Physical Rationale Behind the Nonlinear Enthalpy−Entropy Compensation in DNA Duplex Stability

• Published in: The journal of physical chemistry. B Vol. 113; no. 14; pp. 4698 - 4707
• Main Authors: Starikov, E. B., Nordén, B.
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 09-04-2009
• Subjects: B: Statistical Mechanics, Thermodynamics, Medium Effects; bound water; Chemistry, Physical; conformational maps; DNA - chemistry; heat-capacity; Nucleic Acid Conformation; peptide nucleic-acid; phase-transitions; protein; reca; sequence; statistical-mechanics; Temperature; temperature-dependence; Thermodynamics
• ISSN: 1520-6106; 1520-5207; 1520-5207
• DOI: 10.1021/jp8089424

The physical-chemical sense of nonlinear entropy−enthalpy compensation based upon the standard thermodynamical parameters of high-temperature melting for doublet units in DNA duplexes has been considered. We are able to show that there are three, with no other constraints equally plausible, principal levels of DNA melting/hybridization description. First, DNA structure assembly/disassembly can be seen from the viewpoint of the conventional equilibrium thermodynamics without taking special care of the heat capacity ΔC p value (by simply setting it equal to zero). Second, it is possible to assume that the ΔCp is finite, but independent of temperature. At this approximation level the high-temperature DNA melting cannot be described, but only some special transition between metastable states of DNA duplexes in water solutions in the vicinity of ice melting point. Third, both the latter transition and the high-temperature DNA melting can be reproduced by one and the same approach, if the ΔC p is assumed to be temperature dependent. These three approximation levels are equally justified from the nonlinear entropy−enthalpy compensation standpoint and by a generalized theory of temperature effects on themodynamical stability as is outlined here. Applicability of each of the approximation levels involved is discussed.