THERMAL-STABILITY OF DNA

T-ij and Delta H-ij for stacking of pair i upon j in DNA have been obt ained over the range 0.034-0.114 M Na+ from high-resolution melting cu rves of well-behaved synthetic tandemly repeating inserts in recombina nt pN/MCS plasmids, Results are consistent with neighbor-pair thermody namic additivity, where the stability constant, s(ij) for different do mains of length N depend quantitatively on the product of stability co nstants for each individual pair in domains, s(ij)(N). Unit transition enthalpies with average errors less than +/-5%, were determined by an alysis of two-state equilibria associated with the melting of internal domains and verified from variations of T-ij with [Na+]. Enthalpies i ncrease with T-ij in close agreement with the empirical function: Delt a 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 th e results of an extensive compilation of published Delta H-cal and Del ta S-cal for synthetic and natural DNAs. Neighbor-pair additivity was also observed for (dA . dT)-tracts at melting temperatures; no evidenc e could be detected of the familiar and unusual structural features th at 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 stiffne ss parameters were found applicable to internal domains of all sizes a nd sequences. Statistical mechanical curves calculated with values of T-ij([Na+]), Delta H-ij and these loop parameters are in good agreemen t with observation.