Differential hydration of dA·dT base pairing and da and dT bulges in deoxyoligonucleotides

The role of water in the formation of stable duplexes of nucleic acids is being studied by determining the concurrent volume change, heats, and counterion uptake that accompany the duplexation process. The variability of the volume contraction that we have observed in the formation of a variety of homoduplexes suggests that sequence and conformation acutely affect the degree of hydration. We measured the change in volume and enthalpy resulting from the mixing of two complementary strands to form (a) fully paired duplexes of 10 or 11 base pairs and (b) bulged decameric duplexes with an extra dA or dT unmatched residue.