Energetics of Nucleic Acid Stability:  The Effect of ΔC P

• Published in: Journal of the American Chemical Society Vol. 126; no. 50; pp. 16387 - 16394
• Main Authors: Tikhomirova, Anna, Taulier, Nicolas, Chalikian, Tigran V
• Format: Journal Article
• Language: English
• Published: American Chemical Society 22.12.2004
• ISSN: 0002-7863; 1520-5126
• DOI: 10.1021/ja046387d

We report high-resolution differential scanning calorimetric data on the poly(dAdT)poly(dAdT), poly(dA)poly(dT), poly(dIdC)poly(dIdC), poly(dGdC)poly(dGdC), poly(rA)poly(rU), and poly(rI)poly(rC) nucleic acid duplexes. We use these data to evaluate the melting temperatures, T M, enthalpy changes, ΔH M, and heat capacity changes, ΔCP, 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 ΔC P exhibits a positive, nonzero value, which, on average, equals 268 ± 33 J mol-1 K-1. With ΔC P , we have calculated the transition free energies, ΔG, enthalpies, ΔH, and entropies, ΔS, for the duplexes as a function of temperature. Since, ΔG, ΔH, and ΔS 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, AU, 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.