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]
The non-Watson-Crick base pairs and their associated isostericity matrices by Neocles B. Leontis and others. Introduction, printed p. 3497; Figure 1 and Table 2
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]
The non-Watson-Crick base pairs and their associated isostericity matrices by Neocles B. Leontis and others. Figure 1, identification of edges; Figure 2, canonical contacts
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.
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