straightforward and often relies on \nexpensive trial-and-error experimental protocols. A complementary approach is provided by \ncomputer simulations, which can model biomacromolecules at different levels of detail, ranging \nfrom atomistic to continuous, and can be leveraged to investigate the whole range of time- \nand length-scales relevant for applications. Here we present oxDNA, a software package that \nhas been designed to efficiently run coarse-grained simulations of DNA and RNA and also \nfeatures an analysis suite aimed at post-processing the analysis of oxDNA/oxRNA trajectories.