Sugar base-pair edge

The sugar base-pair edge is the side of a nucleobase adjoining its ribose attachment region, including the ribose $2^{\prime }$-hydroxyl group when it participates in the contact. It is one of the three RNA base-pair edges used to classify RNA base-pair geometry. The original nomenclature also calls it the shallow-groove edge.^[ref]

This definition deliberately extends beyond the base ring. In the usual anti orientation about the glycosidic bond, the ribose $2^{\prime }$-hydroxyl can act as a hydrogen bond donor or hydrogen bond acceptor in the pairing interaction. Some sugar-edge contacts therefore connect a base to its partner's ribose rather than consisting solely of direct base-to-base hydrogen bonds.^[ref]

For an original annotation example, suppose residue 1 contributes its $2^{\prime }$-hydroxyl to an inter-residue hydrogen bond. Recording only the two aromatic base rings would omit that contact. A full record must identify the ribose atom, its partner and the geometry. Calling the interaction sugar-edge does not mean that an additional sugar molecule has joined the RNA; the group belongs to an existing nucleotide.

A complete pair description still needs the other partner's edge and the cis/trans relationship of the two glycosidic bonds. Sugar–sugar and Watson–Crick–sugar contacts are different families. The words “sugar edge” alone do not specify a unique pair of bases or a unique three-dimensional arrangement.

There is also an experimental limitation. The primary structural survey did not infer the $2^{\prime }$-hydroxyl hydrogen's exact position from the available X-ray crystallography coordinates. It represented the group as a unit and used compatible heavy-atom geometry to discuss possible hydrogen bonds. A close oxygen contact is evidence to interpret with donor/acceptor chemistry, not direct observation of the hydrogen's orientation.^[ref]

This distinction is useful when comparing RNA with a modified backbone: removing or replacing a ribose group can change a contact opportunity without changing the attached nucleobase's letter. Whether the whole fold survives that alteration remains a structural and experimental question.