Structure of the 1,4-bis(2′-deoxyadenosin-N⁶-yl)-2S,3S- butanediol intrastrand DNA cross-link arising from butadiene diepoxide in the human N-ras codon 61 sequence

The 1,4-bis(2′-deoxyadenosin-N⁶-yl)-2S,3S-butanediol intrastrand DNA cross-link arises from the bis-alkylation of tandem N ⁶-dA sites in DNA by R,R-butadiene diepoxide (BDO₂). The oligodeoxynucleotide 5′-d(C¹G²G³A ⁴C⁵X⁶Y⁷G⁸A ⁹A¹⁰G¹¹)-3′·5′-d(C ¹²T¹³T¹⁴C¹⁵T¹⁶T ¹⁷G¹⁸T¹⁹C²⁰C²¹G ²²)-3′ contains the BDO₂ cross-link between the second and third adenines of the codon 61 sequence (underlined) of the human N-rai protooncogene and is named the (S,S)-BD-(61-2,3) cross-link (X,Y = cross-linked adenines). NMR analysis reveals that the cross-link is oriented in the major groove of duplex DNA. Watson-Crick base pairing is perturbed at base pair X⁶·T¹⁷, whereas base pairing is intact at base pair Y⁷·T¹⁶. The cross-link appears to exist in two conformations, in rapid exchange on the NMR time scale. In the first conformation, the β-OH is predicted to form a hydrogen bond with T ¹⁶ O⁴, whereas in the second, the β-OH is predicted to form a hydrogen bond with T¹⁷ O⁴. In contrast to the (R,R)-BD-(61-2,3) cross-link in the same sequence (Merritt, W. K., Nechev, L. V., Scholdberg, T. A., Dean, S. M., Kiehna, S. E., Chang, J. C., Harris, T. M., Harris, C. M., Lloyd, R. S., and Stone, M. P. (2005) Biochemistry 44, 10081-10092), the anti-conformation of the two hydroxyl groups at C _β and C_γ with respect to the C _β-C_γ bond results in a decreased twist between base pairs X⁶·T¹⁷ and Y⁷·T ¹⁶, and an approximate 10° bending of the duplex. These conformational differences may account for the differential mutagenicity of the (S,S)- and (R,R)-BD-(61-2,3) cross-links and suggest that stereochemistry plays a role in modulating biological responses to these cross-links (Kanuri, M., Nechev, L. V., Tamura, P. J., Harris, C. M., Harris, T. M., and Lloyd, R. S. (2002) Chem. Res. Toxicol. 15, 1572-1580).