Monitoring the structure of Escherichia coli RNase P RNA in the presence of various divalent metal ions

Lead(II)-induced cleavage can be used as a tool to probe conformational cha nges in RNA, In this report, we have investigated the conformation of M1 RN A, the catalytic subunit of Escherichia coli RNase P, by studying the lead( II)-induced cleavage pattern in the presence of various divalent metal ions . Our data suggest that the overall conformation of M1 RNA is very similar in the presence of Mg2+, Mn2+, Ca2+, Sr2+ and Ba2+, while it is changed com pared to the Mg2+-induced conformation in the presence of other divalent me tal ions, Cd2+ for example, We also observed that correct folding of some M 1 RNA domains is promoted by Pb2+, while folding of other domain(s) require s the additional presence of other divalent metal ions, cobalt(III) hexamin e or spermidine. Based on the suppression of Pb2+ cleavage at increasing co ncentrations of various divalent metal ions, our findings suggest that diff erent divalent metal ions bind with different affinities to M1 RNA as well as to an RNase P hairpin-loop substrate and yeast tRNA(Phe). We suggest tha t this approach can be used to obtain information about the relative bindin g strength for different divalent metal ions to RNA in general, as well as to specific RNA divalent metal ion binding sites. Of these studied in this report, Mn2+ is generally among the strongest RNA binders.