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-N6,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) [SeneviratneU.AntsypovichS.DorrD. Q.DissanayakeT.KotapatiS.TretyakovaN.SeneviratneU.AntsypovichS.DorrD. Q.DissanayakeT.KotapatiS.TretyakovaN.20873715Chem. Res. Toxicol.2010231556]. Herein, the R,R-DHB-dA and S,S-DHB-dA adducts have been incorporated into the 5′-d(C1G2G3A4C5X6A7G8A9A10G11)-3′:5′-d(C12T13T14C15T16T17G18T19C20C21G22)-3′
duplex [X6 = 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-N6 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.