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The structure and folding of kink turns in RNA

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Abstract The kink turn (k‐turn) is a widespread structural motif that introduces a tight kink into the axis of double‐stranded RNA, with an included angle ∼60°. A standard k‐turn comprises a three‐nucleotide bulge followed on the 3′ side by a G•A pair, an A•G pair, and usually further non‐Watson–Crick pairs. The kinked conformation may be stabilized by three processes. These are the addition of metal ions, the binding of proteins such as the L7Ae family, and by the formation of tertiary interactions. The structure is characterized by specific A‐minor interactions with the adenine nucleobases of the G•A pairs, and some very well‐conserved hydrogen bonds involving 2′‐hydroxyl groups. We can identify two classes of k‐turns, that differ in the manner of the hydrogen bonding at the adenine of the bulge‐distal G•A pair. WIREs RNA 2012. doi: 10.1002/wrna.1136 This article is categorized under: RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry RNA Interactions with Proteins and Other Molecules > Protein–RNA Recognition Regulatory RNAs/RNAi/Riboswitches > Riboswitches

Conserved hydrogen bonds in the k‐turn structure. (a)Summary schematic showing the hydrogen bonds commonly observed in k‐turn structures.3 The thickness of the arrows reflects the degree of conservation. (b)A parallel‐eye stereoscopic view of the hydrogen bond (highlighted in red) from L1 O2′ to A1n N1 in the U4 snRNA k‐turn.8 (c)A parallel‐eye stereoscopic view of the hydrogen bond (highlighted in red) between L3 O2′ and the proS non‐bridging O of the phosphate between L1 and L2 that bridges the neck of the loop in the U4 snRNA k‐turn.8

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The A•G pairs of the k‐turn. (a)The structure of the A•G pairs. Both are trans A (Hoogsteen)•G (sugar edge) basepairs held by the two hydrogen bonds shown. The distance between A2b N6 to G2n N3 is longer than a recognized hydrogen bond in many k‐turns, as discussed in the text. (b) A parallel‐eye stereoscopic view of the A•G pairs of the human U4 snRNA k‐turn,8 where the minor groove edges of adenine bases are directed toward viewer.

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Folding of the S‐adenosyl methionine (SAM)‐I k‐turn induced by the binding of Mg2+ ions.19 Folding is accompanied by an increase in fluorescence resonance energy transfer (FRET) between fluorescein (Flu) and Cy3 (Cy3) fluorophores 5′‐terminally attached to a 25 bp RNA duplex with the SAM‐I k‐turn sequence located at its center. The graph shows FRET efficiency (EFRET) plotted as a function of Mg2+ ion concentration. The titration was performed for the unmodified k‐turn sequence (filled circles) and an analogous sequence containing a G2nA substitution (open circles). No ion‐induced folding is observed for the modified k‐turn. The data for the natural k‐turn have been fitted to a model for a two‐state transition (line) giving [Mg2+]1/2 = 50 ± 8 µM and a Hill coefficient n = 0.8 ± 0.1.

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The k‐turn structure. (a) A parallel‐eye stereoscopic structure of a folded k‐turn structure showing the 60° included angle. (b)A parallel‐eye stereoscopic structure of the k‐turn found in a box C/D k‐turn.4 The color scheme matches that of the sequences in Figure 1, and is used throughout.

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The k‐turn motif sequence and nomenclature. The sequence of two standard k‐turns. The upper sequence is Kt‐7 of the H. marismortui 50S ribosomal subunit, and the lower sequence is the k‐turn of the S‐adenosyl methionine (SAM)‐I riboswitch. The nomenclature for nucleotide positions3 is shown on the Kt‐7 sequence.

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The sequence and secondary structures of two complex k‐turns. The gray arrows show the continuity of the non‐bulged strand in both cases. Crystal structures of H. marismortui Kt‐15 and T. thermophilus Kt‐11 have been determined within the context of the 50S and 30S ribosomal subunits respectively.33,35

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The k‐turns with deviations from the conventional A•G pair at the 2b•2n position. (a) WebLogo32 representation of sequence variation within 6325 Kt‐23 sequences found in 16S and 18S rRNA.30 (b) Sequences of examples of k‐turns with A•U and A•A pairs at the 2b•2n position. Crystal structures of the T. thermophilus33 and T. solenopsae31 k‐turns have been determined.

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Induced formation of k‐turn conformation due to secondary structure in the context of the S‐adenosyl methionine (SAM)‐I riboswitch. (a) Schematic showing the secondary structure of the SAM‐I riboswitch. The binding site of the SAM ligand is highlighted in red. Note the k‐turn and the loop–loop interaction. (b) A crystal structure of a modified SAM‐I riboswitch in which the k‐turn contains a G2nA substitution that prevents folding of the isolated motif has been determined. The image shows a superposition of the k‐turn regions of the natural SAM‐I k‐turn (gray) and that of the G2nA variant, with the A at the 2n position highlighted in cyan.

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The structure of a complex between the human 15.5 kDa protein and the U4 snRNA k‐turn.8 The protein is shown in cartoon representation, and the complex is observed from the non‐bulged strand side of the k‐turn.

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RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry
Regulatory RNAs/RNAi/Riboswitches > Riboswitches
RNA Interactions with Proteins and Other Molecules > Protein–RNA Recognition

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