Thermal stability of DNA

T-ij and Delta H-ij for stacking of pair i upon j in DNA have been obtained over the range 0.034-0.114 M Na+ from high-resolution melting curves of well-behaved synthetic tandemly repeating inserts in recombinant pN/MCS plasmids, Results are consistent with neighbor-pair thermodynamic additivity, where the stability constant, s(ij) for different domains of length N depend quantitatively on the product of stability constants for each individual pair in domains, s(ij)(N). Unit transition enthalpies with average errors less than +/-5%, were determined by analysis of two-state equilibria associated with the melting of internal domains and verified from variations of T-ij with [Na+]. Enthalpies increase with T-ij in close agreement with the empirical function: Delta H-ij = 52.78 . T-ij - 9489, and in parallel with a smaller increase in Delta S-ij. Delta H-ij and Delta S-ij are in good agreement with the results of an extensive compilation of published Delta H-cal and Delta S-cal for synthetic and natural DNAs. Neighbor-pair additivity was also observed for (dA . dT)-tracts at melting temperatures; no evidence could be detected of the familiar and unusual structural features that characterize tracts at lower temperatures. The energetic effects of loops were determined from the melting behavior of repeating inserts installed between (G+C)-rich barrier domains in the pN/MCS plasmids, A unique set of values for the cooperativity, loop exponent and stiffness parameters were found applicable to internal domains of all sizes and sequences. Statistical mechanical curves calculated with values of T-ij([Na+]), Delta H-ij and these loop parameters are in good agreement with observation.