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Nucleic Acids Research, 1988, Vol. 16, No. 7 3061-3073
© 1988

Articles

Energetics and stereochemistry of DNA complexation with the antitumor AT specific intercalators tilorone and m-AMSA

Kai-Xian Chen*, Nohad Gresh and Bernard Pullman

Institut de Biologie Physico-Chimique, Laboratoire de Biochimie Théorique associé au CNRS 13 rue Pierre et Marie Curie, 75005 Paris, France

Received December 1, 1987. Revised March 1, 1988. Accepted March 1, 1988.

Computations by the SIBFA method on the lntercaiative interaction energies of tiiorone and m-AMSA with B-DNA representative oiigonucieotides account for the specificity of these antltumor drugs for AT sites and minor groove intercalation. In tilorone this specificity is due to the strong preference of the side chains for the minor groove, which overcomes the preference of the chromophore for a GC intercalation site. In m-AMSA the specificity is due to the combined preference of both the chromophore and the anhiino side chain for AT intercalation site and minor groove, respectively. o-AMSA is shown to manifest a simiiar (although significantly less pronounced specificity) as m-AMSA but a higher affinity for DNA. A comparison of the energetics and stereochemistry of intercalative binding to DNA of m-AMSA (AT minor groove specific) and 9-aminoacr(dine-4- carboxamide (GC major groove specific), which possess the same chromophore and differ oniy by the nature and position of the side chains, shows the possibility of important variations In the intercalative behaviour of chromophoric drugs as a function of the substituent groups attached to them.

*Permanent address: Shanghai Institute of Materia Medica, Academia Sinica, Shanghai, China


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