Reversible B/A Transitions in Single DNA Molecule Immersed in A Water Drop

Abstract

Clarification of the detailed mechanisms involved in the DNA polymorphism is an important challenge for computational molecular biophysics. This paper reports about reversible A/B transitions in DNA observed in silico in a simulated titration experiment by smooth variation of the size of a water drop around a double helical solute. The estimated range of hydration numbers corresponding to the B/A transition roughly agrees with experimental data. The chain length dependence was studied and it appeared that the transition to A-form is hindered when the fragment becomes shorter than one helical turn. Dynamics of the A/B transition at low hydration is cooperative and is driven mainly by medium range electrostatic interactions of counterions sandwiched between phosphate strands in the major groove. The correspondence of these computational observations to common experimental conditions of A/B transitions is discussed.