Thermodynamics of DNA hairpins: Contribution of loop size to hairpin stability and ethidium binding

Dionisios Rentzeperis, Karen Alessi, Luis A. Marky

Research output: Contribution to journalArticlepeer-review

76 Scopus citations


A combination of calorimetric and spectroscopic techniques was used to evaluate the thermodynamic behavior of a set of DNA hairpins with the sequence d(GCGCTnGCGC), where n = 3, 5 and 7, and the interaction of each hairpin with ethidium. All three hairpins melt in two-state monomolecular transitions, with tm's ranging from 79.1°C (T3) to 57.5°C (T7), and transition enthalpies of ∼38.5 kcal mol-1. Standard thermodynamic profiles at 20°C reveal that the lower stability of the T5 and T7 hairpins corresponds to a Δ° term of +0.5 kcal mol-1 perthymine residue, due to the entropic ordering of the thymine loops and uptake of counterions. Deconvolution of the ethldium-hairpin calorimetric titration curves indicate two sets of binding sites that correspond to one ligand in the stem with binding affinity, Kb, of ∼1.8×106 M-1, and two ligands in the loops with Kb, of ∼4.3×104 M-1. However, the binding enthalpy, ΔHb, ranges from -8.6 (T3) to -11.6 kcal mol-1 (T7) for the stem site, and -6.6 (T3) to -12.7 kcal mol-1 (T7) for the loop site. Relative to the T3 hairpin, we obtained an overall thermodynamic contribution (per dT residue) of ΔΔHb = Δ(TΔSb)= -0.75 kcal mol-1 for the stem sites and ΔΔHb = Δ(TΔSb) = -1.5 kcal mol-1 for the loop sites. Therefore, the induced structural perturbations of ethidium binding results in a differential compensation of favorable stacking interactions with the unfavorable ordering of the ligands.

Original languageEnglish (US)
Pages (from-to)2683-2689
Number of pages7
JournalNucleic acids research
Issue number11
StatePublished - Jun 11 1993
Externally publishedYes

ASJC Scopus subject areas

  • Genetics


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