Influence of the 2β€²-Hydroxyl Group Conformation on the Stability of A-form Helices in RNA

Journal of Molecular Biology 356, 280–287 (2006)

The 2β€²-hydroxyl group plays fundamental roles in both the structure and the function of RNA, and is the major determinant of the conformational and thermodynamic differences between RNA and DNA. Here, we report a conformational analysis of 2β€²-OH groups of the HIV-2 TAR RNA by means of NMR scalar coupling measurements in solution.

Our analysis supports the existence of a network of water molecules spanning the minor groove of an RNA A-form helix, as has been suggested on the basis of a high-resolution X-ray study of an RNA duplex. The 2β€²-OH protons of the lower stem nucleotides of the TAR RNA project either towards the O3β€² or towards the base, where the 2β€²-OH group can favorably participate in H-bonding interactions with a water molecule situated in the nucleotide base plane. We observe that the kex rate of the 2β€²-OH proton with the bulk solvent anti-correlates with the base-pair stability, confirming the involvement of the 2β€²-OH group in a collective network of H-bonds, which requires the presence of canonical helical secondary structure.

The methodology and conformational analysis presented here are broadly applicable and facilitate future studies aimed to correlate the conformation of the 2β€²-OH group with both the structure and the function of RNA and RNA–ligand complexes.