Nucleic Acids Research, Vol 24, Issue 11 2095-2103, Copyright © 1996 by Oxford University Press
RD Blake and SG Delcourt
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].
ARTICLES
Thermodynamic effects of formamide on DNA stability
Department of Biochemistry, Microbiology and Molecular Biology, University of Maine, Orono, ME 04469-5735, USA.
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