Mesoscopic modeling for nucleic acid chain dynamics

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 int...

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Bibliographic Details
Published in:arXiv.org 2005-06
Main Authors: Sales-Pardo, M, Guimera, R, Moreira, A A, Widom, J, Amaral, L A N
Format: Article
Language:English
Subjects:
Chain dynamics
Computer simulation
Deoxyribonucleic acid
DNA
Dynamics
Hydrogen bonding
Monomers
Nucleic acids
Online Access:Get full text
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Summary: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.
ISSN:2331-8422
DOI:10.48550/arxiv.0506001