Thermodynamic effects of formamide on DNA stability.
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].
Blake
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RD
Department of Biochemistry, Microbiology and Molecular Biology, University of Maine, Orono, ME 04469-5735, USA.
Delcourt
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SG
D001482:Base Composition; D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000187:drug effects*; D004355:Drug Stability; D005559:Formamides / Q000494:pharmacology*; D006358:Hot Temperature; D006860:Hydrogen Bonding; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010957:Plasmids; D011067:Poly dA-dT / Q000737:chemistry; D013816:Thermodynamics
D005559:Formamides; D011067:Poly dA-dT; C031066:formamide; D004247:DNA