A Reduced Set of Coordinates for Modeling DNA Structures: (I) A B-to-A Transition Pathway Driven by Pseudorotational Angle

Abstract

The A-DNA and the B-DNA are two well characterized polymorphous forms of DNA duplex. By using Metropolis Monte Carlo Simulations in a reduced coordinate space, we have shown that the B ⇔ A transitions can be induced by forcing pseudorotational angle (W) to change between C3′-endo and C2′-endo puckerings. The energy barrier for the transition pathway is less than 10 Kcal · mol ¹. Base-pair parameters x-displacement (D _x) and roll (ρ), which have the largest differences between the two forms of structures, cannot drive the transition. Our results support the view that the bistable states of the DNA duplex are due to the bistable structures of the sugar ring.