DNA double-strand breaks and hairpins in V(D)J recombination

Several lines of evidence have suggested the existence of broken DNA molecules as intermediates in V(D)J recombination. These include sequence alterations at the recombined junctions and the presence of aberrant recombinants. More recently, broken DNA molecules have been directly detected in recombinationally active cells. The signal sequence ends have normal blunt-ended DNA breaks, but the coding ends have a hairpin (self-joined) structure that provides an explanation for the self-complementary P nucleotide insertions often found after V(D)J joining in the antigen receptor genes.