The activation volume of a DNA helix-coil transition

The role of hydration in the kinetics of a DNA helix-coil equilibrium is investigated by studying the effect of hydrostatic pressure on the rate constants describing the reaction. The kinetics were measured using the thermal hysteresis between the denaturation and renaturation curves of the triplex-forming oligonucleotides: (5)'d[AAA-GGAGGAGAAGAAGAAAAAA] (sequence of purine strand) and (5)'d[TTTCCTCCTCTTCTTCTTTTTT] (third strand). The kinetics at atmosphere pressure far this system have been recently reported [Rougee et al. (1992) Biochemistry 31, 9269-9278]. At all pressures the data are consistent with a single-step bimolecular reaction under the conditions of our experiments (100 mM NaCl, 10 mM cacodylate, pH 6.5). The rate of formation of the tripler from the duplex + single strand is accelerated by pressure. At the midpoint of the helix-coil transition (32.5 degrees C), the activation volume for helix formation, V*(1), equals -11.8 (+/-2.4) cm(3) mol(-1) at atmospheric pressure. At the same temperature, the activation volume for helix dissociation, V*(-1), equals +39.9 (+/-5.0) cm(3) mol(-1); that is, the rate of strand separation is slowed by pressure. These findings emphasize the importance of solvent interactions in the stabilization and formation of DNA helices. It is proposed that the activation volume of the forward reaction may arise from the volume change due to charging the cytosine residues and the formation of base-stacking interactions in the third strand. The positive activation volume of strand separation may be a consequence of poor solvent packing of the DNA duplex major groove during dissociation of the third strand.