Stereospecific formation of interstrand carbinolamine DNA cross-links by crotonaldehyde- and acetaldehyde-derived α-CH₃-γ-OH-1, N²-propano-2′-deoxyguanosine adducts in the 5′-CpG-3′ sequence

The crotonaldehyde- and acetaldehyde-derived R- and S-α-CH ₃-γ-OH-1,N²-propanodeoxyguanosine adducts were monitored in single-stranded and duplex oligodeoxynucleotides using NMR spectroscopy. In both instances, the cis and trans diastereomers of the α-CH₃ and γ-OH groups underwent slow exchange, with the trans diastereomers being favored. In single-stranded oligodeoxynucleotides, the aldehyde intermediates were not detected spectroscopically, but their presence was revealed through the formation of N-terminal conjugates with the tetrapeptide KWKK. When annealed into 5′-d(GCTAGCXAGTCC)- 3′·5′-d(GGACTCYCTAGC)-3′ containing the 5′-CpG-3′ sequence context (X = R- or S-α-CH ₃-γ-¹³C-OH-PdG; Y = ¹⁵N²-dG) at pH 7, partial opening of the R- or S-α-CH₃-γ- ¹³C-OH-PdG adducts to the corresponding N²-(3-oxo-1- methyl-propyl)-dG aldehydes was observed at temperatures below the T_m of the duplexes. These aldehydes equilibrated with their geminal diol hydrates; higher temperatures favored the aldehydes. When annealed opposite T, the S-α-CH₃-γ-¹³C-OH-PdG adduct was stable. At 37 °C, an interstrand DNA cross-link was observed spectroscopically only for the R-α-CH₃-γ-OH-PdG adduct. Molecular modeling predicted that the interstrand cross-link formed by the R-α-CH₃-γ- OH-PdG adduct introduced less disruption into the duplex structure than did the cross-link arising from the S-α-CH₃-γ-OH-PdG adduct, due to differing orientations of the R- and S-CH₃ groups. Modeling also predicted that the α-methyl group of the aldehyde arising from the R-α-CH₃-γ-OH-PdG adduct is oriented in the 3′-direction in the minor groove, facilitating cross-linking. In contrast, the α-methyl group of the aldehyde arising from the S-α-CH ₃-OH-PdG adduct is oriented in the 5′-direction within the minor groove, potentially hindering cross-linking. NMR revealed that for the R-α-CH₃-γ-OH-PdG adduct, the carbinolamine form of the cross-link was favored in duplex DNA with the imine (Schiff base) form of the cross-link remaining below the level of spectroscopic detection. Molecular modeling predicted that the carbinolamine linkage maintained Watson-Crick hydrogen bonding at both of the tandem C·G base pairs. Dehydration of the carbinolamine cross-link to an imine, or cyclization of the latter to form a pyrimidopurinone cross-link, required disruption of Watson-Crick hydrogen bonding at one or both of the cross-linked base pairs.