Contribution of Loops and Nicks to the Formation of DNA Dumbbells: Melting Behavior and Ligand Binding

We have evaluated the thermodynamic contribution of thymine loops and nicks to the overall stability of double-helical DNA by investigating (1) the melting behavior of two unligated DNA dumbbells and their corresponding core duplexes and (2) the association of netropsin to the central core of four A-T base pairs of these molecules. Temperature-dependent UV absorption and differential scanning calorimetry techniques have been used to characterize the helix-coil transitions of all four deoxyoligonucleotide duplexes. In 10 mM NaP_i buffer at pH 7.0, all transitions were monophasic. The dumbbells melt with transition temperatures, T_m, independent of strand concentration, while each duplex melts with transition temperature dependence on strand concentration, characteristic of mono-and bimolecular processes, respectively. The T_m's for the dumbbells correspond to those of single hairpins containing only four base pairs in the stem. We obtain dT_m/d log [Na⁺] values of 10.9-12.5 °C for these molecules, which correspond to similar counterion releases and suggest helical structures with similar charge densities and helical strandedness. Standard thermodynamics profiles at 5 °C reveal that the favorable free energy of forming these ordered structures results from the partial compensation of favorable enthalpies with unfavorable entropies. The stabilization of the dumbbells relative to the core duplexes is enthalpic, due to extra stacking of the nearest loop thymines on the G-C base pairs at both ends of the stem. The association of netropsin was used to thermodynamically probe the integrity of the base-pair stacking at the nick point in the center of the dumbbell molecules, GAT^TAC/GTAATC and CAT^TAG/CTAATG, by direct comparison with the similar sequences of the core duplexes without the nicks, GATTAC/GTAATC and CATTAG/CTAATG. In 10 mM NaP_i buffer at pH 7.0, netropsin binds to the central core of A·T base pairs of these four sequences with similar binding affinities of ~10⁸ and similar thermodynamic profiles: ΔG°_b = −10.8 kcal·mol⁻¹, ΔH°_b = −10.6 kcal·mol⁻¹, and TΔS°_b = +0.2 kcal·mol⁻¹, with binding enthalpies independent of salt concentration. Therefore, all four sequences constitute similar binding sites for netropsin. However, we obtained d ln K_b/d ln [Na⁺] values of −1.0 for the dumbbells and −1.1 for the duplexes, consistent with the lower charge density of these helical structures. The difference of 0.1 is attributed to the absence of a phosphate group at the nick point. In the dumbbells, the presence of the loops creates additional sites for netropsin, formed by two G-C pairs at each end of duplex and the constrained loop groups (forming additional stacked base pairs in a double helical geometry), with binding affinities of ~10⁵ and ΔH°_b of −5.1 kcal·mol⁻¹. Both parameters are dependent on salt concentration. Our combined results show that the presence of a nick in the center of the dumbbells is not affecting the overall stacking of the T^T/AA base pair at the center of the dumbbells but interrupts the cooperative melting of the whole molecule.