Thermodynamic Cycle Between DNA and RNA Constituents for Conformation of the Sugar Ring from Nuclear Magnetic Resonance Study

Abstract

The effect of a structural change of ribose to deoxyribose, by replacement of 2′-OH by 2′-H, on the conformational equilibrium of the sugar ring is described in terms of one thermodynamic cycle. The method is based on the observation that conformational correlations of the sugar ring—;side chain ensemble in DNA and RNA components show one general pattern, reflecting an intrinsic physical property of this ensemble. The pattern determines a choice of model systems to study. The systems consist of pairs of DNA and RNA components, nucleosides and nucleotides in aqueous solution, where all conformational factors are fully controlled.

This approach allowed us to describe the thermodynamic cycle and measure its fundamental parameters, equilibrium constants and free energy differences, ΔΔG, from a nuclear magnetic resonance study. The ΔΔG values as determined for pairs of ribo- and deoxyribonucleosides in classes of syn-constrained and anti-preferred models, are comparable and lie in a narrow range, ΔΔG = 1.7 ± 0.1 [kJ/mol]. For pairs of ribo- and deoxyribo- nucleotides, the ΔΔG values also lie in narrow ranges, ΔΔG = 1.7 ± 0.1 [kJ/mol] for 5′-phosphate nucleotides and ΔΔG = 1.9 ± 0.1 [kJ/mol] for 3′-phosphate nucleotides, i.e. similar to those observed for nucleosides.

The measured quantity, ΔΔG, is generally observed in a relatively narrow range, ΔΔG = 1.75 ±0.15 [kJ/mol], irrespective of the class of the model system. This quantity represents a “pure” constant contribution, per one sugar moiety, as a “driving force” for the N—> S shift in the sugar ring conformational equilibrium, when one compares RNA and DNA. This important thermodynamic quantity, ΔΔG, has not hitherto been determined for nucleic acids. Ultimately the AAG quantity is revealed in the tendency to adopt S(C2′endo) sugar puckering domain by the majority of DNA structures, whereas RNA generally adopt an N(C3′endo) puckering domain. A possible biological significance of the ΔΔG quantity may include evolutionary aspects of nucleic acids.