Figure 1.

The adducted regions of the oligodeoxynucleotide duplexes containing the 5′-CpX-3′ sequence, viewed from the minor grooves. A. Average refined structure emergent from rMD calculations of the duplex containing cyclic hemiacetal 8. B. Predicted structure, obtained by molecular mechanics calculations, of the duplex containing aldehyde 6. The dashed arrows indicate the spatial relationship between the reactive aldehyde carbon and the exocyclic amino nitrogen of cross-linking target G¹⁹ (7.1 Å). C. Average refined structure emergent from rMD calculations of the duplex containing cyclic hemiacetal 10. D. Predicted structure, obtained by molecular mechanics calculations, of the duplex containing aldehyde 7. The cyan sticks represent nucleotides. The blue sticks represent the two amino nitrogens of X⁷ and G¹⁹. The white, green, and red sticks represent hydrogens, carbons, and oxygens of the HNE moiety. The dashed arrows indicate the spatial relationship between the reactive aldehyde carbon and the exocyclic amino nitrogen of cross-linking target G¹⁹ (4.4 Å). Adopted with permission from Huang et al., Biochemistry 2008 47: 11457-11472. Copyright 2008 American Chemical Society.