Paper Citing NAMD - Abstract
Izanloo, C.; Parsafar, G. A.; Abroshan, H.; Akbarzadeh, H.
Denaturation of Drew-Dickerson DNA in a High Salt Concentration Medium: Molecular Dynamics Simulations
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:3354-3361, DEC 2011
We have performed molecular dynamics simulation on B-DNA duplex (CGCGAATTGCGC) at different temperatures. The DNA was immerged in a salt-water medium with 1 M NaCl concentration to investigate salt effect on the denaturation process. At each temperature, configurational entropy is estimated using the covariance matrix of atom-positional fluctuations, from which the melting temperature (T(m)) was found to be 349 K. The calculated configuration entropy for different bases shows that the melting process involves more peeling (including fraying from the ends) conformations, and therefore the untwisting of the duplex and peeling states form the transition state of the denaturation process. There is a narrow minor groove in the AATT sequence that becomes wider by increasing temperature which disappears at high temperatures, especially above the melting temperature. We have also calculated the fraction of denatured base pairs, f-curve, from which T(m) was found to be 340 K, close to experimental value of 341 K. We found that DNA at high salt concentrations has few hydrogen bonds even at temperatures higher than the T(m). Our calculations show the fact that adding salt leads to increase of T(m) and stabilization of DNA. (C) 2011 Wiley Periodicals, Inc. J Comput Chem 32: 3354-3361, 2011
