Effects of DNA Adduct Structure and Sequence Context on Strand Opening of Repair Intermediates and Incision by UvrABC Nuclease

Abstract

DNA damage recognition of nucleotide excision repair (NER) in Escherichia coli is achieved by at least two steps. In the first step, a helical distortion is recognized, which leads to a strand opening at the lesion site. The second step involves the recognition of the type of chemical modification in the single-stranded region of DNA during the processing of the lesions by UvrABC. In the current work, by comparing the efficiencies of UvrABC incision of several types of different DNA adducts, we show that the size and position of the strand opening are dependent on the type of DNA adducts. Optimal incision efficiency for the C8-guanine adducts of 2-aminofluorene (AF) and N-acetyl-2-aminofluorene (AAF) was observed in a bubble of three mismatched nucleotides, whereas the same for C8-guanine adduct of 1-nitropyrene and N 2 -guanine adducts of benzo[a]pyrene diol epoxide (BPDE) was noted in a bubble of six mismatched nucleotides. This suggests that the size of the aromatic ring system of the adduct might influence the extent and number of bases associated with the opened strand region catalyzed by UvrABC. We also showed that the incision efficiency of the AF or AAF adduct was affected by the neighboring DNA sequence context, which, in turn, was the result of differential binding of UvrA to the substrates. The sequence context effect on both incision and binding disappeared when a bubble structure of three bases was introduced at the adduct site. We therefore propose that these effects relate to the initial step of damage recognition of DNA structural distortion. The structure-function relationships in the recognition of the DNA lesions, based on our results, have been discussed.Nucleotide excision repair (NER), 1 as one of the primary DNA repair pathways in cells, is capable of removing an extensive variety of bulky lesions, induced by chemicals and radiation, with varying efficiencies (1-3). Its ability to recognize and excise such a broad repertoire of substrates has been the subject of intensive research, and it is generally believed that the success of NER depends on efficient damage recognition. The UvrABC nuclease system, which initiates the NER in Escherichia coli, represents a paradigm for understanding the general mechanism of DNA damage recognition and incision (1). This model system has been widely

Specific and Efficient Binding of Xeroderma Pigmentosum Complementation Group A to Double-Strand/Single-Strand DNA Junctions with 3‘- and/or 5‘-ssDNA Branches

“…The 0-C stands for unmodified DNA with no bending (no carbon tether). Pane B: XPC-HR23B complex (labeled as XPC) had high affinities to DNA bending with the following order: 2-C > 3-C > 4-C > 0-C, which is consistent with the order of their bending-angles: 2-C > 3-C > 4-C > 0-C. Panel C: Binding of E. coli UvrA to the same DNA bending substrates (27)(28)(29).…”

Dynamics of a Benzo[a]pyrene-derived Guanine DNA Lesion in TGT and CGC Sequence Contexts: Enhanced Mobility in TGT Explains Conformational Heterogeneity, Flexible Bending, and Greater Susceptibility to Nucleotide Excision Repair

“…25 This finding represents a case where the same lesion is excised with different efficiencies in two different, natural DNA sequence contexts. A similar sequence context dependence was observed in the excision of C8-guanine adducts of 2-aminofluorene and N-acetyl-2-aminofluorene catalyzed by UvrABC from Escherichia coli, 22 and other base sequence effects on the excision of these lesions have also been reported. 23 Ruan et al attributed their observed sequence effects to the overall weaker base stacking and weaker hydrogen bonding interactions associated with A:T rather than G:C base pairs flanking the lesion.…”

“…17,[19][20][21] Thus, the biological processing of such lesions by DNA polymerases and the cellular DNA repair machinery may be determined by the sequence-dependent conformational state of the DNA lesion. 20,[22][23][24] The relative rate of NER of a DNA adduct and therefore its mutagenic potential can depend on the nature of the neighboring bases, producing mutational hotspots and coldspots. 17,19,20,[22][23][24][25] Remarkable sequence-dependent conformational equilibria have been noted in solution NMR studies 17 of mutagenic DNA adducts derived from the polycyclic aromatic hydrocarbon benzo[a]pyrene (BP), an environmental precarcinogen.…”

“…20,[22][23][24] The relative rate of NER of a DNA adduct and therefore its mutagenic potential can depend on the nature of the neighboring bases, producing mutational hotspots and coldspots. 17,19,20,[22][23][24][25] Remarkable sequence-dependent conformational equilibria have been noted in solution NMR studies 17 of mutagenic DNA adducts derived from the polycyclic aromatic hydrocarbon benzo[a]pyrene (BP), an environmental precarcinogen. 1 Particularly intriguing are the properties of the major 10S (+)-trans-anti-[BP]-N 2 -dG adduct (G*) (Fig.…”

Benzene-derived N2-(4-hydroxyphenyl)-deoxyguanosine adduct: UvrABC incision and its conformation in DNA

“…3, several minor incisions were also observed on the 5' side of the major incision, which are further away from the adduct. Similar 5' extra cuts by UvrABC have also been described previously for other DNA adducts (Moolenaar et al, 1998;Zou et al, 2003). No specific incision(s) was detected for the unmodified 40-mer under the same UvrABC concentration used (Fig.…”