Solution Conformation of the (-)-trans-anti-5-Methylchrysene-dG Adduct opposite dC in a DNA Duplex: DNA Bending Associated with Wedging of the Methyl Group of 5-Methylchrysene to the 3'-Side of the Modification Site

Abstract

This paper reports on NMR-molecular mechanics structural studies of the (-)-trans-anti-[MC]dG adduct positioned opposite dC in the sequence context of the d(C1-C2-A3-T4-C5-[MC]G6-C7-T8-A9-C10-C11).d(G12-G13-T14++ +-A15-G16-C17-G18- A19-T20-G21-G22) duplex [designated (-)-trans-anti-[MC]dG.dC 11-mer duplex]. This adduct is derived from the trans addition at C4 of (-)-anti-1(S),2(R)-dihydroxy-3(R),4(S)-epoxy-1,2,3,4-tetrahydro-5-met hylchrysen e [(-)-anti-5-MeCDE] to the N2 position of dG6 in this duplex sequence. The 5-methyl group is located adjacent to the MC(C4) binding site, with these groups juxtaposed in a sterically crowded bay region in the adduct duplex. The 5-methylchrysenyl and the nucleic acid exchangeable and nonexchangeable protons were assigned following analysis of two-dimensional NMR data sets in H2O and D2O buffer solution. The solution structure of the (-)-trans-anti-[MC]dG.dC 11-mer duplex has been determined by incorporating DNA-DNA and carcinogen-DNA proton-proton distances defined by lower and upper bounds deduced from NOESY data sets as restraints in molecular mechanics computations in torsion angle space. The results establish that the [MC]dG6.dC17 base pair and flanking dC5.dG18 and dC7.dG16 base pairs retain Watson-Crick alignments upon adduct formation. The aromatic chrysenyl ring is positioned in the minor groove of a right-handed B-DNA helix and stacks predominantly over the sugar of the dC17 residue across from it on the unmodified complementary strand. The chrysenyl ring points toward the 3'-end of the modified strand with its 5-methyl group inserting between the modified [MC]dG6.dC17 and dC7.dG16 base pairs. The adduct duplex bends by approximately 47 degrees as a result of the wedged insertion of the 5-methyl group from the minor groove face of the duplex. The solution structure of the (-)-trans-anti-[MC] dG.dC 11-mer duplex is compared with that of the corresponding (-)-trans-anti-[BP]dG.dC 11-mer [De los Santos et al. (1992) Biochemistry 31, 5245-5252] in which the [BP]dG adduct is derived from the binding of (-)-anti-BPDE [7(S),8(R)-dihydroxy-9(R),10(S)-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene] to the N2 position in the same DNA sequence context. Although the solution structures of the (-)-trans-anti-stereoisomers of 5-methylchrysenyl-dG and benzo[a]pyrenyl-dG adducts opposite dC exhibit many features in common with each other, the [MC]dG adduct which contains a bay region methyl group bends the DNA helix to a greater extent than in the corresponding [BP]dG adduct, which lacks a bay region methyl group.(ABSTRACT TRUNCATED AT 400 WORDS)

Site-specific adducts derived from the binding of anti-5-methylchrysene diol epoxide enantiomers to DNA: Synthesis and characteristics

“…The adduct duplexes derived from both of these tumorigenic (-l-)-enantiomers are characterized by greater apparent extents of bending or flexibilities at the sites of the lesions than the stereoisomeric adducts derived from the chiral, non-tumorigenic (-)-enantiomers (Table I). These differences appear to be primarily linked to stereochemical factors, even though the methyl group in the case of the (-)-anr/-5-MeCDEmodified 11-mer duplexes does cause significant alterations in the local DNA conformation (21). However, the relationships between the structural differences between DNA lesions derived from the ( + )-and (-)-enantiomers, and the differences in their biological activities, are not yet clear.…”

“…The T m values are similar in all cases. Most likely this is due to the fact that the PAH residues are positioned in the minor grooves in at least three of these duplexes (19)(20)(21). sequences in a native gel are shown in Figure 8.…”

“…Total and post-oligomerization methods can be used to synthesize sitespecifically modified oligonucleotides with PAH-substituted bases (13)(14)(15)(16)(17)(18). We have successfully adopted a direct synthesis approach to generate a variety of site-specifically substituted PAH-oligonucleotide adducts (17,18) in milligram quantities for NMR (19)(20)(21) and other structural studies (22,23).…”

“…NMR structural studies for sitespecific (+)-and (-)-BPDE-dG-modified oligonucleotides in the same sequence have been described (19,20). Analogous NMR structural studies for (-)-5-MeCDE-N 2 -dG lesions in the same sequence context have also been published (21), and are in progress in the case of the analogous (+)-5-MeCDE-N 2 -dG adducts.…”

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

“…When placed opposite C 4 , the 1R-B[c]Ph dG adduct modestly inhibited enzymatic activity, and when opposite C 3 , it completely abolished enzymatic activity (25). (26), including stereochemistry (27,28), PAH topology (29)(30)(31), DNA sequence (32), and whether the adducts are incorporated into model primer-template junctions (33,34) or interact with DNA polymerases (35,36). The need to accommodate the bulky fjord region PAH into the DNA helix, concomitant with maximizing aromatic stacking interactions of the PAH, provides a primary determinant of the conformations of N 6 -dA and N 2 -dG trans-anti-B[c]Ph adducts in DNA.…”