Multi-resolution methods, taken from signal processing, and a tree formalism, re-define and expand the RNA motif concept, unifying what previously appeared to be disparate groups of structures. The simplest, smallest and most frequent RNA motif is known as the tetraloop. Tetraloops are terminal loops, with characteristic four-residue sequences first observed in early phylogenetic comparisons of RNAs. We find RNA tetraloops at high frequencies, in new contexts, with unexpected lengths, and in novel topologies. The results, with broad implications for RNA structure in general, show that even at this most elementary level of organization, RNA tolerates astounding variation in conformation, length, sequence and context. However the variation is not random; it is well-described by four distinct modes, which are 3-2 switches (backbone topology variations), insertions, deletions and strand clips. The four types of polymorphism arise from common enabling factors, which are the high RNA backbone length per residue and numerous degrees of freedom of RNA backbone conformation.
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