Structures of exocyclic R,R - And S,S - N⁶, N ⁶-(2,3-dihydroxybutan-1,4-diyl)-2′-deoxyadenosine adducts induced by 1,2,3,4-diepoxybutane

1,3-Butadiene (BD) is an industrial and environmental chemical present in urban air and cigarette smoke, and is classified as a human carcinogen. It is oxidized by cytochrome P450 to form 1,2,3,4-diepoxybutane (DEB); DEB bis-alkylates the N⁶ position of adenine in DNA. Two enantiomers of bis-N⁶-dA adducts of DEB have been identified: R,R-N ⁶,N⁶-(2,3-dihydroxybutan-1,4-diyl)-2′- deoxyadenosine (R,R-DHB-dA), and S,S-N⁶,N⁶-(2,3- dihydroxybutan-1,4-diyl)-2′-deoxyadenosine (S,S-DHB-dA) [ Seneviratne, U., Antsypovich, S., Dorr, D. Q., Dissanayake, T., Kotapati, S., and Tretyakova, N. (2010) Chem. Res. Toxicol. 23, 1556-1567 ]. Herein, the R,R-DHB-dA and S,S-DHB-dA adducts have been incorporated into the 5′-d(C ¹G²G³A⁴C⁵X ⁶A⁷G⁸A⁹A¹⁰G ¹¹)-3′:5′-d(C¹²T¹³T ¹⁴C¹⁵T¹⁶T¹⁷G¹⁸T ¹⁹C²⁰C²¹G²²)-3′ duplex [X ⁶ = R,R-DHB-dA (R⁶) or S,S-DHB-dA (S⁶)]. The structures of the duplexes were determined by molecular dynamics calculations, which were restrained by experimental distances obtained from NMR data. Both the R,R- and S,S-DHB-dA adducts are positioned in the major groove of DNA. In both instances, the bulky 3,4-dihydroxypyrrolidine rings are accommodated by an out-of-plane rotation about the C6-N⁶ bond of the bis-alkylated adenine. In both instances, the directionality of the dihydroxypyrrolidine ring is evidenced by the pattern of NOEs between the 3,4-dihydroxypyrrolidine protons and DNA. Also in both instances, the anti conformation of the glycosyl bond is maintained, which combined with the out-of-plane rotation about the C6-N ⁶ bond, allows the complementary thymine, T¹⁷, to remain stacked within the duplex, and form one hydrogen bond with the modified base, between the imine nitrogen of the modified base and the T¹⁷ N3H imino proton. The loss of the second Watson-Crick hydrogen bonding interaction at the lesion sites correlates with the lower thermal stabilities of the R,R- and S,S-DHB-dA duplexes, as compared to the corresponding unmodified duplex. The reduced base stacking at the adduct sites may also contribute to the thermal instability.