Lessons learned in atomistic simulation of double-stranded DNA: Solvation and salt concerns [Article v1.0].

Abstract

Nucleic acids are highly charged macromolecules sensitive to their surroundings of water, salt, and other biomolecules. Molecular dynamics simulations with accurate biomolecular force fields provide a detailed atomistic view into DNA and RNA that has been useful to study the structure and dynamics of these molecules and their biological relevance. In this work we study the Drew-Dickerson dodecamer duplex with the sequence d(GCGCAATTGCGC)₂ in three different salt concentrations and using different monvalent salt types to detect possible structural influence. Overall, the DNA shows no major structural changes regardless of amount or type of monovalent ions used. Our results show that only at very high salt conditions (5M) is a small structural effect observed in the DNA duplex, which mainly consist of narrowing of the grooves due to increased residence of ions. We also present the importance of sampling time to achieve a converged ensemble, which is of major relevance in any simulation to avoid biased or non-meaningful results.