Secondary Structure of an RNA Interacting with a Hairpin RNA

Abstract

Enzymes and chemical which have mainlybeen used for probing RNA structure in solution, are double-strand-specific RNase V1, single-strand-specific nucleaseS1, RNase T1 which has a specificity for a guanine in singlestrand region, and kethoxal (3-ethoxy-1,1-dihydroxy-2-butanone), which modify the N1 and N2 of guanine in thesingle strand. Hydroxyl radical (·OH) has also been used forthe structural analysis of RNA. Exposed nucleotides aredamaged by hydroxyl radical while nucleotides involved intertiary contacts are protected from damage, making it afavorable approach for establishing exterior/interior relationsfor RNA.