DNA Bearing Bulky Fluorescent and Photoreactive Damage in Both Strands as Substrates of the Nucleotide Excision Repair System

Model DNA molecules that contain bulky lesions in both strands have been created, and their properties as substrates of the nucleotide excision repair (NER) system have been analyzed. The modified nucleoside, 5-[3-(4-azido-2,3,5,6-tetrafluorobenzamido)-1-propoxypropyl]-2′-deoxycytidine (dC^FAB), or the nonnucleoside fragment, N-[6-(9-anthracenylcarbamoyl)hexanoyl]-3-amino-1,2-propanediol (nAnt), have been inserted as damage in certain positions of the first DNA strand (“0”). The position of N-[6-5(6)- fluoresceinylcarbamoyl]hexanoyl]-3-amino-1,2-propanediol (nFlu) has been varied within the second DNA strand. This residue has been located opposite the removable damaging fragment of the first strand at positions–20,–10,–4, 0, +3, and +8 relative to the first lesion). It has been demonstrated that the presence of nFlu at the–4, 0, or +3 position of the second strand significantly reduces the thermostability of DNA duplexes, especially in the case of nAnt-DNA and completely excludes the possibility of NER-catalyzed excision from dC^FAB- and nAnt-containing 137-meric DNA with the second lesion at these positions. The introduction of nFlu at positions–20,–10, or +8 differently affects the excision efficiency of dC^FAB- and nAntcontaining fragments from the first strand. The excision efficiency of dC^FAB-containing fragments from extended double-damaged DNA is as high as from DNA that contains a single dC^FAB damage, while the excision of nAnt-containing fragments occurs with 80–90% lower efficiency from double-damaged DNA occurs from DNA that contains the single nAnt insert. The nFlu insert differently affects the interaction of the sensory XPC-HR23B dimer with dC^FAB- and nAnt-containing DNAs, although in all cases, this interaction occurs with increased efficiency compared to that with single-damaged DNAs. No direct correlation between the thermostability of the DNA duplex and XPC-DNA affinity on the one hand, and the excision efficiency of lesions on the other hand has been shown. The absence of the correlation may be caused by both functional features of variable multiprotein complexes involved in the recognition and verification of damage during NER and the sensitivity of the complexes to the structure of the damage and damage-surrounding DNA. The results are important for understanding the NER mechanism of elimination of bulky damage located in both DNA strands.