RNA Structural Motifs

Abstract

Chemically, ribonucleic acid (RNA) is a close cousin of deoxyribonucleic acid (DNA). RNA is, however, involved in a wide range of cellular activities (e.g. translating genetic information, serving as a structural scaffold, catalysing biological reactions) that often require the molecule to fold into a specific structure in order to perform its targeted function. Structurally and functionally it is therefore more closely related to proteins than to DNA. An RNA structural motif is defined as a collection of residues that fold into a stable three‐dimensional (3D) structure and which can be found in naturally occurring RNAs in unexpected abundance. Owing to the fact that stable 3D structures are associated with RNA structural motifs, these motifs often served as nucleation sites for RNA folding.

Key Concepts:

  • RNA motifs can help stabilise a global RNA structure, as well as guide the RNA folding process.

  • Hairpins are essential in constituting RNA tertiary architecture and in forming binding sites for other molecules.

  • Owing to variation of the lengths of loops and stems, as well as the types of interactions between them, pseudoknots represent a structurally diverse group.

  • Triloops and tetraloops with specific sequences are stable and frequently observed hairpin loops.

  • Self‐folding RNA structures, including the adenosine platform, ribose zipper, bulge–helix–bulge motif and G‐bulge motif, can provide the nucleation sites for RNA folding.

Keywords: helix and loop; hairpin; junction; kissing loop; pseudoknot; RNA folding; RNA self‐folding structure

Figure 1.

RNA molecule in an A‐form helix structure. The bases are shown in grey and the sugar–phosphate backbones in yellow. The minor and major grooves are indicated by arrows. Figure generated using the UCSF Chimera package (Pettersen et al., ).

Figure 2.

Triloop structure. Figure generated using the UCSF Chimera package (Pettersen et al., ) and structure 1JJ2 from Protein Data Bank (Berman et al., ).

Figure 3.

Three tetraloop hairpins. (a) UUCG tetraloop; (b) GAGA tetraloop; (c) CUUG on the right. Figure generated using the UCSF Chimera package (Pettersen et al., ) and structures 1BGZ, 430D and 1RNG from Protein Data Bank (Berman et al., ).

Figure 4.

An example of an RNA pseudoknot. The hairpin stem is shown in grey; the hairpin loop is indicated by a curved arrow. The additional stem in the pseudoknot is shown in yellow. The two loops that connect the two stems are shown in cyan. Figure generated using the UCSF Chimera package (Pettersen et al., ) and structure 1HVU from Protein Data Bank (Berman et al., ).

Figure 5.

Kissing loop structure. Two hairpins forming the kissing loop are coloured in blue and yellow, respectively. Figures generated using the UCSF Chimera package (Pettersen et al., ) and structures 1KIS (left, showing a 6 bp kissing loop), 1JJ2 (right, showing two red‐coloured unpaired bases in the kissing loop) from Protein Data Bank (Berman et al., ).

Figure 6.

Three‐way junction and four‐way junction structures. Figure generated using the UCSF Chimera package (Pettersen et al., ) and structure 1JJ2 from Protein Data Bank (Berman et al., ).

Figure 7.

The structure of an adenosine platform. The two consecutive A bases (purple) that constitute the platform are almost planar. This structural motif brings two helices (cyan and grey) and hairpin (yellow) into close proximity. Figure generated using the UCSF Chimera package (Pettersen et al., ) and structure 1GID from Protein Data Bank (Berman et al., ).

Figure 8.

The structure of a ribose zipper. This motif allows two different RNA duplexes to come into close proximity. Figure generated using the UCSF Chimera package (Pettersen et al., ) and structure 1GID from Protein Data Bank (Berman et al., ).

Figure 9.

The sequence and structure of a bulge–helix–bulge motif. The two bulges are on two opposite strands (purple). The central helix is shown in yellow. Figure generated using the UCSF Chimera package (Pettersen et al., ) and structure 2A9L from Protein Data Bank (Berman et al., ).

Figure 10.

The structure of a G‐bulge motif. The nucleotide guanine involved in the G‐bulge motif is shown in purple. The three hydrogen bonds formed between the guanine and the helix are shown as dotted lines. Figure generated using the UCSF Chimera package (Pettersen et al., ) and structure 430D from Protein Data Bank (Berman et al., ).

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Zhang, Ming, Perelson, Alan S, and Tung, Chang‐Shung(Aug 2011) RNA Structural Motifs. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0003132.pub2]