Entropy Calculations of Hoogsteen and Watson-Crick Conformations

Abstract

The conformations that DNA takes are often vital in many biological processes. The physical effects Hoogsteen conformation base pairs have on the full strand of DNA are still being determined. Through molecular dynamics simulations in CHARMM, the effect Hoogsteen conformation has on the entropy of the strand can be examined. The absolute entropy of both Hoogsteen and Watson-Crick conformations can be calculated with the use of a quasi-harmonic approximation using the trajectories of each simulation. Using this method, the entropy contribution of varying amounts of neighboring base pairs can be estimated. This work can be compared with experimental entropy values for entire double-strands. Our calculations show how a localized conformational change can affect the entropy in neighboring site and over longer-range base pairs.