DNA, RNA, and DNA/RNA Oligomer Duplexes: A Comparative Study of Their Stability, Heat, Hydration, and Mg²⁺ Binding Properties

We used a combination of spectroscopic, calorimetric, density, and ultrasonic techniques to determine complete thermodynamic profiles, including hydration effects, for the formation of a set of DNA, RNA, and DNA/ RNA oligomer duplexes, from the mixing of their complementary strands. UV melting curves show that at room temperature all four molecules are in the duplex state while the circular dichroism spectra indicate that the DNA duplex is in the "B" conformation and the RNA and DNA/RNA hybrid duplexes are in the "A" conformation. The favorable formation of these duplexes at 20°C is characterized with exothermic enthalpies and unfavorable entropies, the RNA duplex is the more stable one, resulting from a more favorable heat of 7-17 kcal/mol. The volume and compressibility measurements show that the formation of each duplex is accompanied by an uptake of water molecules and that the overall hydration of a duplex is mainly determined by its conformation; the DNA duplex is 2-fold more hydrated than any of the other three duplexes. We also used density and ultrasonic techniques to determine the changes in the apparent molar volume, ΔΦV, and adiabatic compressibility, ΔΦK_s, for the interaction of Mg²⁺ with each duplex and its component single strands. These ΔΦV and ΔΦK_s values range from 2.2 cm³/mol and 6.0 × 10^-4 cm³/(mol bar) to 10.0 cm³/ mol and 21.9 × 10^-4 cm³/(mol bar), respectively. The magnitude of the lowest values for the interaction of Mg²⁺ with the RNA duplex suggests the formation of Mg²⁺-RNA outer-sphere complexes. However, the magnitude of the higher values for the interaction of Mg²⁺ with the DNA duplex, and two of the single strands, may be consistent with the formation of Mg²⁺-nucleic acid inner-sphere complexes. Furthermore, the resulting ΔΦV/ΔΦK_s ratios of ∼0.75 × 10⁴ (formation of duplexes) and ∼0.48 × 10^-4 (Mg²⁺ binding) suggest the uptake of mostly hydrophobic water and release of mostly electrostricted water, respectively.