Crystallographic Characterization of an Exocyclic DNA Adduct: 3,N4-etheno-2′-deoxycytidine in the Dodecamer 5′-CGCGAATTεCGCG-3′

Abstract

Exocyclic DNA adducts are formed from metabolites of chemical carcinogens and have also been detected as endogenous lesions in human DNA. The exocyclic adduct 3,N4-etheno-2′-deoxycytidine (εdC), positioned opposite deoxyguanosine in the B-form duplex of the dodecanucleotide d(CGCGAATTεCGCG), has been crystallographically characterized at 1.8Å resolution. This self-complementary oligomer crystallizes in space group P3212, containing a single strand in the asymmetric unit. The crystal structure was solved by isomorphous replacement with the corresponding unmodified dodecamer structure. Exposure of both structures to identical crystal packing forces allows a detailed investigation of the influence of the exocyclic base adduct on the overall helical structure and local geometry. Structural changes are limited to the εC:G and adjacent T:A and G:C base-pairs. The standard Watson–Crick base-pairing scheme, retained in the T:A and G:C base-pairs, is blocked by the etheno bridge in the εC:G pair. In its place, a hydrogen bond involving O2 of εC and N1 of G is present. Comparison with an εdC-containing NMR structure confirms the general conformation reported for εC:G, including the hydrogen bonding features. Superposition with the crystal structure of a DNA duplex containing a T:G wobble pair shows similar structural changes imposed by both mismatches. Evaluation of the hydration shell of the duplex with bond valence calculations reveals two sodium ions in the crystal.