NMR Solution Structure of an Oligodeoxynucleotide Duplex Containing the Exocyclic Lesion 3,N⁴-Etheno-2‘-deoxycytidine Opposite Thymidine:  Comparison with the Duplex Containing Deoxyadenosine Opposite the Adduct

Abstract

The exocyclic 3,N4-etheno-2'-deoxycytidine adduct was incorporated at the center of the oligodeoxynucleotide duplex d(C-G-T-A-C-epsilon C-C-A-T-G-C).d (G-C-A-T-G-T-G-T-A-C-G), and its solution structure was analyzed using high-resolution proton NMR spectroscopy and molecular dynamics simulations. The experimental data indicate that the oligodeoxynucleotide duplex adopts a right-handed helical structure with sugar puckers in the C2'-endo/C3'-exo range and Watson-Crick hydrogen bond alignments for all base pairs. NOE connectivities established a syn orientation for the glycosidic torsion angle of the exocyclic adduct. Restrained molecular dynamics simulations, using the full relaxation matrix approach, produced a three-dimensional model in agreement with the experimental data. The structure shows only minor perturbations in the sugar-phosphate backbone and a 27 degrees bend of the helical axis at the lesion site. On the refined model a well-formed hydrogen bond between T (N3H) and epsilon C(N4) stabilizes the epsilon C(syn).T(anti) base pair alignment, reflecting the preference of the adduct for the syn orientation. Furthermore, the epsilon C(syn).T(anti) base pair stacks with flanking base pairs. We discuss a correlation between the mutagenic properties of the adduct and the three-dimensional structure of the epsilon C.dA and epsilon C.T duplexes.

Structure of the 1,N2-Etheno-2′-Deoxyguanosine Adduct in Duplex DNA at pH 8.6

“…NMR studies reveal that PdG disrupts duplex DNA (39,40,43,44). At neutral pH, and similar to the present observations for the 1,N 2 -εdG adduct, it has not been possible to obtain a refined structure for PdG positioned opposite cytosine in duplex DNA.…”

“…When the εdC•G base pair was examined by NMR (43), both nucleotides were in the anti conformation about the glycosyl bond. On the other hand, in the εdC•T base pair, εdC existed in the syn orientation about the glycosyl bond, whereas the mismatched T remained in the anti conformation (43).…”

Replication of non-hydrogen bonded bases by DNA polymerases: A mechanism for steric matching

“…Analogue C has been shown to adopt a syn orientation with a hydrogen bond to T opposite it in a duplex, for example. 48 The adduct dA cannot form hydrogen bonds in standard anti orientation since both of the underlying adenine H-bonding groups are blocked by the etheno substitution. However, as with C, A can form hydrogen bonds by adopting a syn orientation, which allows it to form up to two hydrogen bonds with a partner base.…”

3, N 4 -ethenocytosine, a highly mutagenic adduct, is a primary substrate for Escherichia coli double-stranded uracil-DNA glycosylase and human mismatch-specific thymine-DNA glycosylase

“…Sci. USA 95 (1998) duplexes containing C͞T, C͞G, or C͞A mismatches (42)(43)(44), will be of interest for structural investigations aiming to elucidate the molecular mechanisms involved in the catalytic action of the dsUDG. Therefore, the human and the E. coli enzymes exhibit the same substrate specificity.…”