Repair efficiency of (5′S)-8,5′-cyclo-2′-deoxyguanosine and (5′S)-8,5′-cyclo-2′-deoxyadenosine depends on the complementary base

Abstract

5’-R and 5’-S diastereoisomers of 8,5’-cyclo-2’-deoxyadenosine (cdA) and 8,5’-cyclo-2’-deoxyguanosine (cdG) containing a base-sugar covalent bond are formed by hydroxyl radicals. R-cdA and S-cdA are repaired by nucleotide excision repair (NER) in mammalian cellular extracts. Here, we have examined seven purified base excision repair enzymes for their ability to repair S-cdG or S-cdA. We could not detect either excision or binding of these enzymes on duplex oligonucleotide substrates containing these lesions. However, both lesions were repaired by HeLa cell extracts. Dual incisions by human NER on a 136-mer duplex generated 24–32 base-pair fragments. The time course of dual incisions were measured in comparison to cis-anti-B[a]P-N2-dG, an excellent substrate for human NER, which showed that cis-anti-B[a]P-N2-dG was repaired more efficiently than S-cdG, which, in turn, was repaired more efficiently than S-cdA. When NER efficiency of S-cdG with different complementary bases was investigated, the wobble pair S-cdG•dT was excised more efficiently than the S-cdG•dC pair that maintains nearly normal Watson-Crick base pairing. But S-cdG•dA mispair with no hydrogen bonds was excised less efficiently than the S-cdG•dC pair. Similar pattern was noted for S-cdA. The S-cdA•dC mispair was excised much more efficiently than the S-cdA•dT pair, whereas the S-cdA•dA pair was excised less efficiently. This result adds to complexity of human NER, which discriminates the damaged base pairs on the basis of multiple criteria.

Removal of oxidatively generated DNA damage by overlapping repair pathways

“…The cdG and cdA DNA lesions are characterized by a covalent C-C bond between the purine C8 and the 2′-deoxyribose C5′ atoms within the same nucleoside. The N-glycosidic bond of the 5′,8-cyclopurine lesions is resistant to acid/base-catalyzed hydrolysis [81, 82], and is also resistant to base excision repair in mammalian cell extracts [83, 84], as well as to purified NEIL1, NEIL2, Fpg, OGG1, Endo III, and Endo VIII BER proteins [85]. However, the 5′,8-cyclopurines cause significant local distortions to the DNA double helix [86] and are therefore good substrates of mammalian [83, 84] and prokaryotic E. coli nucleotide excision repair systems [87].…”

“…The NER dual incision efficiencies of the diastereomeric cdA lesions are about four times greater in the case of the (5′R)- than the (5′S)-cdA lesion incorporated into plasmid DNA [83]. In linear 135-mer DNA duplexes, the 5′R cdG stereoisomer is incised ~ 1.5 more efficiently than the 5′S cdA lesion in 135-mer DNA duplexes in HeLa cell extracts [85]. More recently, the relative NER efficiencies of all four 5′R and 5′S diastereomeric 5′,8-cyclopurines were compared in human HeLa cell extracts [86] and the results are summarized in Table 1.…”

Oxidatively Generated Guanine(C8)-Thymine(N3) Intrastrand Cross-links in Double-stranded DNA Are Repaired by Base Excision Repair Pathways

“…It is well established that the 8,5Ј-cyclo-2Ј-deoxypurine lesions are not repaired by DNA glycosylase-mediated BER mechanisms, but are excellent substrates of mammalian NER (12,13,16,41,42) and prokaryotic NER repair pathways (43). However, a limited amount of information is available about IntraCLs that involve covalent bonds between two different nucleotides on the same strand.…”

“…1A). Like the cdG and cdA lesions embedded in double-stranded DNA (12)(13)(14)(15)(16), the G*T* and G*CT* lesions are moderate to good substrates, respectively, of the human nucleotide excision repair (NER) system in extracts from HeLa cells (17). Furthermore, evidence was presented that both types of IntraCL lesions are also incised at the sites of the lesions.…”

Ribonucleotides as nucleotide excision repair substrates

“…This study revealed that each embedded rNTP adopts the C3′-endo sugar pucker that is characteristic of A-form double stranded RNAs [41]; however, the rest of the duplex is essentially normal B form, with only modest local disturbances in helical parameters at the site of the lesion and the adjacent base pairs. These disturbances do not seem quite in line with the more severe distortions in Watson-Crick pairing, groove dimensions, bending, unwinding, impaired stacking, and local dynamics that have been characteristic of NER-susceptible lesions in both prokaryotes [17, 22, 24, 42, 43] and eukaryotes [15-18, 20, 21, 26, 44, 45]. Such types of disturbances have also been observed in a crystal structure of UvrA containing a bulky fluorescein-modified thymine [1, 43], and were considered as recognition signals.…”