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

Abstract

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, ∆ΦV, and adiabatic compressibility, ∆ΦK S , for the interaction of Mg 2+ with each duplex and its component single strands. These ∆ΦV and ∆ΦK S values range from 2.2 cm 3 /mol and 6.0 × 10 -4 cm 3 /(mol bar) to 10.0 cm 3 / mol and 21.9 × 10 -4 cm 3 /(mol bar), respectively. The magnitude of the lowest values for the interaction of Mg 2+ with the RNA duplex suggests the formation of Mg 2+ -RNA outer-sphere complexes. However, the magnitude of the higher values for the interaction of Mg 2+ with the DNA duplex, and two of the single strands, may be consistent with the formation of Mg 2+ -nucleic acid inner-sphere complexes. Furthermore, the resulting ∆ΦV/∆ΦK S ratios of ∼0.75 × 10 4 (formation of duplexes) and ∼0.48 × 10 -4 (Mg 2+ binding) suggest the uptake of mostly hydrophobic water and release of mostly electrostricted water, respectively.

Efficient Initiation of HIV-1 Reverse Transcriptionin Vitro

“…As expected, the all-RNA duplex was more stable than the all-DNA duplex (66,70,71), whereas the chimeras were intermediate in their thermal stability. The relative stability of chimeric DNA-RNA duplexes is difficult to predict and depends strongly on base composition (65-67, 70, 71).…”

A guide to ions and RNA structure

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The presence of two modes of binding to calf thymus DNA by metal-free bleomycin: A low frequency Raman study

“…40 It is reasonable to suppose that a localized dehydration may signify some loss of water from the structural water spine found in the DNA grooves as this is considered a primary site of dehydration. 40,41 In the Blm/DNA case, this could probably occur via displacement of water in the minor groove by the drug as there are indications from previous NMR studies that the bithiazole moiety of ZnBlm does bind in the minor groove. 3,4,9 Other evidence for minor groove binding of the bithiazole group comes from a previous resonance Raman study of metal-free bleomycin.…”