Differentiate RNA single-stranded region of the branched structures and hairpin loops by an octahedral cobalt(II) complex

Single-stranded RNA molecules usually include secondary structural elements such as bulges, internal loops, and hairpin loops. These RNA secondary structural elements are often essential for the biological activity and functions of the RNA molecule. Chemical probe Co11(HAPP)(TFA) 2 in the presence of H2O2 is found to differentiate single-stranded RNA from branched structures and hairpin loops. This study uses Co11(HAPP)(TFA)2 to analyze the structures of two RNA molecules: a fragment of HIV TAR RNA (TAR-27) and the catalytic domain 5 of group II intron (D5-29). The electrophoretic mobility of TAR-27 does not shift in the presence of Co11(HAPP)(TFA)2, suggesting that the reagent does not change the conformation of RNA substrate. Cleavage of the RNA substrates by Co11(HAPP)(TFA)2 unambiguously differentiated RNA internal looped structures from hairpin loops. The results show that Co11(HAPP)(TFA)2 is a sensitive, informative and convenient tool for analysis of RNA secondary structures.