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

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Abstract
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 ΔV accompanying the formation of four duplexes was interpreted to reflect changes in hydration based on the electrostriction phenomenon. In 10 mM sodium phosphate buffer at pH 7, the magnitude of the measured ΔV'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 mM 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 ΔV results. © 1993 John Wiley & Sons, Inc.