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Mesoscopic modeling for nucleic acid chain dynamics

M. Sales-Pardo·R. Guimera·A. A. Moreira·J. Widom·L. A. N. Amaral
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Abstract

To gain a deeper insight into cellular processes such as transcription and translation, one needs to uncover the mechanisms controlling the configurational changes of nucleic acids. As a step toward this aim, we present here a novel mesoscopic-level computational model that provides a new window into nucleic acid dynamics. We model a single-stranded nucleic as a polymer chain whose monomers are the nucleosides. Each monomer comprises a bead representing the sugar molecule and a pin representing the base. The bead-pin complex can rotate about the backbone of the chain. We consider pairwise stacking and hydrogen-bonding interactions. We use a modified Monte Carlo dynamics that splits the dynamics into translational bead motion and rotational pin motion. By performing a number of tests we first show that our model is physically sound. We then focus on the study of a the kinetics of a DNA hairpin--a single-stranded molecule comprising two complementary segments joined by a non-complementary loop--studied experimentally. We find that results from our simulations agree with experimental observations, demonstrating that our model is a suitable tool for the investigation of the hybridization of single strands.

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M. Sales-Pardo, R. Guimera, A. A. Moreira, J. Widom, L. A. N. Amaral. 2005-06-01. Mesoscopic modeling for nucleic acid chain dynamics. https://doi.org/10.1103/physreve.71.051902

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