MOLECULAR ANCHORING OF DUPLEX AND TRIPLEX DNA BY DISUBSTITUTED ANTHRACENE-9,10-DIONES - CALORIMETRIC, UV MELTING, AND COMPETITION DIALYSIS STUDIES

Isothermal titration calorimetry, UV melting, and competition dialysis techniques have been used to examine the binding of isomeric 1,4- and 2,6-bis(omega-aminopropionamido)-substituted anthracene-9,10-diones ( anthraquinones) with dA(n) . dT(n) duplexes and dT(n)-dA(n) . dT(n) tr iplexes. Recent footprinting studies [Fox, K. R.; Polucci, P.; Jenkins , T. C.; Neidle, S. Proc. Natl. Acad. Sci. U.S.A. 1995, 92, 7887-7891] indicate that 2,6 derivatives, but not their 1,4 counterparts, differ entially stabilize triple-stranded DNA and may have application in ant igene chemotherapy. Thermodynamic investigations are here reported for interaction with dA(18). dT(18) and dT(18)-dA(18). dT(18). The 2,6 co mpound shows preferential tripler binding, with K-b values of 1.8 x 10 (4) M (duplex)(-1) and 2.2 x 10(5) M (tripler)(-1) at 25 degrees C in aqueous solution, pH 6.0, whereas the 1,4 isomer favors duplex binding , with K-b values of 1:1 x 10(5) M (duplex)(-1) and 3.5 x 10(4) M (tri pler)(-1). Binding to the preferred DNA is enthalpically driven for ea ch ligand, whereas binding to the disfavored DNA is either entropicall y driven or enthalpy/entropy compensated. Further, the binding site si zes (3.6 base pairs/base triplets) suggest DNA intercalation. Competit ion dialysis studies with poly(dA). poly(dT) and poly(dA). poly(dT)(2) confirm these binding preferences, and qualitative support is provide d from UV melting experiments. Such studies reveal tripler disruption by the 1,4 isomer at low drug concentrations while the 2,6 compound ef fects stabilization toward thermal tripler denaturation. Spectrophotom etric studies of each free ligand indicate self-association in aqueous solution; with dimerization constants at 25 degrees C of (2.9 +/- 0.2 ) x 10(3) and (3.2 +/- 0.1) x 10(3) M(-1) respectively for the 1,4 and 2,6 isomers. Taken together, these data provide a firm thermodynamic basis for the contrasting duplex/tripler binding preferences of this i someric family of ligands.