title: Safer one-pot synthesis of the 'SHAPE' reagent 1-methyl-7-nitroisatoic anhydride (1m7).
abstract: Estimating the reactivity of 2'-hydroxyl groups along an RNA chain of interest aids in the modeling of the folded RNA structure; flexible loops tend to be reactive, whereas duplex regions are generally not. Among the most useful reagents for probing 2'-hydroxyl reactivity is 1-methyl-7-nitroisatoic anhydride (1m7), but the absence of a reliable, inexpensive source has prevented widespread adoption. An existing protocol for the conversion of an inexpensive precursor 4-nitroisatoic anhydride (4NIA) recommends the use of NaH in dimethylformamide (DMF), a reagent combination that most molecular biology labs are not equipped to handle, and that does not scale safely in any case. Here we describe a safer, one-pot method for bulk conversion of 4NIA to 1m7 that reduces costs and bypasses the use of NaH. We show that 1m7 produced by this method is free of side products and can be used to probe RNA structure in vitro.
authors.forename: Rushia
authors.initials: R
authors.lastname: Turner
authors.forename: Kinneret
authors.initials: K
authors.lastname: Shefer
authors.forename: Manuel
authors.initials: M
authors.lastname: Ares
mesh_terms: D000215:Acylation; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D005821:Genetic Techniques; D055772:Green Chemistry Technology; D007202:Indicators and Reagents / Q000138:chemical synthesis; D009690:Nucleic Acid Conformation; D010078:Oxazines / Q000138:chemical synthesis*; D012329:RNA, Bacterial / Q000737:chemistry* / Q000378:metabolism; D012343:RNA, Transfer / Q000737:chemistry* / Q000378:metabolism; D013194:Staining and Labeling
chemical_list: C585663:1-methyl-7-nitroisatoic anhydride; D007202:Indicators and Reagents; D010078:Oxazines; D012329:RNA, Bacterial; D012343:RNA, Transfer
keywords: 1-methyl-7-nitroisatoic anhydride; 1m7; RNA structure; SHAPE