A more unified picture for the thermodynamics of nucleic acid duplex melting: A characterization by calorimetric and volumetric techniques

We use a combination of calorimetric and volumetric techniques to detect an d to characterize the thermodynamic changes that accompany helix-to coil tr ansitions for five polymeric nucleic acid duplexes. Our calorimetric measur ements reveal that melting of the duplexes is accompanied by positive chang es in heat capacity (Delta C-P) of similar magnitude, with an average Delta C-P value of 64.6 +/- 21.4 cal deg(-1) mol(-1). When this heat capacity va lue is used to compare significantly different transition enthalpies (Delta H-o) at a common reference temperature, T-ref, we find Delta H-Trel for du plex melting to be far less dependent on duplex type, base composition, or base sequence than previously believed on the basis of the conventional ass umption of a near-zero value for Delta C-P. Similarly, our densimetric and acoustic measurements reveal that, at a given temperature, all the AT- and AU-containing duplexes studied here melt with nearly the same volume and co mpressibility changes. In the aggregate, our results, in conjunction with l iterature data, suggest a more unified picture for the thermodynamics of nu cleic acid duplex melting. Specifically, when compared at a common temperat ure, the apparent large differences present in the literature for the trans ition enthalpies of different duplexes become much more compressed, and the melting of all-AT- and all-AU-containing duplexes exhibits similar volume and compressibility changes despite differences in sequence and conformatio n. Thus, insofar as thermodynamic properties are concerned, when comparing duplexes, the temperature under consideration is as important as, if not mo re important than, the duplex type, the base composition, or the base seque nce. This general behavior has significant implications for our basic under standing of the forces that stabilize nucleic acid duplexes. This behavior also is of practical significance in connection with the use of thermodynam ic databases for designing probes and for assessing the affinity and specif icity associated with hybridization-based protocols used in a wide range of sequencing, diagnostic, and therapeutic applications.