Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.05.238485v1?rss=1

Authors: Zerze, G., Stillinger, F., Debenedetti, P.

Abstract:

Studying the DNA hybridization equilibrium via brute force molecular dynamics (MD) or commonly used advanced sampling approaches is notoriously difficult at the atomistic length scale. However, besides providing more realistic modeling of this microscopic phenomenon, the atomistic resolution is a necessity for some fundamental research questions, such as the ones related to DNA's chirality. Here, we describe an order parameter-based advanced sampling technique to calculate the free energy surface of hybridization and estimate the melting temperature of DNA oligomers at the atomistic resolution, using a native topology-based order parameter. We show that the melting temperatures estimated from our atomistic simulations follow an order consistent with the predictions from melting experiments and those from the nearest neighbor model, for a range of DNA sequences of different GC content. Moreover, free energy surfaces and melting temperatures are calculated to be identical for D- and L-enantiomers of Drew-Dickerson dodecamer.

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