Major Groove Orientation of the (2<i>S</i>)‑<i>N</i><sup>6</sup>‑(2-Hydroxy-3-buten-1-yl)-2′-deoxyadenosine
DNA Adduct Induced by 1,2-Epoxy-3-butene
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Abstract
1,3-Butadiene (BD) is an environmental
and occupational toxicant
classified as a human carcinogen. It is oxidized by cytochrome P450
monooxygenases to 1,2-epoxy-3-butene (EB), which alkylates DNA. BD
exposures lead to large numbers of mutations at A:T base pairs even
though alkylation of guanines is more prevalent, suggesting that one
or more adenine adducts of BD play a role in BD-mediated genotoxicity.
However, the etiology of BD-mediated genotoxicity at adenine remains
poorly understood. EB alkylates the <i>N</i><sup>6</sup> exocyclic nitrogen of adenine to form <i>N</i><sup>6</sup>-(hydroxy-3-buten-1-yl)-2′-dA ((2<i>S</i>)-<i>N</i><sup>6</sup>-HB-dA) adducts (Tretyakova, N., Lin, Y., Sangaiah, R., Upton, P. B., and Swenberg, J. A. (1997) Carcinogenesis 18, 137−147). The structure
of the (2<i>S</i>)-<i>N</i><sup>6</sup>-HB-dA
adduct has been determined in the 5′-d(C<sup>1</sup>G<sup>2</sup>G<sup>3</sup>A<sup>4</sup><u>C</u><sup><u>5</u></sup><u>Y</u><sup><u>6</u></sup><u>A</u><sup><u>7</u></sup>G<sup>8</sup>A<sup>9</sup>A<sup>10</sup>G<sup>11</sup>)-3′:5′-d(C<sup>12</sup>T<sup>13</sup>T<sup>14</sup>C<sup>15</sup>T<sup>16</sup>T<sup>17</sup>G<sup>18</sup>T<sup>19</sup> C<sup>20</sup>C<sup>21</sup>G<sup>22</sup>)-3′ duplex [Y = (2<i>S</i>)-<i>N</i><sup>6</sup>-HB-dA] containing codon 61 (underlined) of
the human N-<i>ras</i> protooncogene, from NMR spectroscopy.
The (2<i>S</i>)-<i>N</i><sup>6</sup>-HB-dA adduct
was positioned in the major groove, such that the butadiene moiety
was oriented in the 3′ direction. At the C<sub>α</sub> carbon, the methylene protons of the modified nucleobase Y<sup>6</sup> faced the 5′ direction, which placed the C<sub>β</sub> carbon in the 3′ direction. The C<sub>β</sub> hydroxyl
group faced toward the solvent, as did carbons C<sub>γ</sub> and C<sub>δ</sub>. The C<sub>β</sub> hydroxyl group
did not form hydrogen bonds with either T<sup>16</sup> <i>O</i><sup>4</sup> or T<sup>17</sup> <i>O</i><sup>4</sup>. The
(2<i>S</i>)-<i>N</i><sup>6</sup>-HB-dA nucleoside
maintained the <i>anti</i> conformation about the glycosyl
bond, and the modified base retained Watson–Crick base pairing
with the complementary base (T<sup>17</sup>). The adduct perturbed
stacking interactions at base pairs C<sup>5</sup>:G<sup>18</sup>,
Y<sup>6</sup>:T<sup>17</sup>, and A<sup>7</sup>:T<sup>16</sup> such
that the Y<sup>6</sup> base did not stack with its 5′ neighbor
C<sup>5</sup>, but it did with its 3′ neighbor A<sup>7</sup>. The complementary thymine T<sup>17</sup> stacked well with both
5′ and 3′ neighbors T<sup>16</sup> and G<sup>18</sup>. The presence of the (2<i>S</i>)-<i>N</i><sup>6</sup>-HB-dA resulted in a 5 °C reduction in the <i>T</i><sub>m</sub> of the duplex, which is attributed to less favorable
stacking interactions and adduct accommodation in the major groove