Differential incision of bulky carcinogen-DNA adducts by the UVrABC nuclease: Comparison of incision rates and the interactions of Uvr subunits with lesions of different structures

The UvrABC nuclease system from Escherichia coli removes DNA damages induce d by a wide range of chemical carcinogens with variable efficiencies. The i nteractions with UvrABC proteins of the following three lesions site-specif ically positioned in DNA, and of known conformations, were investigated: (i ) adducts derived from the binding of the (-)-(7S,8R,9R,10S) enantiomer of 7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene [(-)-anti-BPDE] by cis-covalent addition to N-2-2'-deoxyguanosine [(-)-cis-anti-BP-N-2-dG], (ii) an adduct derived from the binding of the (+)-(1R,2S,3S,4R) enantiome r of 1,2-dihydroxy-3,4-epoxy- 1,2,3,4-tetrahydro-5-methylchrysene [(+)-anti -5-MeCDE] by trans addition to N-2-2'-deoxyguanosine [(+)-trans-anti-MC-N-2 -dG], and (iii) a C8-2'-deoxyguanosine adduct (C8-AP-dG) formed by reductiv ely activated I-nitropyrene (1-NP). The influence of these three different adducts on UvrA binding affinities, formation of UvrB-DNA complexes by quan titative gel mobility shift analyses, and the rates of UvrABC incision were investigated. The binding affinities of UvrA varied among the three adduct s, UvrA bound to the DNA adduct (+)-trans-anti-MC-N-2-dG with the highest a ffinity (K-d = 17 +/- 2 nM) and to the DNA containing C8-AP-dG with the lea st affinity (K-d = 28 +/- 1 nM). The extent of complex formation with UvrB was also the lowest with the C8-AP-dG adduct. 5' Incisions occurred at the eighth phosphate from the modified guanine, The major 3' incision site corr esponded to the fifth phosphodiester bond for all three adducts. However, a dditional 3' incisions were observed at the fourth and sixth phosphates in the case of the C8-AP-dG adduct, whereas in the case of the (-)-cis-anti-BP -N-2-dG and (+)-trans-anti-MC-N-2-dG lesions additional 3' cleavage occurre d at the sixth and seventh phosphodiester bonds. Both the initial rate and the extent of 5' and 3' incisions revealed that C8-AP-dG was repaired less efficiently in comparison to the (-)-cis-anti-BP-N-2-dG and (+)-trans-anti- MC-N-2-dG containing DNA adducts. Our study showed that UvrA recognizes con formational changes induced by structurally different lesions and that in c ertain cases the binding affinities of UvrA and UvrB can be correlated with the incision rates. The size of the bubble formed around the damaged site with mismatched bases also appears to influence the incision rates. A parti cularly noteworthy finding in this study is that UvrABC repair of a substra te with no base opposite C8-AP-dG was quite inefficient as compared to the same adduct with a C opposite it. These findings are discussed in terms of the available NMR solution structures.