title: An introduction to recurrent nucleotide interactions in RNA.
abstract: RNA secondary structure diagrams familiar to molecular biologists summarize at a glance the folding of RNA chains to form Watson–Crick paired double helices. However, they can be misleading: First of all, they imply that the nucleotides in loops and linker segments, which can amount to 35% to 50% of a structured RNA, do not significantly interact with other nucleotides. Secondly, they give the impression that RNA molecules are loosely organized in three-dimensional (3D) space. In fact, structured RNAs are compactly folded as a result of numerous long-range, sequence-specific interactions, many of which involve loop or linker nucleotides. Here, we provide an introduction for students and researchers of RNA on the types, prevalence, and sequence variations of inter-nucleotide interactions that structure and stabilize RNA 3D motifs and architectures, using Escherichia coli (E. coli) 16S ribosomal RNA as a concrete example. The picture that emerges is that almost all nucleotides in structured RNA molecules, including those in nominally single-stranded loop or linker regions, form specific interactions that stabilize functional structures or mediate interactions with other molecules. The small number of noninteracting, ‘looped-out’ nucleotides make it possible for the RNA chain to form sharp turns. Base-pairing is the most specific interaction in RNA as it involves edge-to-edge hydrogen bonding (H-bonding) of the bases. Non-Watson–Crick base pairs are a significant fraction (30% or more) of base pairs in structured RNAs.
authors: Blake A
authors: BA
authors: Sweeney
authors: Poorna
authors: P
authors: Roy
authors: Neocles B
authors: NB
authors: Leontis
mesh_terms: D020029:Base Pairing; D004926:Escherichia coli / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D009711:Nucleotides / Q000378:metabolism*; D059370:RNA Folding; D012336:RNA, Ribosomal, 16S / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D009711:Nucleotides; D012336:RNA, Ribosomal, 16S