Calculation of melting temperature and transition curve for Dickerson DNA dodecamer on the basis of configurational entropy, hydrogen bonding energy, and heat capacity: A molecular dynamics simulation study

Abstract

A familiarity with denaturation process is highly significant in understanding the DNA replication, m anipulation, and interactions involving DNA double helix stability. We have performed molecular dynamics simulation on B-DNA duplex (CGCGAATTGCGC) at different temperatures. At each temperature, configurational entropy was estimated u sing the covariance matrix of atom-positional fluctuations. By plotting the configuration entropy versus temperature, we c alculated the melting temperature which was found to be 329.7 K. We also calculated the hydrogen bonding energy and heat cap acity for the atoms participating in the hydrogen bonding between two s trands of DNA. Moreover, their temperature dependencies were investigated to obtain the melting temperature which was found t o be 330.9 K. Finally, by comparing the melting tem perature and the shape of the transition curve obtained from different method s, it is concluded that the stacking interactions a ffect the shape of transition curve, while the hydrogen bonding and columbic interactions determine the position of the melting poin t temperature.