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

Repair of broken double-stranded RNAs by AvaPnkp/Hen1. (A–D) Schematic depiction of different secondary structures of RNA repair substrates with single RNA break in the regions of double-stranded RNA (Nick) and bulges (Bulge, Double Bulge1, and Double Bulge2). Only Tail RNA, which is depicted with white cycles, is radiolabeled (with *). Lead RNA, the potential repair partner of Tail, is colored black, and the complementary strand bridging Tail and Lead RNAs (Bridge1 to Bridge4) is in gray. (E) Analysis of RNA repair products by DPAGE. B1 to B4 indicate Bridge1 to Bridge4.