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A two-dimensional mutate-and-map strategy for non-coding RNA structure.
- Source :
- Nature Chemistry; Dec2011, Vol. 3 Issue 12, p954-962, 9p
- Publication Year :
- 2011
-
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. [ABSTRACT FROM AUTHOR]
Details
- Language :
- English
- ISSN :
- 17554330
- Volume :
- 3
- Issue :
- 12
- Database :
- Complementary Index
- Journal :
- Nature Chemistry
- Publication Type :
- Academic Journal
- Accession number :
- 67366809
- Full Text :
- https://doi.org/10.1038/nchem.1176