Structural Alignment of the (+)-trans-anti-Benzo[a]pyrene-dG Adduct Positioned Opposite dC at a DNA Template-Primer Junction
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This study reports on the solution conformation of thecovalent (+)-trans-anti-[BP]dG adduct(derived from the binding of the highly mutagenic and tumorigenic(+)-anti-benzo[a]pyrene diolepoxideto the N2 of deoxyguanosine)positioned opposite dC at a junctional site in thed(A1-A2-C3-[BP]G4-C5-T6-A7-C8-C9-A10-T11-C12-C13)·d(G14-G15-A16-T17-G18-G19-T20-A21-G22-C23)13/10-mer DNAsequence. The 13-mer represents the template strand containing thejunction [BP]dG4 lesion while thecomplementary 10-mer models a primer strand which extends upto and iscomplementary to the modifieddG4 residue. The solution conformation has been determined byinitially incorporating intramolecularand intermolecular proton-proton distances defined by lower and upperbounds deduced from NOESYspectra as restraints in molecular mechanics computations in torsionangle space and subsequently throughrestrained molecular dynamics calculations based on a NOE distance andintensity refinement protocol.The duplex segment retains a minimally perturbed B-DNAconformation with all base pairs, includingthe junctional [BP]dG4·dC23 pair, in Watson-Crickhydrogen-bonded alignments. The pyrenyl ring isnot stacked over the adjacent dC5·dG22 base pair but ispositioned on the minor groove-side of the[BP]dG moiety and directed toward the 5'-end of the templatestrand. The pyrenyl ring stacks over thebase of the non-adjacent dA2 residue in one direction and the sugarring of dC23 in the other direction.The solution structure of the(+)-trans-anti-[BP]dG adduct opposite dC in the13/10-mer in which themodified deoxyguanosine adopts an anti glycosidic torsionangle (this study) is in striking contrast to thestructure of the same (+)-trans-anti-[BP]dG moietyin a 13/9-mer of the same sequence but without thedC23 residue positioned opposite the adduct site [Cosman, M., et al.(1995) Biochemistry 34, 15334-15350]. For the latter case, the aromatic portion of the BPresidue stacks over the adjacent dC5·dG22base pair, the modified deoxyguanosine adopts a synglycosidic torsion angle and is displaced toward themajor groove direction. Insights into the factors that affect thesequence and context dependentconformations of stereoisomeric [BP]dG lesions have emergedfollowing comparison of these two structureswith the minor groove conformations of the same(+)-trans-anti-[BP]dG lesion in the fullycomplementary11-mer duplex [Cosman, M., et al. (1992) Proc. Natl. Acad. Sci.U.S.A. 89, 1914-1918] and inthe basedisplaced-intercalative conformation of the 11/10-mer deletion duplexcontaining a -1 deletion site oppositethe lesion [Cosman, M., et al. (1994) Biochemistry 33,11507-11517]. The contributing factors whereapplicable include Watson-Crick base pairing at the site of thelesion, positioning of the carcinogenwithin the floor of the minor groove, and the tendency of the bulkyhydrophobic aromatic BP residue toassume stacked or intercalative conformations.

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