Influence of strongly stabilized sites on DNA melting: A comparison of theory with experiment

¹ Institute of Physics, Academia Sinica - Nankang, Taipei 11529, Taiwan
² Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus - 5/2, Kuprevich St., 220141, Minsk, Belarus
³ Center for Nonlinear and Complex Systems and Department of Physics, Chung-Yuan Christian University Chungli 32023, Taiwan

^a huck@phys.sinica.edu.tw

Received: 26 May 2010
Accepted: 26 July 2010

Abstract

Strong local stabilization of the double helix can be an alternative to the interstrand crosslinks formed in DNA by some antitumor drugs. Therefore, we have carried out a computer modeling of the thermodynamic properties of DNA that contains strongly stabilized sites (SSSs). Melting of DNA locally fastened by SSSs was compared with DNA that includes interstrand crosslinks. Using experimental data from the literature and the results of our calculations, we have shown that SSSs really exist: some irreversibly bound protein molecules and chemical modifications caused by some ruthenium and antitumor platinum compounds form such sites in DNA. The theoretical calculated results for the increase of melting temperatures for random distribution of SSSs are consistent with experimental data.