() Structure of the different pATSer variants used

Copyright information:Taken from "The naturally -acting ribozyme RNase P RNA has leadzyme properties"Nucleic Acids Research 2005;33(21):6920-6930.Published online 6 Dec 2005PMCID:PMC1310964.© The Author 2005. Published by Oxford University Press. All rights reserved Y indicates U or C at this position, I = inosine, 2AP = 2-aminopurine, DAP = 2, 6-diaminopurine, Pu = purine, dG = deoxyG, ddG = c7deoxyG, Rib = ribavirin, 3 mU = 3-methyl U, Δ denotes that the base at this position was deleted while cs and red arrow = canonical RNase P cleavage site between positions −1 and +1. Blue arrows indicate Pb-induced cleavage sites (note that Pb also promoted cleavage at position +2, not indicated in the figure but see text) and in the case of the U variants the blue arrows indicate that cleavage was observed at +1 in addition to cleavage at the other positions. The elips denote the residues that had been deleted in these variants. () The structures of guanosine (G; top) and uridine (U; bottom), the red circles indicate the chemical groups that were substituted while the grey area corresponds to the part of G that is missing in ribavirin, for details see text. () Model of the A–RNase P RNA interaction (interacting residues underlined). The letters A–C refer to divalent metal ions that have been identified in the substrate and in the P15 loop (for references see text). The A/N interaction is indicated () Suggested mechanism for Me-induced e.g. Pb or Mg cleavage of RNA. The Me acts as a general base and activates the 2′OH resulting in 5′OH and 2′;3′P as cleavage products (left). In RNase P RNA mediated cleavage available data suggest that Me-OH acts as the nucleophile resulting in 5′P and 3′OH as cleavage products (right). Me encircled in red denotes the divalent metal ion.