RNA Structure: Pseudoknots


An RNA pseudoknot results from Watson–Crick base pairing of a single‐stranded segment, located between two regions, paired to each other, with a sequence that is not located between these paired regions. This leads to a structure with at least two helical stems and two loops crossing the grooves of the helices. Pseudoknots are further stabilised by coaxial stacking between stems and the formation of triple ribonucleic acid (RNA) interactions between stems and loops. RNA pseudoknots adopt different folding topologies and are an essential part of various functional RNA molecules, including ribosomal RNAs, ribozymes and riboswitches. In this review, the thermodynamics and main structural features of pseudoknots, important for their function, are discussed: amongst others, viral tRNA‐like structures, ribosomal frameshifter pseudoknots and pseudoknots formed by S‐adenosylmethionine and pre‐queuosine riboswitches upon binding of their respective ligands.

Key Concepts:

  • The simplest RNA pseudoknot is formed by base‐pairing of nucleotides within a hairpin loop to a complementary sequence outside the hairpin (H‐pseudoknot).

  • Classical H‐pseudoknots consist of two coaxially stacked helical stems and two loops that cross one deep groove of one helix and the shallow groove of the other helical stem.

  • Pseudoknots are usually stabilised by coaxial stacking between stems and triple base pairs formed between the bases of the stems and loops.

  • Many complex pseudoknots may be interpreted as classical pseudoknots containing additional structural elements inserted in the pseudoknot loops.

  • Pseudoknots are folded in various types of RNA molecules and have diverse functions.

  • Limited information is available on thermodynamic stability of pseudoknots.

  • Computer‐assisted prediction of pseudoknots is partially hampered by a lack of knowledge about the thermodynamics of pseudoknot folding.

Keywords: RNA folding; RNA secondary structure; RNA tertiary structure; ribozyme; ribosome; reprogramming; frameshifting

Figure 1.

Formation of the H‐pseudoknot from two alternative hairpins. The equilibria in the shown model oligonucleotide were studied by UV‐melting and NMR spectroscopy (Puglisi et al., ).

Figure 2.

Three different topologies of two stems stacked coaxially in the H‐pseudoknots. In classical pseudoknot (with no loop L2), loop L3 is frequently named L2.

Figure 3.

Examples of triple helices (dotted lines) in H‐pseudoknots with different functions. (a) The pseudoknot of the tRNA‐like structure from TYMV (Kolk et al., ); (b) Frameshifting pseudoknot from BWYV (Su et al., ; Nixon et al., ); (c) Modified SRV‐1 frameshifting pseudoknot (Michiels et al., ; Olsthoorn et al., ); (d) the Kluyveromyces lactis telomerase pseudoknot (Shefer et al., ).

Figure 4.

Examples of complex pseudoknot topologies. (a) A ‘nonclassical’ stacking topology in the pseudoknot from influenza A virus (Gultyaev et al., ); (b) additional hairpin inserted in loop L2 of the HIV‐1 group O frameshifting pseudoknot (Baril et al., ); (c) additional hairpin insertion in L1 of the pseudoknot from PYVV (Livieratos et al., ); (d) formation of a pseudoknot by the pairing of the loop in branched structure with a downstream region in yellow fever virus (YFV) (Olsthoorn and Bol, ).

Figure 5.

Pseudoknot formation in the riboswitches, induced by a ligand binding. (a) SAM‐II riboswitch from the metX gene in the Sargasso Sea metagenome (Gilbert et al., ); (b) Bacillus subtilisqueC PreQ1 riboswitch (Klein et al., ). Ligands are shown in red, triple interactions are shown by dotted lines. Non‐Watson–Crick edge‐to‐edge base pairs are depicted by symbols according to their nomenclature (Leontis and Westhof, ).



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Further Reading

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Taufer M, Licon A, Araiza R et al. (2009) PseudoBase++: an extension of PseudoBase for easy searching, formatting and visualization of pseudoknots. Nucleic Acids Research 37: D127–D135.

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Gultyaev, Alexander P, Olsthoorn, René CL, Pleij, Cornelis WA, and Westhof, Eric(Sep 2012) RNA Structure: Pseudoknots. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0003134.pub2]