Characterization of structure and metal ions specificity of CO2+-binding RNA aptamers

Studies on RNA motifs capable of binding metal ions have largely focused on Mg2+-specific motifs, therefore information concerning interactions of other metal ions with RNA is still very limited. Application of the in vitro selection approach allowed us to isolate two RNA aptamers that bind Co2+ ions. Structural analysis of their secondary structures revealed the presence of two motifs, loop E and kissing loop complex, commonly occurring in RNA molecules. The Co2+-induced cleavage method was used for identification of Co2+-binding sites after the determination of the optimal cleavage conditions. In the aptamers, Co2+ ions seem to bind to N7 atoms of purines, inducing cleavage of the adjacent phosphodiester bonds, similarly as is the case with yeast tRNA(Phe). Although the in vitro selection experiment was carried out in the presence of Co2+ ions only, the aptamers displayed broader metal ions specificity. This was shown by inhibition of Co2+-induced cleavages in the presence of the following transition metal ions: Zn2+, Cd2+, Ni2+, and Co(NH3)(6)(3+) complex. On the other hand, alkaline metal ions such as Mg2+, Ca2+, Sr2+, and Ba2+ affected Co2+-induced cleavages only slightly. Multiple metal ions specificity of Co2+-binding sites has also been reported for other in vitro selected or natural RNAs. Among many factors that influence metal specificity of the Co2+-binding pocket, chemical properties of metal ions, such as their hardness as well as the structure of the coordination site, seem to be particularly important.