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Mesoscopic modeling for nucleic acid chain dynamics M. Sales-Pardo,1
 

Summary: Mesoscopic modeling for nucleic acid chain dynamics
M. Sales-Pardo,1
R. Guimerą,1
A. A. Moreira,1
J. Widom,2
and L. A. N. Amaral1
1
Department Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, USA
2
Department of Biochemistry, Molecular Biology and Cell Biology, and Department of Chemistry, Northwestern University,
2153 Sheridan Road, Evanston, Illinois 60208, USA
Received 2 July 2004; revised manuscript received 8 November 2004; published 5 May 2005
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 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

  

Source: Amaral, Luis A.N. - Department of Chemical and Biological Engineering, Northwestern University

 

Collections: Physics; Biology and Medicine