Observation of H-Bond Mediated 3hJH2H3 Coupling Constants Across Watson-Crick AU Base Pairs in RNA

Published

October 1, 2002

Author(s)

B. Luy, U Richter, E S. DeJong, O W. Sorensen, John Marino

Abstract

^3hJ_H2H3 trans-hydrogen bond scalar couplings have been observed for the first time in Watson-Crick AU base pairs in uniformly ¹⁵N-labeled RNA oligonucleotides using a new ^2hJ_NN-HNN-E.COSY experiment. The experiment, utilizes adenosine H2 (AH2) for original polarization and detection, while employing ^2hJ_NN couplings for coherence transfer across the hydrogen bonds (H-bonds). The H3 protons of uracil bases are unperturbed throughout the experiment so that these protons appear as passive spins in E.COSY patterns. ^3hJ^H2H3 coupling constants can therefore be accurately measured in the acquisition dimension from the displacement of the E.COSY multiplet components, which are separated by the relatively large 1J_H3N3 coupling constants in the indirect dimension of the two-dimensional experiment. The ^3hJ_H2H3 scalar coupling constants determined for AU base pairs in the two RNA hairpins examined here have been found to be positive and range in magnitude up to 1.8 Hz. Using a molecular fragment representation of an AU base pair, density functional theory/finite field perturbation theory (DFT/FPT) methods have been applied to attempt to predict the relative contributions of H-bond length and angular geometry to the magnitude of ^3hJ_H2H3 coupling constants. Although the DFT/FPT simulations did not reproduce the full range of magnitude observed experimentally for the ^3hJ_H2H3 couplings, the calculations do predict the correct sign and general trends in variation in size of these couplings. The simulations suggest that the magnitude of the coupling constants depends largely on H-bond length, but can also vary with differences in pair geometry. The dependency of the ^3hJ_H2H3 coupling constant on H-bond strength and geometry makes it a new probe for defining pairs in NMR studies of nucleic acids.

Citation

Journal of Biomolecular Nmr

Volume

24

Issue

No. 2

Pub Type

Journals

Keywords

^3hJ_HH Coupling Constant, E. COSY, hydrogen bond, RNA

Citation

Luy, B. , Richter, U. , DeJong, E. , Sorensen, O. and Marino, J. (2002), Observation of H-Bond Mediated ^3hJ_H2H3 Coupling Constants Across Watson-Crick AU Base Pairs in RNA, Journal of Biomolecular Nmr (Accessed October 10, 2025)