Probing RNA Hairpins with Cobalt(III)hexammine and Electrospray Ionization Mass Spectrometry

In this work, electrospray ionization mass spectrometry (ESI MS) was employed to study the interactions of cobalt(III) hexammine, Co(NH3)63+, with five RNA hairpins representing the 790 loop of 16S ribosomal RNA and 1920 loop of 23S ribosomal RNA. The RNAs varied in mismatch identity (G·U versus A·C) and level of base modification (pseudouridine versus uridine). Co(NH3)63+ binding was observed with the four RNA hairpins that contained a G·U wobble pair in the stem region. ESI MS revealed 1:1 and 1:2 complex formation with all RNAs. Weaker binding was observed with the fifth RNA hairpin that contained an A·C wobble pair in the stem region. The effects of pH on Co(NH3)63+ binding were also examined.