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The central dogma of DNA enzymology has long held that for two pieces of DNA to be ligated, the respective DNA pieces must bear a hydroxyl on the 3′-end and a phosphate on the 5′-end. All of the other types of DNA ends are considered incorrect or “dirty,” as they cannot be joined by classic DNA ligases. However, intrinsic and extrinsic DNA damage often results in broken DNA with dirty ends. Thus, there are a variety of DNA repair enzymes that function to “clean up” or “heal” such dirty ends to promote the restoration of a continuous DNA phosphodiester backbone. Until now, DNA breaks with phosphate at the 3′-end and hydroxyl at the 5′-end also fell into the category of dirty ends. The study in PNAS by Das et al. (1) demonstrates that a recently identified RNA-processing enzyme, RtcB, can directly ligate a DNA 3′-phosphate end with a DNA 5′-OH end (Fig. 1). Comparison of the end-joining mechanisms between classic ligases (A) and RtcB (B). (A) First, the catalytic lysine residues of classic DNA and RNA ligases are charged by adenylylation. Second, the transfer of adenylate to the 5′-phosphate end of DNA or RNA activates the 5′-end with a pyrophosphate linkage. Third, the attack by the 3′-OH on the 5′-phosphoanhydride generates the 3′-5′ phosphodiester bond, releasing AMP. (B) In a GTP-dependent step, RtcB first becomes charged by guanylylation at a conserved histidine residue located at the catalytic site. Next, the transfer of guanylate from the histidine residue to the RNA or DNA 3′-phosphate end generates …

Cross-over of RNA 3′-phosphate ligase into the DNA world