Solution Structure of a Cis-Opened (10R)-N⁶-Deoxyadenosine Adduct of (9S,10R)-9,10-Epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene in a DNA Duplex^,

Abstract

The solution structure of an 11-mer DNA duplex, d(CGGTCA*CGAGG) x d(CCTCGTGACCG), containing a 10R adduct at dA* that corresponds to the cis addition of the N(6)-amino group of dA(6) to (+)-(9S,10R)-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene was studied by 2D NMR methods. The NOESY cross-peak patterns indicate that the hydrocarbon is intercalated on the 5'-side of the modified base. This observation is the same as that observed for other oligonucleotides containing (10R)-dA adducts but opposite to that observed for the corresponding (10S)-dA adducts which are intercalated on the 3'-side of the modified base. The hydrocarbon is intercalated from the major groove without significant disruption of either the anti glycosidic torsion angle of the modified residue or the base pairing of the modified residue with the complementary residue on the opposite strand. The ensemble of 10 structures determined exhibits relatively small variations (6-15 degrees) in the characteristic hydrocarbon-base dihedral angles (alpha' and beta') as well as the glycosidic torsion angle chi. These angles are similar to those in a previously determined cis-opened benzo[a]pyrene diol epoxide-(10R)-dA adduct structure. Comparison of the present structure with the cis-opened diol epoxide adduct suggests that the absence of the 7- and 8-hydroxyl groups results in more efficient stacking of the aromatic moiety with the flanking base pairs and deeper insertion of the hydrocarbon into the helix. Relative to normal B-DNA, the duplex containing the present tetrahydroepoxide adduct is unwound at the lesion site, whereas the diol epoxide adduct structure is more tightly wound than normal B-DNA. Buckling of the adducted base pair as well as the C(5)-G(18) base pair that lies immediately above the hydrocarbon is much less severe in the present adducted structure than its cis-opened diol epoxide counterpart.

Crystal structure of a benzo[ a ]pyrene diol epoxide adduct in a ternary complex with a DNA polymerase

“…1 A), which perfectly match a predicted favorable conformation of the adduct (21) and are practically identical to those found in NMR structures determined in the absence of a polymerase (Fig. 3A) (6,22). Because of the intercalation of the PAH, the dA*⅐dT base pair is distorted by 36°of buckle, 31°of propeller twist, and 10°o f base opening (23), and only one hydrogen bond is retained between this base pair (Fig.…”

“…3A) and higher temperature factors. Structural characterization of BPDE-dA adducts by NMR to date has found the hydrocarbon intercalated only between base pairs and not in the major groove (5,6,24). To accommodate the PAH in the major groove without clashing with the neighboring base pairs, the dA* slides toward the major groove by nearly 2 Å (Fig.…”

“…1 A). Two-dimensional NMR studies (5,6) suggest that BPDE-dA adducts are intercalated between base pairs whereas BPDE-dG adducts either reside in the minor groove or are intercalated with base displacement depending on the trans or cis stereochemistry of the adducts. These bulky polycyclic aromatic hydrocarbon (PAH) adducts impede DNA replication and induce mutations by perturbing the double-helical structure.…”

The Spacious Active Site of a Y-Family DNA Polymerase Facilitates Promiscuous Nucleotide Incorporation Opposite a Bulky Carcinogen-DNA Adduct

“…A recent crystal structure has revealed the accommodation of a BPDE-adenine adduct, linked to N 6 of dA, within Dpo4. Two structures were resolved, including a proposed blocking structure with the BP moiety intercalated between adjacent base pairs, similar to that seen by high resolution NMR in duplex DNA (106), and a proposed bypass structure, with the BP moiety solvent-exposed in the major groove (76). The major groove structure showed that the enzyme can coerce the adduct into adopting a conformation that is disfavored in duplex DNA (106, 107) and on the nucleoside level (108).…”

Inhibition of Werner Syndrome Helicase Activity by Benzo[a]pyrene Diol Epoxide Adducts Can Be Overcome by Replication Protein A

“…The stereoisomeric BaP DE adducts at dG and dA provide a variety of structural motifs within duplex DNA that have been well characterized by NMR studies (24,25). For cis-opened BaP DE-dG adducts, both 10R and 10S enantiomers cause flipping out of both the modified base and its complement from the DNA helix (26,27).…”