Structure of the 1,N²-Propanodeoxyguanosine Adduct in a Three-Base DNA Hairpin Loop Derived from a Palindrome in the Salmonella typhimurium hisD3052 Gene

The solution structure of the 1,N²-propanodeoxyguanosine (PdG) adduct was determined in a 3-base hairpin loop formed by d(CGCGGTXTCCGCG) (X = PdG). This sequence is contained within the Salmonella typhimurium hisD3052 gene, a hotspot for frameshift mutagenesis. PdG provides a structural model for the primary adduct induced in DNA by malondialdehyde, the 3-(2‘-deoxy-β-d-erythro-pentofuranosyl)pyrimido[1,2-a]-purin-10(3H)-one (M₁G) lesion. The solution structure of the PdG-containing hairpin was refined by molecular dynamics calculations restrained by a combination of NMR-derived distances and dihedral angles, using a simulated annealing protocol. The structure of the PdG-modified hairpin consisted of a five-base-pair stem and a three-base loop consisting of T⁶, X⁷, and T⁸. T⁶ projected into the minor groove of the stem adjacent to G⁴. The modified base X⁷ stacked on top of the duplex stem and wedged between bases T⁸ and C⁹. The PdG moiety was oriented such that the imidazole proton was facing the minor groove of the stem and the exocyclic protons projected into the major groove. The structure of the adducted hairpin was compared with the structure of the corresponding unmodified oligodeoxynucleotide, and was found to be similar. There was a minor difference in the backbone angles of the G and PdG Hairpins at the phosphate linkage between G⁵ and T⁶ involving the G⁵ ε angle and T⁶ α and β angles. The PdG-modified hairpin exhibited an increase in T_m of ∼2 °C compared to the unmodified hairpin. The structural and thermodynamic similarities suggested that PdG does not stabilize this hairpin and thus may not promote its extrusion in duplex DNA. The structural results are correlated with the results of site-specific mutagenesis experiments in the same sequence, which do not show evidence of frameshift mutations associated with hairpin loop formation. The geometry of this three-base loop is similar to that of other DNA hairpins containing three-base loops, and suggests a common motif for the folding of these loops.