Nicking is asynchronous and stimulated by synapsis in 12/23 rule-regulated V(D)J cleavage

The first step in DNA cleavage at V(D)J recombination signals by RAG1 and RAG2 is creation of a nick at the heptamer/coding flank border. Under proper conditions in vitro the second step, hairpin formation, requires two signals with spacers of 12 and 23 bp, a restriction referred to as the 12/23 rule. Under these conditions hairpin formation occurs at the two signals at or near the same time. In contrast, we find that under the same conditions nicking occurs at isolated signals and hence is not subject to the 12/23 rule. With two signals the nicking events are not concerted and the signal with a 12 bp spacer is usually nicked first. However, the extent and rate of nicking at a given signal are diminished by mutations of the other signal. The appearance of DNA nicked at both signals is stimulated by more than an order of magnitude by the ability of the signals to synapse, indicating that synapsis accelerates nicking and often precedes it. These observations allow formulation of a more complete model of catalysis of DNA cleavage and how the 12/23 rule is enforced.