Probing the substrate specificity of the bacterial Pnkp/Hen1 RNA repair system using synthetic RNAs

Repair of broken stem–loop RNAs by AvaPnkp/Hen1. (A) Schematic view of three sets of broken stem–loop RNAs used for the assay. Since each substrate is reconstituted by mixing and annealing separately prepared 5′-half and 3′-half RNAs, its breaking point is marked with an arrow and labeled as Asp (for nucleotide sequence matching tRNA^Asp) or Arg (for nucleotide sequence matching tRNA^Arg). (B) Analysis of phosphorylation and repair reactions by DPAGE. Pnkp-N indicates the N-terminal half of Pnkp consisting of the kinase and phosphatase domains. SM indicates RNA size marker.