The conformation of the crotonaldehyde-derived N(2)-[3-oxo-1(S)-methyl-propyl]-dG adduct in the oligodeoxynucleotide 5'-d(G(1)C(2)T(3)A(4)G(5)C(6)X(7)A(8)G(9)T(10)C(11)C(12))-3'.5'-d(G(13)G(14)A(15)C(16)T(17)C(18)G(19)C(20)T(21)A(22)G(23)C(2)(4))-3', where X = N(2)-[3-oxo-1(S)-methyl-propyl]-dG, is reported. This adduct arises from opening of the cyclic N(2)-(S-alpha-CH(3)-gamma-OH-1,N(2)-propano-2')-dG adduct when placed opposite dC in duplex DNA. This oligodeoxynucleotide contains the 5'-CpG-3' sequence in which the N(2)-(R-alpha-CH(3)-gamma-OH-1,N(2)-propano-2')-dG but not the N(2)-(S-alpha-CH(3)-gamma-OH-1,N(2)-propano-2')-dG adduct preferentially formed an interstrand carbinolamine cross-link [Kozekov, I. D., Nechev, L. V., Moseley, M. S., Harris, C. M., Rizzo, C. J., Stone, M. P., and Harris, T. M. (2003) J. Am. Chem. Soc. 125, 50-61; Cho, Y.-J., Wang, H., Kozekov, I. D., Kurtz, A. J., Jacob, J., Voehler, M., Smith, J., Harris, T. M., Lloyd, R. S., Rizzo, C. J., and Stone, M. P. (2006) Chem. Res. Toxicol. 19, 195-208]. Analysis of (1)H NOE data, chemical shift perturbations, and deoxyribose pseudorotations and backbone torsion angles suggested the presence of a stable and ordered DNA conformation at pH 9.3 and 30 degrees C, with minimal conformational perturbation. The spectral line widths of the adduct protons were comparable to those of the oligodeoxynucleotide, suggesting that the correlation times of these protons were similar to those of the overall duplex. The crotonaldehydic-derived methyl protons showed NOEs in the 5'-direction to C(18) H1', G(19) H1', and G(19) H4' in the complementary strand of the duplex. The aldehyde proton of the adduct exhibited NOEs in the 3'-direction to A(8) H1' and A(8) H4' in the modified strand. All of these NOEs involved DNA protons facing the minor groove. Molecular dynamics calculations, restrained by distances and torsion angles derived from the NMR data, revealed that within the minor groove, the aldehyde of the N(2)-[3-oxo-1(S)-methyl-propyl]-dG adduct oriented in the 3'-direction, while the 1(S) methyl group oriented in the 5'-direction. This positioned the aldehyde distal to the G(19) exocyclic amine and provided a rationale as to why the N(2)-(S-alpha-CH(3)-gamma-OH-1,N(2)-propano-2')-dG adduct generated interstrand cross-links less efficiently than did the N(2)-(R-alpha-CH(3)-gamma-OH-1,N(2)-propano-2')-dG adduct.