Rewriting the rules for end joining via enzymatic splicing of DNA 3′-PO4 and 5′-OH ends

Abstract There are many biological contexts in which DNA damage generates “dirty” breaks with 3′-PO4 (or cyclic-PO4) and 5′-OH ends that cannot be sealed by DNA ligases. Here we show that the Escherichia coli RNA ligase RtcB can splice these dirty DNA ends via a unique chemical mechanism. RtcB transfers GMP from a covalent RtcB–GMP intermediate to a DNA 3′-PO4 to form a “capped” 3′ end structure, DNA3′pp5′G. When a suitable DNA 5′-OH end is available, RtcB catalyzes attack of the 5′-OH on DNA3′pp5′G to form a 3′–5′ phosphodiester splice junction. Our findings unveil an enzymatic capacity for DNA 3′ capping and the sealing of DNA breaks with 3′-PO4 and 5′-OH termini, with implications for DNA repair and DNA rearrangements.