A novel pathway of DNA end-to-end joining

Repair mechanisms related to illegitimate recombination can join nonhomologous DNA ends that terminate as protruding single strands (PSS). Here we analyze in Xenopus egg extracts joining reactions between 3′ PSS termini and various partner termini. In junctions, 3′ PSS termini are preserved by fill-in DNA synthesis, although their 5′ recessed ends cannot serve as a primer. Alternative priming from a partner terminus ligated to the 3′ PSS end appears unlikely, because no single strand-specific DNA ligases are detectable. We show that fill-in of 3′ PSS termini precedes ligation and can even be primed in the absence of any ligation. Therefore, priming requires precise alignment of terminus pairs by a novel mechanism. We postulate that this is achieved by unique DNA binding proteins that align ends in various types of joining reactions.