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3′-Intercalation of a N2-dG 1R-trans-anti-Benzo[c]phenanthrene DNA Adduct in an Iterated (CG)3 Repeat

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posted on 2008-07-21, 00:00 authored by Yazhen Wang, Nathalie C. Schnetz-Boutaud, Heiko Kroth, Haruhiko Yagi, Jane M. Sayer, Subodh Kumar, Donald M. Jerina, Michael P. Stone
The conformation of the 1R,2S,3R,4S-benzo[c]phenanthrene-N2-dG adduct, arising from trans opening of the (+)-1S,2R,3R,4S-anti-benzo[c]phenanthrene diol epoxide, was examined in 5′- d(ATCGCXCGGCATG)-3′·5′-d(CATGCCGCGCGAT)-3′, where X = 1R,2S,3R,4S-B[c]P-N2-dG. This duplex, derived from the hisD3052 frameshift tester strain of Salmonella typhimurium, contains a (CG)3 iterated repeat, a hotspot for frameshift mutagenesis. NMR experiments showed a disconnection in sequential NOE connectivity between X4 and C5, and in the complementary strand, they showed another disconnection between G18 and C19. In the imino region of the 1H NMR spectrum, a resonance was observed at the adducted base pair X4·C19. The X4 N1H and G18 N1H resonances shifted upfield as compared to the other guanine imino proton resonances. NOEs were observed between X4 N1H and C19 N4H and between C5 N4H and G18 N1H, indicating that base pairs X4·C19 and C5·G18 maintained Watson−Crick hydrogen bonding. No NOE connectivity was observed between X4 and G18 in the imino region of the spectrum. Chemical shift perturbations of greater than 0.1 ppm were localized at nucleotides X4 and C5 in the modified strand and G18 and C19 in the complementary strand. A total of 13 NOEs between the protons of the 1R-B[c]Ph moiety and the DNA were observed between B[c]Ph and major groove aromatic or amine protons at base pairs X4·C19 and 3′-neighbor C5·G18. Structural refinement was achieved using molecular dynamics calculations restrained by interproton distances and torsion angle restraints obtained from NMR data. The B[c]Ph moiety intercalated on the 3′-face of the X4·C19 base pair such that the terminal ring of 1R-B[c]Ph threaded the duplex and faced into the major groove. The torsion angle α′ [X4]−N3−C2−N2−B[c]Ph]−C1 was calculated to be −177°, maintaining an orientation in which the X4 exocyclic amine remained in plane with the purine. The torsion angle β′ [X4]−C2−N2−[B[c]Ph]−C1−C2 was calculated to be 75°. This value governed the 3′-orientation of the B[c]Ph moiety with respect to X4. The helical rise between base pairs X4·C19 and C5·G18 increased and resulted in unwinding of the right-handed helix. The aromatic rings of the B[c]Ph moiety were below the Watson−Crick hydrogen-bonding face of the modified base pair X4·C19. The B[c]Ph moiety was stacked above nucleotide G18, in the complementary strand.

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