Conformational features of 2′‐O‐methyl‐adenosylyl‐adenosine
Authors: Singh Harwant , Herbut Marion H. , Lee Che‐Hung , Sarma Ramaswamy H. 
Published: December 2004

In order to obtain information about the conformational features of a 2′‐O‐methylated polyribonucleotide at the nearest neighbor level, a detailed nuclear magnetic resonance study of AmpA was undertaken. AmpA was isolated from alkali hydrolysates of yeast RNA, and proton spectra were recorded at 100 MHz in the Fourier transform mode in D2O solutions, 0.01 M, pH 5.4 and 1.5 at 25°C. 31P spectra were recorded at 40.48 MHz. Complete, accurate sets of nmr parameters derived for each nucleotidyl unit by simulation iteration methods.

The nmr data were translated into conformational parameters for all the bonds using procedures developed in earlier studies from these laboratories. It is shown that AmpA exists in aqueous solution with a flexible molecular framework, which shows preferences for certain orientations. The ribose rings exist as a 2E ⇄ 3E equilibrium with the —pA ribose showing a bias for the 3E pucker. The C(4′)—C(5′) bonds of both nucleotidyl units show significant preference (75–80%) to exist in gg conformation. The dominant conformer (80%) about C(5′)—O(5′) of the 5′‐nucleotidyl unit is g′g′. Even though an unambiguous determination of the orientation of the 3′‐phosphate group cannot be made, tentative evidence shows that it preferentially occupies g+ domains [O(3′)—P trans to C(3′)—C(2′)] in which the H(3′) —C(3′)—O(3′)—P(3′) dihedral angle is about 31°. There is reasonable evidence that the 2′‐O‐methyl preferentially occupies the domain in which the O(2′)—CH3 bond is trans to C(2′)—C(1′).

Lowering of pH to 1.5, which results in protonation of both the adenine moieties, causes destacking of AmpA. Such destacking is accompanied by small, but real, perturbations in the conformations about most of the bonds in the backbone.

A detailed comparison of the solution conformations of ApA and AmpA clearly shows that 2′‐O‐methylation strongly influences the conformational preference about the C(3′)—O(3′) bond of the 3′‐nucleotidyl unit, in addition to inducing small changes in the overall ribophosphate backbone conformational equilibria. The effect of 2′‐O‐methylation is such that the C(3′)—O(3′) is forced to occupy preferentially the g+ domain rather than the normally preferred g− domain [O(3′)—P trans to C(3′)—C(4′)] in ApA. The data on ApA and AmpA further reveal that the extent of stacking interaction is less in AmpA compared to ApA.

It is suggested that stacked species of AmpA exist as right‐handed stacks where the magnitude of ω and ω′ about O(5′)—P and P—O(3′) is about 290°. The reason for the lesser degree of stacking in AmpA compared to ApA is intramolecular interaction between 2′‐O‐methyl and the flexible O(3′)—P—O(5′) bridge, the interaction causing some perturbation in the magnitudes of ω/ω′, causing destacking. The destacking will lead to an increase in χCN by a few degrees, causing an increase in 2E populations; the latter in turn will shift the 3′ phosphate group from g− to g+ domains. In short, a coupled series of conformational events is envisioned at the onset of destacking, made feasible by the interaction between the 2′‐O‐methyl group and the swivel O(3′)—P—O(5′) bridge.