Molecular dynamics study of single-stranded DNA in aqueous solution confined in a nanopore

Abstract

Molecular dynamics simulations have been carried out to study the molecular behaviours of single-strand DNA molecules in aqueous solution in a cylindrical pore of 2–3 nm diameter. We examined the solvent and the ion distribution in the nanopore. We studied the conformational properties of the single-strand DNA and the dependence of the conformation on the diameter of the nanopore and on the length of the single-stranded DNA, and the interaction between the single-stranded DNA and the ions. We found that the ions in the nanopore show a preference to the centre of the pore. In addition, the sodium ions exhibit an oscillatory density distribution in the radial direction correlated with the density distribution of the water molecules. The end-to-end distance, and the orientation of the end-to-end vector of the single-stranded DNA are strongly affected by the confinement. The counter-ions adsorb strongly to the charged sites on the single-stranded DNA, most dominantly the backbone phosphate groups. There exists, however, substantial freedom for the counter-ion to desorb from the DNA.

Acknowledgments

The author acknowledges very helpful discussions with T. E. Cheatham III at the early stage of this work. The author would like to thank H. D. Cochran and J. M. Ramsey for useful discussions. The work is supported in part by the NSF at UT under contract BES-0103140, by DARPA at ORNL, and by the Chemical Sciences Division of DOE at ORNL. ORNL is operated for the US DOE by UT-Battelle, LLC, under contract DE-AC05-00OR22725.