Thermodynamic effects of formamide on DNA stability

Abstract

Formamide lowers melting temperatures (T(m)) of DNAs linearly by 2.4-2.9°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. dT(m)/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 Δ̄H̄(m) exhibits a biphasic dependence on formamide concentration. The initial drop of -0.8 kcal/mol bp at low formamide concentrations is attributable to a δΔ̄H̄(m) 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.