Sequence-dependent modulation of nucleotide excision repair: the efficiency of the incision reaction is inversely correlated with the stability of the pre-incision UvrB-DNA complex

The UvrABC excinuclease is involved in the nucleotide excision repair (NER) pathway. Sequence-dependent differences in repair efficiency have been reported for many different lesions, and it is often suggested that sites with poor repair contribute to the occurrence of mutation hot spots. However, guanine bases modified by N-2-acetylaminofluorence (AAF) within the NarI site (5′-G1G2CG3CC-3′) are incised by the UvrABC excinuclease with different efficiencies in a pattern not correlated with the potency of mutation induction. To gain insight into the mechanism of sequence-dependent modulation of NER, we analyzed the formation, the structure and the stability of UvrB-DNA pre-incision complexes formed at all three positions of the AAF-modified NarI site. We show that the efficiency of release of UvrA2 from specific UvrA2B-DNA complexes is sequence-dependent and that the efficiency of incision is inversely related to the stability of the pre-incision complex. We propose that the pre-incision complex, [UvrB-DNA], when formed upon dissociation of UvrA2, undergoes a conformational change (isomerization step) giving rise to an unstable but incision-competent complex that we call [UvrB-DNA]′. The [UvrB-DNA] complex is stable and unable to form an incision-competent complex with UvrC. As the release of UvrA2, this isomerization step is sequence-dependent. Both steps contribute to modulate NER efficiency.