Hidden Conformation Events in DNA Base Extrusions: A Generalized-Ensemble Path Optimization and Equilibrium Simulation Study

Abstract

DNA base extrusion is a crucial component of many biomolecular processes. Elucidating how bases are selectively extruded from the interiors of double-strand DNAs is pivotal to accurately understanding and efficiently sampling this general type of conformational transitions. In this work, the on-the-path random walk (OTPRW) method, which is the first generalized-ensemble sampling scheme designed for finite-temperature-string path optimizations, was improved and applied to obtain the minimum free-energy path (MFEP) and the free-energy profile of a classical B-DNA major-groove base-extrusion pathway. Along the MFEP, an intermediate state and the corresponding transition state were located and characterized. The MFEP result suggests that a base-plane-elongation event rather than the commonly focused base-flipping event is dominant in the transition-state (TS) formation portion of the pathway; and the energetic penalty at the transition state is mainly introduced by the stretching of the Watson–Crick base pair. Moreover, to facilitate the essential base-plane-elongation dynamics, the surrounding environment of the flipped base must be intimately involved. Further taking advantage of the extended-dynamics nature of the OTPRW Hamiltonian, an equilibrium generalized ensemble simulation was performed along the optimized path; based on the collected samples, several base-flipping (opening) angle collective variables were evaluated. In correspondence with the MFEP result, the collective variable analysis result reveals that none of these commonly employed flipping (opening) angles alone can adequately represent the base-extrusion pathway, especially in the pre-TS portion. As further revealed by the collective variable analysis, the base-pairing partner of the extrusion target undergoes a series of in-plane rotations to facilitate the base-plane-elongation dynamics. A base-plane rotation angle is identified to be a possible reaction coordinate to represent these in-plane rotations. Notably, these in-plane rotation motions may play a pivotal role in determining the base-extrusion selectivity