Influence of Local Excitations in Dna Conformation on Binding of Nonintercalating Antitumor Antibiotic in the Minor Groove

Computer model building with damped least-square minimization procedure has been used to study the stereochemistry and energetics of incorporation of a trinucleoside diphosphate fragment with C1/2-endo-C1/3-endo-C1/2-endo sugar puckers in pentanucleotide duplexes d(A)5·d(T)5 (DNA 1) and d(G)5·(C)5 (DNA 2) in B-form. These deformed models were used to study the binding of non-intercalating antitumor antibiotic, netropsin, in the minor groove of DNA. Results show, that in comparison with the normal DNA, the deformed DNA has higher conformational energy and its binding with nonintercalating ligands is stronger. It also shows a higher sequence specificity. The role of these conformational excitations in DNA recognition is discussed in this article.