Quantum Mechanical Characterization of Nucleic Acids in Solution:? A Linear-Scaling Study of Charge Fluctuations in DNA and RNA

The Journal of Physical Chemistry B vol. 106  p. 7693-7703  DOI: 10.1021/jp0146667  Published: 2002-08-08 

Jana Khandogin, Darrin M. York [ ]

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Atom-centered point charges are a convenient and computationally efficient way to approximately represent the electrostatic properties of biological macromolecules. Atomic charges are routinely used in molecular modeling applications such as molecular simulations, molecular recognition, and ligand binding studies and for determining quantitative structure activity relationships. In the present paper a divide-and-conquer linear-scaling semiempirical method combined with a conductor-like screening model is applied to the calculation of charge distributions of solvated DNA and RNA duplexes in canonical A- and B-forms. The atomic charges on A-DNA, B-DNA, and A-RNA duplex decamers are analyzed to characterize the convergence of the linear-scaling method, and the effects of the charge model and semiempirical Hamiltonian. Furthermore, the inter- and intramolecular charge variations on DNA and RNA duplex 72-mers are investigated to gain insight into the influence of conformation, base stacking, and solvent polarization on the charge distributions. The charges derived from the linear-scaling semiempirical calculations reflect the electronic relaxation in the solvated macromolecular environment and therefore provide a better reference charge state for biomolecular modeling applications.