= RNA base-pair geometry
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<RNA base-pair geometry> specifies how two <nucleobases> contact and orient relative to one another, beyond their letter identities. It distinguishes different <base pairing> arrangements, including <noncanonical base pairs>, that can organize <RNA secondary structure> and three-dimensional folding.
A primary classification uses the contacting <RNA base-pair edge> of each partner: Watson–Crick, Hoogsteen or sugar edge. It also distinguishes cis and trans orientations of the two <glycosidic bonds> relative to the interbase <hydrogen bonds>. These are pairwise geometric descriptors; they are not simply labels for parallel versus <antiparallel nucleic acid strands>.<Geometric nomenclature and classification of RNA base pairs by N. B. Leontis and E. Westhof>[Abstract, edges and relative glycosidic-bond orientation.]{ref}
An original counting explanation clarifies the twelve basic families. Ignoring exchange of the two partner labels, three edge types allow three same-edge combinations and three mixed-edge combinations: six possibilities. Combining each with cis or trans orientation gives $6\times2=12$. This counts contact-geometry families, not twelve possible <nucleotide sequences> or twelve equally common structures.
For example, knowing only that a contact is <guanine>–<adenine> does not specify which <RNA base-pair edges> participate. Replacing that pair by another two-base combination also does not guarantee the new contact fits the same surrounding backbone. Geometry can therefore explain why one sequence substitution preserves a structural motif while another disrupts it. The classification was designed to support structural comparison and recognition of geometrically similar pairs.<Geometric nomenclature and classification of RNA base pairs by N. B. Leontis and E. Westhof>[Abstract, structural annotation and isosteric relationships.]{ref}
Experimental coordinates or solution restraints are needed to assign an actual contact. A proposed <hydrogen bond> requires a compatible arrangement of donor and acceptor groups, not merely a favorable pair of letters. A secondary-structure arc records a relationship between residues; a full <RNA base-pair geometry> adds spatial information that the arc alone cannot encode.
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