CHARACTERIZATION OF BROKEN DNA-MOLECULES ASSOCIATED WITH V(D)J RECOMBINATION

We previously demonstrated that DNA molecules with double-strand break s at variable-(diversity)-joining [V(D)J] recombination signal sequenc es are relatively abundant in mouse thymocytes. This abundance strongl y suggests that the mechanism of V(D)J recombination involves double-s trand cleavage at recombination signals. As a first step toward unders tanding the mechanism of cleavage, we used a sensitive PCR assay to ch aracterize the structure of one class of cleavage products, the signal ends, in detail. Here we demonstrate that most of these ends are blun t and terminate in 5' phosphoryl groups. Virtually all of the flush si gnal ends are full length. A minor subpopulation of broken ends termin ates in short single-strand extensions. We have found no evidence for covalent DNA-protein linkages involving the signal ends. These data al low further refinement of the double-strand cleavage model for V(D)J r ecombination.