Paper Citing NAMD - Abstract
Izanloo, C.; Parsafar, G. A.; Abroshan, H.; Akbarzade, H.
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
JOURNAL OF THE IRANIAN CHEMICAL SOCIETY, 8:708-716, SEP 2011
A familiarity with denaturation process is highly significant in understanding the DNA replication, manipulation, 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 using the covariance matrix of atom-positional fluctuations. By plotting the configuration entropy versus temperature, we calculated the melting temperature which was found to be 329.7 K. We also calculated the hydrogen bonding energy and heat capacity for the atoms participating in the hydrogen bonding between two strands of DNA. Moreover, their temperature dependencies were investigated to obtain the melting temperature which was found to be 330.9 K. Finally, by comparing the melting temperature and the shape of the transition curve obtained from different methods, it is concluded that the stacking interactions affect the shape of transition curve, while the hydrogen bonding and columbic interactions determine the position of the melting point temperature.
