1axu
From Proteopedia
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SOLUTION NMR STRUCTURE OF THE [AP]DG ADDUCT OPPOSITE DA IN A DNA DUPLEX, NMR, 9 STRUCTURES
Overview
Solution structural studies have been undertaken on the, aminopyrene-C(8)-dG ([AP]dG) adduct in the d(C5-[AP]G6-C7). d(G16-A17-G18), sequence context in an 11-mer duplex with dA opposite [AP]dG, using, proton-proton distance and intensity restraints derived from NMR data in, combination with distance-restrained molecular mechanics and, intensity-restrained relaxation matrix refinement calculations. The, exchangeable and nonexchangeable protons of the aminopyrene and the, nucleic acid were assigned following analysis of two-dimensional NMR data, sets on the [AP]dG.dA 11-mer duplex in H2O and D2O solution. The, broadening of several resonances within the d(G16-A17-G18) segment, positioned opposite the [AP]dG6 lesion site resulted in weaker NOEs, involving these protons in the adduct duplex. Both proton and carbon NMR, data are consistent with a syn glycosidic torsion angle for the [AP]dG6, residue in the adduct duplex. The aminopyrene ring of [AP]dG6 is, intercalated into the DNA helix between intact Watson-Crick dC5.dG18 and, dC7.dG16 base pairs and is in contact with dC5, dC7, dG16, dA17, and dG18, residues that form a hydrophobic pocket around it. The intercalated AP, ring of [AP]dG6 stacks over the purine ring of dG16 and, to a lesser, extent dG18, while the looped out deoxyguanosine ring of [AP]dG6 stacks, over dC5 in the solution structure of the adduct duplex. The dA17 base, opposite the adduct site is not looped out of the helix but rather, participates in an in-plane platform with adjacent dG18 in some of the, refined structures of the adduct duplex. The solution structures are quite, different for the [AP]dG.dA 11-mer duplex containing the larger, aminopyrene ring (reported in this study) relative to the previously, published [AF]dG.dA 11-mer duplex containing the smaller aminofluorene, ring (Norman et al., Biochemistry 28, 7462-7476, 1989) in the same, sequence context. Both the modified syn guanine and the dA positioned, opposite it are stacked into the helix with the aminofluorene chromophore, displaced into the minor groove in the latter adduct duplex. By contrast, the aminopyrenyl ring participates in an intercalated base-displaced, structure in the present study of the [AP]dG.dA 11-mer duplex and in a, previously published study of the [AP]dG.dC 11-mer duplex (Mao et al., Biochemistry 35, 12659-12670, 1996). Such intercalated base-displaced, structures without hydrogen bonding between the [AP]dG adduct and dC or, mismatched dA residues positioned opposite it, if present at a replication, fork, may cause polymerase stalling and formation of a slipped, intermediate that could produce frameshift mutations, the most dominant, mutagenic consequence of the [AP]dG lesion.
About this Structure
1AXU is a Protein complex structure of sequences from [1] with AP as ligand. Full crystallographic information is available from OCA.
Reference
Solution structure of the N-(deoxyguanosin-8-yl)-1-aminopyrene ([AP]dG) adduct opposite dA in a DNA duplex., Gu Z, Gorin A, Krishnasamy R, Hingerty BE, Basu AK, Broyde S, Patel DJ, Biochemistry. 1999 Aug 17;38(33):10843-54. PMID:10451381
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