= Noncanonical base pair
A <noncanonical base pair> joins two <nucleobases> in an arrangement other than the standard Watson–Crick <base pairing> geometry. For <RNA>, the canonical Watson–Crick combinations are <adenine>–<uracil> and <guanine>–<cytosine>. Other combinations and contact geometries can contribute to an organized, functional <RNA secondary structure>; noncanonical does not mean an experimental mistake.
<RNA base-pair geometry> describes more than the two base letters. Which parts of the <nucleobases> contact each other, their relative orientation and their <hydrogen bonds> distinguish arrangements that a letter-only sequence description cannot specify. For a concrete structural example, solution <NMR spectroscopy> studies of GCAA and GAAA <GNRA tetraloops> identified a <guanine>–<adenine> <base pair> between the first and last loop residues, alongside other stabilizing contacts.<Structural features that give rise to the unusual stability of RNA hairpins containing GNRA loops by H. A. Heus and others>[Abstract, loop G–A pairing and solution structures.]{ref}
An original counting example makes the distinction useful. A three-pair stem capped by a GAAA <RNA tetraloop> contains ten <nucleotides>: six in the stem and four in the loop. A contact between the loop's first <guanine> and last <adenine> can add a <noncanonical base pair> without adding any <nucleotides> or turning the four-residue loop into a different-length sequence. Sequence length, stem-pair count and the complete three-dimensional contact inventory answer different questions.
Conventions should be stated. Some <RNA> analyses include the common <guanine>–<uracil> wobble arrangement among their canonical pairs even though it differs from Watson–Crick geometry. The tetraloop survey, for example, explicitly adopts that broader convention.<Thermodynamic characterization of naturally occurring RNA tetraloops by Justin P. Sheehy and others>[Materials and Methods, Compiling and searching a database for RNA tetraloops.]{ref} Comparing reported counts therefore requires checking what each author counted as canonical.
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