Enthalpy-entropy contribution to carcinogen-induced DNA conformational heterogeneity

Abstract

DNA damage by adduct formation is a critical step for the initiation of carcinogenesis. Aromatic amines are strong inducers of environmental carcinogenesis. Their DNA adducts are known to exist in an equilibrium between the major groove (B) and base-displaced stacked (S) conformations. However, the factors governing such heterogeneity remain unclear. Here we conducted extensive calorimetry/NMR/CD studies on the model DNA lesions caused by fluorinated 2-aminfluorene (FAF) and 4-aminobiphenyl (FABP) in order to gain thermodynamic and kinetic insights into the S/B conformational equilibrium. We demonstrate that there are large differences in enthalpy-entropy compensations for FABP and FAF. The small and flexible FABP exclusively adopts the less perturbed B conformer with small enthalpy (DeltaDeltaH-2.7 kcal/mol)/entropy (DeltaDeltaS-0.7 eu) change. In contrast, FAF stacks better and exists as a mixture of B and S conformers with large enthalpy (DeltaDeltaH-13.4 kcal/mol)/entropy (DeltaDeltaS-34.2 eu) compensation. van't Hoff analysis of dynamic (19)F NMR data indicated DeltaH(B<-->S) = 4.1 kcal/mol in favor of the B conformer and DeltaS(B<-->S) = 15.6 cal mol(-1) K(-1) in favor of the intercalated S conformer. These findings demonstrate that the favorable entropy of the S conformer over B conformer determines the S/B population ratios at physiological temperatures.

Fig. 1

(a) Chemical structures of FABP and FAF-modified DNA. (b) AF-induced S/B-conformational heterogeneity. B and S refers to B-type and stacked conformers, respectively.

Fig. 2

(a) ¹⁹F NMR Spectra of FABP and FAF-modified 11-mer duplexes at 20 ° C. (b) Overlays of (b) CD and (c) UV spectra for FABP and FAF-modified duplexes.

Fig. 3

(a) DSC and (b) Thermodynamic plots of the FABP- and FAF-modified, and the control DNA duplexes.

Fig. 4

Dynamic ¹⁹F NMR of the FABP- and FAF-modified DNA duplexes as a function of temperatures.

Fig. 5

(a) van’t Hoff plot of the FAF-induced B/S conformational equilibrium as a function of 1/T (0 ~ 30°C). (b) Conformational thermodynamics of B–S equilibrium derived from van’t Hoff parameters.