Base Pairing in RNA: Unusual Patterns


Ribonucleic acids (RNAs) consist of linear arrays of bases, some of which have the hydrogen‐bonding capacity to interact with others to form base pairs. In addition to the standard Watson–Crick base pairings, RNAs have unusual base pairings that give rise to the many tertiary structures that are now known to be important for a variety of biological functions.

Keywords: wobble; recognition of unusual base pairs; chemical modification of unusual base pairs; alternative ‘cloverleaf’ structures; unusual termination signals; alternative splicing

Figure 1.

The Watson–Crick G•C and A•U base pairs in RNA. The unusual base pairs in RNA include the reverse Watson–Crick G•C and reverse Watson–Crick A•U base pairs; the G•U wobble base pair; the U•A Hoogsteen and reverse Hoogsteen base pairs; and base triples such as [U12•A23]•A9 and [C13•G22]•G46 that are found in the crystal structure of yeast tRNAPhe (Kim et al., ; Robertus et al., ).

Figure 2.

The cloverleaf (a) and L‐shaped (b) structure of yeast tRNAPhe in the unmodified sequence. Conserved and semiconserved nucleotides are indicated by squares and circles, respectively. Watson–Crick base pairings are indicated by black dots; unusual base pairs are connected by thin lines in the cloverleaf structure, and lines connecting nucleotides in the L‐shaped structure represent the sugar‐phosphate backbone. Numbers next to selected nucleotides are the positions in the sequence framework of the tRNA. The anticodon of the tRNA is GAA at positions 34–36.

Figure 3.

The alternative ‘cloverleaf’ structure of bovine and human mt tRNASer/AGY, missing the normal D stem–loop. The Watson–Crick base pairings are indicated by black dots.



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Hou, Ya‐Ming(Oct 2002) Base Pairing in RNA: Unusual Patterns. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1038/npg.els.0003131]