title: A two-dimensional mutate-and-map strategy for non-coding RNA structure.
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.
authors: Department of Biochemistry, Stanford University, Stanford, California                 94305, USA.
authors: Wipapat
authors: W
authors: Kladwang
authors: Christopher C
authors: CC
authors: VanLang
authors: Pablo
authors: P
authors: Cordero
authors: Rhiju
authors: R
authors: Das
mesh_terms: D005998:Glycine / Q000737:chemistry; D008958:Models, Molecular; D009154:Mutation; D009690:Nucleic Acid Conformation; D022661:RNA, Untranslated / Q000737:chemistry*; D058928:Riboswitch
chemical_list: D022661:RNA, Untranslated; D058928:Riboswitch; D005998:Glycine