Enthalpy-entropy compensations in nucleic acids: Contribution of electrostriction and structural hydration

Investigations have been carried out on the interaction of nucleic acids with a wide variety of ligands, the most pervasive and least understood of these is water itself. Experimental evidence indicates that helical nucleic acid structures are heavily hydrated. Sequence-independent DNA hydration sites exist near the edges of the bases facing the grooves, in the vicinity of the sugars, and around the phosphate groups. The fact that the hydration of DNA is sequence dependent has been inferred from X-ray analysis of the crystal structures of oligonucleotides. An investigation on the formation of four duplexes is discussed from mixing its complementary single strands: two fully paired duplexes and two decamer duplexes containing a bulge. Complete thermodynamic profiles are obtained for the formation of each duplex at 20°. By setting up appropriate thermodynamic cycles, for pairs of reactions, differential thermodynamic profiles are obtained that correspond to specific changes such as the inclusion of an extra base pair, or a nonpaired base or bulge, in a fully paired decamer duplex. The comparison of the sign of the resulting differential enthalpy-entropy compensation with the sign of the differential volume change allows distinguishing the type of hydration contribution, electrostricted versus structural that is responsible for the particular change.