Differential Binding of Ions and Water in the Unfolding of DNA Hairpins

Abstract

Stem-loop motifs are appropriate models for the thermodynamic description of the stability and melting behavior of native DNA. In order to improve our understanding of the role of both ions and water in the stability and melting behavior of DNA secondary structures, we used a combination of UV and CD spectroscopies, and DSC calorimetric techniques to determine standard thermodynamic profiles, the differential binding of ions (Δnion) and water (ΔnW) for the unfolding of 22 hairpin loops with different stem sequence and loops of 5 thymines. The CD spectra indicated that all hairpins adopted the B-conformation at low temperatures. The UV and DSC data showed all hairpins unfold in two-state transitions, and accompanied by water releases of 12-24 mol H2O/mol hairpin and ion releases of 0.38-0.76 mol Na+/mol hairpin. Therefore, the folding of each hairpin is accompanied by a favorable free energy term, resulting from the compensation of a favorable enthalpy and unfavorableentropy contributions, due to formation of base-pair stacks and uptake of both water and counterions, respectively. Complete thermodynamic parameters, including ΔnW and Δnion, for all 10 W-C nearest-neighbor contributions were determined by solving the matrix of the thermodynamic data. This allows us to predict the overall thermodynamics, hydration and ion binding properties for the unfolding of a hairpin loop from knowledge of its stem sequence. Supported by Grant MCB-0616005 from the National Science Foundation.