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Association of anthracyclines and synthetic hexanucleotides. Structural factors influencing sequence specificity

The equilibrium and kinetic aspects of the interaction between four anthracyclines and two synthetic self‐complementary hexanucleotides was investigated by fluorescence detection. Two of the studied anthracyclines are widely used antitumor drugs: doxorubicin (1, formerly adriamycin) and daunorubicin (2, formerly daunomycin). The other two 9‐deoxydoxorubicin (3) and 3′‐deamino‐3′‐hydroxy‐4′‐epidoxorubicin (4), are doxorubicin analogues with modifications of the chemical groups that have been proposed as responsible for sequence specificity (Chen, K.‐X., Gresh, N. and Pullman, B. (1985). J. Biomol. Struct. Dyn. 3, 445–466). One of the oligonucleotides, d(CGTACG), is identical to that used in the high resolution x‐ray structure determination of the daunorubicin intercalative complex (Wang, A. H.‐J., Ughetto, G., Quigley, G. J. & Rich, A. (1987). Biochemistry 26, 1152–1163). Binding to this hexanucleotide is compared with intercalation into the d(CGCGCG) duplex, revealing sequence preferences of the four anthracyclines. Taking into account the anthracycline aggregation and the dissociation of the hexanucleotide double stranded form, results can be interpreted with a model that assumes complete fluorescence quenching at intercalative sites containing the CG base pair, and a large residual fluorescence after intercalation within the TpA fragment. All four anthracyclines show preferential intercalation at sites near the ends of both hexanucleotide duplexes, partly as a result of positive cooperativity in the formation of di‐intercalated species at these sites. Within the limits of experimental error, complete site specificity for the CpG fragment is found in the intercalation of 1 and 2 into d(CGTACG) duplex, whereas analogues 3 and 4 give increasing evidence of intercalation at other sites including the fluorescence‐preserving TpA fragment. Site specificity is less pronounced in the association with d(CGCGCG), when cooperativity is taken into account. Kinetic data corroborate the results of equilibrium studies and are interpreted with a mechanism that includes formation of an intermediate bound species followed by drug redistribution to preferential sites. Finally, from a comparison of pertinent site binding constants, approximate free energy contributions to sequence specific DNA interaction, due to C9OH on the aglycone and NH  3+ on daunosamine, are estimated not to exceed 2 kcal/mol.