Volume changes correlate with entropies and enthalpies in the formation of nucleic acid homoduplexes: Differential hydration of A and B conformations

We have used a combination of densimetric, calorimetric, and uv absorption techniques to obtain a complete thermodynamic characterization for the formation of nucleic acid homoduplexes of known sequence and conformation. The volume change Δ V accompanying the formation of four duplexes was interpreted to reflect changes in hydration based on the electrostriction phenomenon. In 10 m M sodium phosphate buffer at pH 7, the magnitude of the measured Δ V 's ranged from −2.0 to +7.2 ml/mol base pair and followed the order of poly(rA) · poly(dT) ∼ poly(dA) · poly(dT) < poly(rA) · poly(dU) ∼ poly(rA) · poly(rU). Inclusion of 100 m M NaCl in the same buffer gave the range of −17.4 to −2.3 mL/mol base pair and the following order: poly(dA) · poly(dT) < poly(rA) · poly(dT) < poly(rA) · poly(rU) ∼ poly(rA) ∼ polyr(dU). Standard thermodynamic profiles of forming these duplexes from their corresponding complementary single strands indicated similar free energies that resulted from the compensation of favorable enthalpies with unfavorable entropies along with a similar counterion uptake at both ionic strengths. The differences in these compensating effects of entropy and enthalpy correlated very well with the volume change measurements in a manner suggesting that the homoduplexes in the B conformation are more hydrated than are those in the A conformation. Moreover, the increased thermal stability of these homoduplexes resulted from an increase in the salt concentration corresponding to larger hydration levels as reflected by the Δ V results. © 1993 John Wiley & Sons, Inc.