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 ultrason ic techniques to determine complete thermodynamic profiles, including hydra tion 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 w hile 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" con formation. The favorable formation of these duplexes at 20 degrees C is cha racterized with exothermic enthalpies and unfavorable entropies, the RNA du plex is the more stable one, resulting from a more favorable heat of 7-17 k cal/mol. The volume and compressibility measurements show that the formatio n of each duplex is accompanied by an uptake of water molecules and that th e overall hydration of a duplex is mainly determined by its conformation; t he 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, Delta Phi V, and adiabatic compressibility, Del ta Phi K-S, for the interaction of Mg2+ with each duplex and its component single strands. These Delta Phi V and Delta Phi K-S values range from 2.2 c m(3)/mol and 6.0 x 10(-4) cm(3)/(mol bar) to 10.0 cm(3)/ mol and 21.9 x 10( -4) cm(3)/(mol bar), respectively. The magnitude of the lowest values for t he interaction of Mg2+ with the RNA duplex suggests the formation of Mg2+-R NA 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 com plexes. Furthermore, the resulting Delta Phi V/Delta Phi K-S ratios of simi lar to 0.75 x 10(4) (formation of duplexes) and similar to 0.48 x 10(-4) (M g2+ binding) suggest the uptake of mostly hydrophobic water and release of mostly electrostricted water, respectively.