Ion motions in molecular dynamics simulations on DNA

doi:10.1073/pnas.0406435101

Ion motions in molecular dynamics simulations on DNA

Departments of ^*Physics, ^‡Molecular Biology and Biochemistry, and ^§Chemistry and ^†Molecular Biophysics Program, Wesleyan University, Middletown, CT 06459

Communicated by Mark A. Ratner, Northwestern University, Evanston, IL, August 31, 2004 (received for review March 26, 2004)

Abstract

Counterions play a significant role in DNA structure and function, and molecular dynamics (MD) simulations offer the prospect of detailed description of the dynamical structure of ions at the molecular level. However, the motions of mobile counterions are notably slow to converge in MD on DNA. Obtaining accurate and reliable MD simulations requires knowing just how much sampling is required for convergence of each of the properties of interest. To address this issue, MD on a d(CGCGAATTCGCG) duplex in a dilute aqueous solution of water and 22 Na⁺ counterions was performed until convergence was achieved. The calculated first shell ion occupancies and DNA–Na⁺ radial distribution functions were computed as a function of time to assess convergence, and compared with relaxation times of the DNA internal parameters shift, slide, rise, tilt, roll, and twist. The sequence dependence of fractional occupancies of ions in the major and minor grooves of the DNA is examined, and the possibility of correlation between ion proximity and DNA minor groove widths is investigated.

Footnotes

↵ ¶ To whom correspondence should be addressed. E-mail: dbeveridge{at}wesleyan.edu.
Author contributions: S.Y.P. performed research and analyzed data; and K.M.T. and D.L.B. designed research and wrote the paper.
Abbreviations: CC, counterion condensation; PB, Poisson Boltzmann; MD, molecular dynamics.
Note Added in Proof. While this article was being reviewed, a related article comparing the behavior of Na+ and K+ counterions around DNA was published (65).