Differential Scanning Calorimetry to measure the binding of ions, water and protons in the unfolding of DNA molecules

The overall stability of DNA molecules globally depends on base-pair stacking, base-pairing, polyelectrolyte effect and hydration contributions. In order to improve our understanding of the role of ions, water and protons in the stability and melting behavior of DNA structures, we report an experimental approach to determine the differential binding of ions (Δnion), water (ΔnW) and protons (ΔnH+) in the helix-coil transition of DNA molecules. A combination of differential scanning calorimetry (DSC) and temperature-dependent UV spectroscopic techniques were used to investigate the unfolding of a variety of DNA molecules: salmon testes DNA (ST- DNA), one dodecamer, one undecamer and one decamer duplexes, nine hairpin loops as a function of the GC content of their stem, and two triplexes. We determined complete thermodynamic profiles, including all three linking numbers, for the unfolding of each molecule. The favorable folding of a DNA helix results from the typical compensation of favorable enthalpy, unfavorable entropy contributions, and negligible heat capacity effects. DSC thermograms and UV melts as a function of salt, osmolyte and proton concentrations yielded releases of ions, water and protons (for the triplex with C+GC base triplets).µ