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Netropsin binding to poly[d(IC)].poly[IC)] and poly[d(GC].poly[d(GC)]: a computer simulation

F Gago and WG Richards

Oxford Centre for Molecular Sciences, Oxford University, UK.

The thermodynamic cycle perturbation approach has been used to calculate the difference in the free energy of binding of netropsin to two different DNA molecules. In the computer simulations, all the inosine residues have been gradually 'mutated' into guanosine in a DNA dodecamer and in a complex of the same dodecamer with netropsin. The difference in binding free energy of about 4.3 kcal mol-1 agrees well with the experimentally determined value of 4.0 kcal mol-1. One structural determinant of the specificity seems to be the width of the minor groove in the two complexes.

Volume 37, Issue 3, pp. 341-346, 03/01/1990
Copyright © 1990 by American Society for Pharmacology and Experimental Therapeutics




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E. Marco, A. Negri, F. J. Luque, and F. Gago
Role of stacking interactions in the binding sequence preferences of DNA bis-intercalators: insight from thermodynamic integration free energy simulations
Nucleic Acids Res., November 10, 2005; 33(19): 6214 - 6224.
[Abstract] [Full Text] [PDF]


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