MELTSIM 1.0 is available at: //www.uml.edu/Dept/Chem/UMLBIC/Apps/MEL TSIM/MELTSIM-1.0-Win/meltsim. zip. Melting curve plots in this paper were made with GNUPLOT 3.5, available at: http://www.cs.dartmouth.edu/gnuplot_inf o.html Contact : blake@maine.maine.edu;
Tij and Delta Hij 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, sij , for different domains of length N depend quantitatively on the product of stability constants for each individual pair in domains, sijN . 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 Tij with [Na+]. Enthalpies increase with Tij , in close agreement with the empirical function: Delta Hij = 52.78@ Tij - 9489, and in parallel with a smaller increase in Delta Sij . Delta Hij and Delta Sij are in good agreement with the results of an extensive compilation of published Delta Hcal and Delta Scal 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/MCSplasmids. 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 Tij([Na+]) , Delta Hij and these loop parameters are in good agreement with observation.
Formamide lowers melting temperatures (Tm) of DNAs linearly by 2.4-2.9 degrees C/mole of formamide (C(F)) depending on the (G+C) composition, helix conformation and state of hydration. The inherent cooperativity of melting is unaffected by the denaturant. dTm/dC(F)for 11 plasmid domains of 0.23 < (G+C)<0.71 generally fit to a linear dependence on (G+C)-content, which, however, is consistent with a (G+C)-independent alteration in the apparent equilibrium constant for thermally induced helix <--> coil transitions. Results indicate that formamide has a destabilizing effect on the helical state, and that sequence-dependent variations in hydration patterns are primarily responsible for small variations in sensitivity to the denaturant. The average unit transition enthalpy delta H(m)[see text for complete expression], exhibits a biphasic dependence on formamide concentration. The initial drop of -0.8 kcal/mol bp at low formamide concentrations is attributable to a delta delta H(m)[see text for complete expression], for exchange of solvent in the vicinity of the helix: displacement by formamide of weakly bound hydrate or counterion. The phenomenological effects are equivalent to lowering the bulk counterion concentration. Poly(dA.dT) exhibits a much lower sensitivity to formamide, due to the specific pattern of tightly bound, immobilized water bridges that buttress the helix from within the narrow minor groove. Tracts of three (A.T)-pairs behave normally, but tracts of six exhibit the same level of reduced sensitivity as the polymer, suggesting a conformational shift as tracts are elongated beyond some critical length [McCarthy J.G. and Rich,A. (1991) Nucleic Acids Res. 19, 3421-3429].
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