Energetics of nucleic acid stability:: The effect of ΔCP

We report high-resolution differential scanning calorimetric data on the poly(dAdT)poly(dAdT), poly(dA)poly(dT), poly(dldC)poly(dldC), poly(dGdC)poly(dGdC), poly(rA)poly(rU), and poly(rl)poly(rC) nucleic acid duplexes. We use these data to evaluate the melting temperatures, T-M, enthalpy changes, DeltaH(M), and heat capacity changes, DeltaC(P), accompanying helix-to-coil transitions of each polymeric duplex studied in this work at different NaCl concentrations. In agreement with previous reports, we have found that DeltaC(P) exhibits a positive, nonzero value, which, on average, equals 268 +/- 33 J mol(-1) K-1. With DeltaC(P), we have calculated the transition free energies, DeltaG, enthalpies, DeltaH, and entropies, DeltaS, for the duplexes as a function of temperature. Since, DeltaG, DeltaH, and DeltaS all strongly depend on temperature, the thermodynamic comparison between DNA and/or RNA duplexes (that may differ from one another with respect to sequence, composition, conformation, etc.) is physically meaningful only if extrapolated to a common temperature. We have performed such comparative analyses to derive differential thermodynamic parameters of formation of GC versus AT, U, and IC base pairs as well as B' versus A and B helix conformations. We have proposed some general microscopic interpretations for the observed sequence-specific and conformation-specific thermodynamic differences between the duplexes.