A simple physical description of DNA dynamics: quasi-harmonic analysis as a route to the configurational entropy

It has become increasingly apparent that the dynamic as well as the structural properties of biological macromolecules are important to their function. However, information concerning molecular flexibility can be difficult to obtain experimentally at the atomic level. Computer modelling techniques s...

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Bibliographic Details
Published in:Journal of physics. Condensed matter 2007-02, Vol.19 (7), p.076103-076103
Main Authors: Harris, S A, Laughton, C A
Format: Article
Language:English
Subjects:
Analytical, structural and metabolic biochemistry
Biological and medical sciences
Fundamental and applied biological sciences. Psychology
General aspects, investigation methods
Nucleic acids
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Summary:It has become increasingly apparent that the dynamic as well as the structural properties of biological macromolecules are important to their function. However, information concerning molecular flexibility can be difficult to obtain experimentally at the atomic level. Computer modelling techniques such as molecular dynamics (MD) have therefore proved invaluable in advancing our understanding of biomolecular flexibility. This paper describes how a combination of atomistic MD simulations and quasi-harmonic analysis can be used to describe the dynamics of duplex DNA, with a particular emphasis on methods for calculating differences in configurational entropies. We demonstrate that DNA possesses remarkably simple mechanical properties relative to globular proteins, making it an ideal system for exploring biomolecular flexibility in general. Our results also highlight the importance of solvent viscosity in determining the dynamic behaviour of DNA in aqueous solution.
ISSN:0953-8984
1361-648X
DOI:10.1088/0953-8984/19/7/076103