1BPS

MINOR CONFORMER OF A BENZO[A]PYRENE DIOL EPOXIDE ADDUCT OF DA IN DUPLEX DNA

Summary for 1BPS

• Entry DOI: 10.2210/pdb1bps/pdb
• Descriptor: DNA (5'-D(*GP*GP*TP*CP*(BAP)AP*CP*GP*AP*G)-3'), DNA (5'-D(*CP*TP*CP*GP*GP*GP*AP*CP*C)-3'), 1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE (3 entities in total)
• Functional Keywords: deoxyribonucleic acid, benzo[a]pyrene diol epoxide adduct, duplex dna, dna
• Biological source: synthetic construct; More
• Total number of polymer chains: 2
• Total formula weight: 5801.96

Authors

Schwartz, J.S.,Rice, J.S.,Luxon, B.A.,Sayer, J.M.,Xie, G.,Yeh, H.J.C.,Liu, X.,Jerina, D.M.,Gorenstein, D.G. (deposition date: 1998-08-06, release date: 1998-08-19, Last modification date: 2023-12-27)

Primary citation

Schwartz, J.L.,Rice, J.S.,Luxon, B.A.,Sayer, J.M.,Xie, G.,Yeh, H.J.,Liu, X.,Jerina, D.M.,Gorenstein, D.G.
Solution structure of the minor conformer of a DNA duplex containing a dG mismatch opposite a benzo[a]pyrene diol epoxide/dA adduct: glycosidic rotation from syn to anti at the modified deoxyadenosine.
Biochemistry, 36:11069-11076, 1997

PubMed Abstract: Polycyclic aromatic hydrocarbons (PAHs) are widespread environmental contaminants whose metabolism in mammals results in deleterious cell transformation. Covalent modification of DNA by diol epoxides metabolically formed from PAHs such a benzo[a]pyrene (BaP) provides a mechanism for the genotoxicity, mutagenicity, and carcinogenicity of PAHs. We had previously reported NMR evidence for a minor conformer of the duplex d(G1G2T3C4A5*C6G7A8G9).d(C10T11C12G13G14G15A16C17C18) containing a dG14 mismatch opposite a dA5* residue modified at the exocyclic amino group by trans addition to (+)-(7R,8S,9S,10R)-7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a] pyrene [Yeh, H.J.C., Sayer, J.M., Liu, X., Altieri, A.S., Byrd, R.A., Lashman, M.K., Yagi, H., Schurer, E.J., Gorenstein, D.G., & Jerina, D.M. (1995) Biochemistry 34, 13570-13581]. In the present work, we describe the structure of this minor conformer (ca. 17% of the total conformer population). This represents the first structural determination of a minor conformer of a carcinogen-lesion DNA adduct. Two-dimensional NOESY, ROESY, TOCSY, and exchange-only spectra at 750 MHz allowed nearly complete sequential assignment of both conformers. In the minor conformer, the adducted base assumes an anti-glycosidic torsion angle whereas in the major conformer it assumes an unusual syn-glycosidic torsion angle. The aromatic hydrocarbon in the minor conformer is intercalated between dG13 and dG14, preserving the energetically favorable stacking interactions found in the major conformer. The major structural differences between the two conformers appear to be near the lesion site as evidenced by the large chemical shift differences between major and minor conformer protons near the lesion site; away from this site, the chemical shifts of the major and minor conformer protons are nearly identical. Because any of the conformations of benzo[a]pyrene diol epoxide-modified DNA may contribute to tumorigenic activity, structural determination of all conformations is essential for the elucidation of the mechanism of cell transformation initiated by covalent modification of DNA by PAHs.

PubMed: 9333324
DOI: 10.1021/bi971306u

Experimental method

SOLUTION NMR