DNA Dynamics in a Water Drop without Counterions

Because of its polyionic character, the DNA double helix is stable and biologically active only in salty aqueous media where its charge is compensated by solvent counterions. Monovalent metal ions are ubiquitous in DNA environment, and they are usually considered as the possible driving force of sequence-dependent modulations of DNA structure that make it recognizable by proteins. In an effort to directly examine this hypothesis, MD simulations of DNA in a water drop surrounded by vacuum were carried out, which relieves the requirement of charge neutrality. Surprisingly, with zero concentration of counterions, a dodecamer DNA duplex appears metastable, and its structure remains similar to that observed in experiment, including the minor groove narrowing in the dodecamer d(CGCGAATTCGCG)(2) often considered as the most evident cation effect. It is suggested that the same computational approach will allow one to simulate dynamics of long DNA chains more efficiently than with periodical boundary conditions.