ArticleNucleic acids research2016
A critical base pair in k-turns determines the conformational class adopted, and correlates with biological function.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Origins of Reactivity in SAM-Utilizing Ribozyme SAMURI-Catalyzed RNA Alkylation.Journal of the American Chemical Society · 2026Article
- RNAprecis: Prediction of full-detail RNA conformation from the experimentally best-observed sparse parameters.PLoS computational biology · 2026Article
- The Kink-Turn 7 Motif: An Additional Test for RNA Force Field Performance.Journal of chemical theory and computation · 2025Article
- Discovery of small molecule probes targeting the 5' stem-loop in the yeast U4/U6 snRNA.bioRxiv : the preprint server for biology · 2025Article
- A general strategy for engineering GU base pairs to facilitate RNA crystallization.Nucleic acids research · 2025Article
- RIP-PEN-seq identifies a class of kink-turn RNAs as splicing regulators.Nature biotechnology · 2024Article
- Article
- Structure and folding of four putative kink turns identified in structured RNA species in a test of structural prediction rules.Nucleic acids research · 2021Article
- Limits in accuracy and a strategy of RNA structure prediction using experimental information.Nucleic acids research · 2019Article
- Effects of Noncanonical Base Pairing on RNA Folding: Structural Context and Spatial Arrangements of G·A Pairs.Biochemistry · 2019Article
- The role of RNA structure in translational regulation by L7Ae protein in archaea.RNA (New York, N.Y.) · 2019Article
- Structure and ligand binding of the SAM-V riboswitch.Nucleic acids research · 2018Article
- Adventures with RNA graphs.Methods (San Diego, Calif.) · 2018Review
- Article
- Sequence determinants of the folding properties of box C/D kink-turns in RNA.RNA (New York, N.Y.) · 2017Article
- Opportunities and Challenges in RNA Structural Modeling and Design.Biophysical journal · 2017Article
- Using sequence signatures and kink-turn motifs in knowledge-based statistical potentials for RNA structure prediction.Nucleic acids research · 2017Article
- Article
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3 authors.
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Abstract
k-turns are commonly-occurring motifs that introduce sharp kinks into duplex RNA, thereby facilitating tertiary contacts. Both the folding and conformation of k-turns are determined by their local sequence. k-turns fall into two conformational classes, called N3 and N1, that differ in the pattern of hydrogen bonding in the core. We show here that this is determined by the basepair adjacent to the critical G•A pairs. We determined crystal structures of a series of Kt-7 variants in which this 3b,3n position has been systematically varied, showing that this leads to a switch in the conformation. We have previously shown that the 3b,3n position also determines the folding characteristics of the k-turn, i.e. whether or not the k-turn can fold in the presence of metal ions alone. We have analyzed the distribution of 3b,3n sequences from four classes of k-turns from ribosomes, riboswitches and U4 snRNA, finding a strong conservation of properties for a given k-turn type. We thus demonstrate a strong association between biological function, 3b,3n sequence and k-turn folding and conformation. This has strong predictive power, and can be applied to the modeling of large RNA architectures.
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