ArticleNucleic acids research2009
The UA_handle: a versatile submotif in stable RNA architectures.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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Who cites it
56 citing papers in PubMed.
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- Utilizing RNA origami scaffolds in Saccharomyces cerevisiae for dCas9-mediated transcriptional control.Nucleic acids research · 2022Article
- Computer-aided comprehensive explorations of RNA structural polymorphism through complementary simulation methods.QRB discovery · 2022Review
- Thermostability, Tunability, and Tenacity of RNA as Rubbery Anionic Polymeric Materials in Nanotechnology and Nanomedicine-Specific Cancer Targeting with Undetectable Toxicity.Chemical reviews · 2021Review
- In vitro selected GUAA tetraloop-binding receptors with structural plasticity and evolvability towards natural RNA structural modules.Nucleic acids research · 2021Article
- In silico survey of the central conserved regions in viroids of theRNA (New York, N.Y.) · 2019Article
- Responsive self-assembly of tectoRNAs with loop-receptor interactions from the tetrahydrofolate (THF) riboswitch.Nucleic acids research · 2019Article
- Deducing putative ancestral forms of GNRA/receptor interactions from the ribosome.Nucleic acids research · 2019Article
- Using Rosetta for RNA homology modeling.Methods in enzymology · 2019Article
- How to fold and protect mitochondrial ribosomal RNA with fewer guanines.Nucleic acids research · 2018Article
- A metastable rRNA junction essential for bacterial 30S biogenesis.Nucleic acids research · 2018Article
- Mining for recurrent long-range interactions in RNA structures reveals embedded hierarchies in network families.Nucleic acids research · 2018Article
- Blind prediction of noncanonical RNA structure at atomic accuracy.Science advances · 2018Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Single-Molecule Fluorescence Reveals Commonalities and Distinctions among Natural and in Vitro-Selected RNA Tertiary Motifs in a Multistep Folding Pathway.Journal of the American Chemical Society · 2017Article
- Composing RNA Nanostructures from a Syntax of RNA Structural Modules.Nano letters · 2017Article
- RNA quaternary structure and global symmetry.Trends in biochemical sciences · 2015Review
- Ligand-responsive RNA mechanical switches.RNA biology · 2015Article
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3 authors.
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Abstract
Stable RNAs are modular and hierarchical 3D architectures taking advantage of recurrent structural motifs to form extensive non-covalent tertiary interactions. Sequence and atomic structure analysis has revealed a novel submotif involving a minimal set of five nucleotides, termed the UA_handle motif (5'XU/AN(n)X3'). It consists of a U:A Watson-Crick: Hoogsteen trans base pair stacked over a classic Watson-Crick base pair, and a bulge of one or more nucleotides that can act as a handle for making different types of long-range interactions. This motif is one of the most versatile building blocks identified in stable RNAs. It enters into the composition of numerous recurrent motifs of greater structural complexity such as the T-loop, the 11-nt receptor, the UAA/GAN and the G-ribo motifs. Several structural principles pertaining to RNA motifs are derived from our analysis. A limited set of basic submotifs can account for the formation of most structural motifs uncovered in ribosomal and stable RNAs. Structural motifs can act as structural scaffoldings and be functionally and topologically equivalent despite sequence and structural differences. The sequence network resulting from the structural relationships shared by these RNA motifs can be used as a proto-language for assisting prediction and rational design of RNA tertiary structures.
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