ArticleNature chemistry2011
A two-dimensional mutate-and-map strategy for non-coding RNA structure.
Article in Nature chemistry, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 81 papers.
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Who cites it
81 citing papers in PubMed.
- De novo design of RNA pseudoknots with deep learning.bioRxiv : the preprint server for biology · 2026Article
- Measuring intramolecular connectivity in long RNA molecules using two-dimensional DNA patch-probe arrays.Nucleic acids research · 2025Article
- The role of structure in regulatory RNA elements.Bioscience reports · 2024Review
- Evaluating Performance of Different RNA Secondary Structure Prediction Programs Using Self-cleaving Ribozymes.Genomics, proteomics & bioinformatics · 2024Article
- Diversity of ribosomes at the level of rRNA variation associated with human health and disease.Cell genomics · 2024Article
- Ribonanza: deep learning of RNA structure through dual crowdsourcing.bioRxiv : the preprint server for biology · 2024Article
- Rational design of oligonucleotides for enhanced in vitro transcription of small RNA.RNA (New York, N.Y.) · 2024Article
- Diversity and modularity of tyrosine-accepting tRNA-like structures.RNA (New York, N.Y.) · 2024Article
- RNA structure determination: From 2D to 3D.Fundamental research · 2023Review
- Full-Length Model of SaCas9-sgRNA-DNA Complex in Cleavage State.International journal of molecular sciences · 2023Article
- Chemical crosslinking and ligation methods for in vivo analysis of RNA structures and interactions.Methods in enzymology · 2023Article
- Programmable antivirals targeting critical conserved viral RNA secondary structures from influenza A virus and SARS-CoV-2.Nature medicine · 2022Article
- Crowdsourced RNA design discovers diverse, reversible, efficient, self-contained molecular switches.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Protein synthesis control in cancer: selectivity and therapeutic targeting.The EMBO journal · 2022Review
- Short- and long-range interactions in the HIV-1 5' UTR regulate genome dimerization and packaging.Nature structural & molecular biology · 2022Article
- Chemical reversible crosslinking enables measurement of RNA 3D distances and alternative conformations in cells.Nature communications · 2022Article
- Review
- Three-dimensional structure of a flavivirus dumbbell RNA reveals molecular details of an RNA regulator of replication.Nucleic acids research · 2021Article
- Direct Mapping of Higher-Order RNA Interactions by SHAPE-JuMP.Biochemistry · 2021Article
- An expanded class of histidine-accepting viral tRNA-like structures.RNA (New York, N.Y.) · 2021Article
21 more citing papers are in PubMed but not listed here.
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4 authors.
Funding
Abstract
Non-coding RNAs fold into precise base-pairing patterns to carry out critical roles in genetic regulation and protein synthesis, but determining RNA structure remains difficult. Here, we show that coupling systematic mutagenesis with high-throughput chemical mapping enables accurate base-pair inference of domains from ribosomal RNA, ribozymes and riboswitches. For a six-RNA benchmark that has challenged previous chemical/computational methods, this 'mutate-and-map' strategy gives secondary structures that are in agreement with crystallography (helix error rates, 2%), including a blind test on a double-glycine riboswitch. Through modelling of partially ordered states, the method enables the first test of an interdomain helix-swap hypothesis for ligand-binding cooperativity in a glycine riboswitch. Finally, the data report on tertiary contacts within non-coding RNAs, and coupling to the Rosetta/FARFAR algorithm gives nucleotide-resolution three-dimensional models (helix root-mean-squared deviation, 5.7 Å) of an adenine riboswitch. These results establish a promising two-dimensional chemical strategy for inferring the secondary and tertiary structures that underlie non-coding RNA behaviour.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.