capture of a transition state using molecular dynamics creation of an intercalation site in dsdna with ethidium cation捕获的过渡态使用分子动力学建立夹层网站dsdna ethidium阳离子.pdfVIP

SAGE-Hindawi Access to Research Journal of Nucleic Acids Volume 2010, Article ID 702317, 4 pages doi:10.4061/2010/702317 Research Article Capture of a Transition State Using Molecular Dynamics: Creation of an Intercalation Site in dsDNA with Ethidium Cation Regina R. Monaco Department of Environmental Chemistry, Mailman School of Public Health, Columbia University, New York NY, 10032, USA Correspondence should be addressed to Regina R. Monaco, rm2441@ Received 3 June 2009; Revised 17 November 2009; Accepted 28 January 2010 Academic Editor: John A. Hartley Copyright © 2010 Regina R. Monaco. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The mechanism of intercalation and the ability of double stranded DNA (dsDNA) to accommodate a variety of ligands in this manner has been well studied. Proposed mechanistic steps along this pathway for the classical intercalator ethidium have been discussed in the literature. Some previous studies indicate that the creation of an intercalation site may occur spontaneously, with the energy for this interaction arising either from solvent collisions or soliton propagation along the helical axis. A subsequent 1D diffusional search by the ligand along the helical axis of the DNA will allow the ligand entry to this intercalation site from its external, electrostatically stabilized position. Other mechanistic studies show that ethidium cation participates in the creation of the site, as a ligand interacting closely with the external surface of the DNA can cause unfavorable steric interactions depending on the ligands’ orientation, which are relaxed during the creation of an intercalation site.