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An RNA base-pair edge is a region around a nucleobase presenting groups that can participate in an edge-to-edge contact with another nucleobase. It is a chemical contact surface in RNA base-pair geometry, rather than an edge of a drawn secondary-structure graph. The arrangement of hydrogen bond donors and hydrogen bond acceptors constrains possible partners.

The Leontis–Westhof classification distinguishes the Watson-Crick base-pair edge, Hoogsteen base-pair edge and sugar base-pair edge. The last category includes the ribose $2^{\prime }$-hydroxyl contribution and is also called the shallow-groove edge in the original classification.^[ref] Thus an edge label does not necessarily refer only to atoms in the aromatic ring.

An edge belongs to one partner. A complete pair description identifies the edge used by each nucleobase and the relative orientation of their glycosidic bonds. For example, specifying that one adenine uses its Hoogsteen base-pair edge still leaves the second partner's identity, contacting edge and orientation to be determined. It does not by itself specify a unique noncanonical base pair.

For an original classification exercise, label two partners A and B. The record “A uses Watson–Crick; B uses sugar; orientation trans” contains more geometric information than “A contacts B”. Exchanging the names A and B reverses the written edge order but does not create a second physical contact. In contrast, moving B to a different contact surface changes the proposed structure.

Structural coordinates or solution restraints are needed to establish the contact. A plausible hydrogen bond donor near an appropriate hydrogen bond acceptor is a necessary geometric clue, not proof that a proposed RNA structure is populated under every condition. Edge labels make comparisons precise while retaining the need for experimental evidence.

The Watson-Crick base-pair edge is the nucleobase contact surface used in ordinary canonical base pairing. In RNA, the familiar adenine–uracil and guanine–cytosine contacts use this edge on both partners with cis-oriented glycosidic bonds in the geometric classification.^[ref]

For adenine, this edge includes its N1 ring nitrogen and N6 amino group. These provide a hydrogen bond acceptor and a hydrogen bond donor, respectively, in the ordinary neutral chemical form. The N6 group also borders the Hoogsteen base-pair edge; the classification divides contact regions, not disjoint lists in which every atom must belong to only one edge.^[ref]

A simple canonical A–U example has the uracil N3 hydrogen directed toward adenine N1 and an adenine N6 hydrogen directed toward uracil O4. These are the two conventional hydrogen bonds. In the corresponding G–C geometry, three conventional hydrogen bonds can form. The number of bonds is a property of the chemical pairing arrangement, not the definition of the edge.

The term also does not require the second base to use its own Watson–Crick edge. A Watson–Crick–Hoogsteen contact uses the named edge on one partner and the Hoogsteen base-pair edge on the other. Even a Watson–Crick–Watson–Crick edge combination can have a trans relationship of glycosidic bonds, placing it in a different family from the ordinary cis contact.^[ref]

An original comparison separates the information being recorded. “A contacts U” supplies two identities. “Both use Watson–Crick edges” adds two contact surfaces. “The glycosidic bonds are cis” adds their relative orientation. Only the full description identifies the canonical family; sequence identity alone cannot determine the geometry. Experimental structural coordinates or restraints are needed to decide which arrangement occurs in a particular molecule.

The edge framework consequently covers both canonical and noncanonical base pairs without equating every use of a familiar contact surface with the familiar double-helix geometry. It also makes RNA base-pair isostericity a geometric question rather than a simple count of hydrogen bonds.