Solution Structure of a DNA Duplex Containing the Exocyclic Lesion 3,N⁴-Etheno-2‘-deoxycytidine Opposite 2‘-Deoxyguanosine

Abstract

Vinyl chloride reacts with cellular DNA producing 3,N4-etheno-2'-deoxycytidine (epsilonC) along with other exocyclic adducts. The solution structure of an oligodeoxynucleotide duplex containing an epsilonC.dG base pair was determined by high-resolution NMR spectroscopy and molecular dynamics simulations. NMR data indicated that the duplex adopts a right-handed helical structure having all residues in anti orientation around the glycosylic torsion angle. The epsilonC adduct has a sugar pucker in the C3'-endo/C4'-exo region while the rest of the residues are in the C2'-endo/C3'-exo range. NOE interactions established Watson-Crick alignments for canonical base pairs of the duplex. The imino proton of the lesion-containing base pair resonated as a sharp signal that was resistant to water exchange, suggesting hydrogen bonding. Restrained molecular dynamics simulations generated three-dimensional models in excellent agreement with the spectroscopic data. The refined structures are slightly bent at the lesion site without major perturbations of the sugar-phosphate backbone. The adduct is displaced and shifted toward the major groove of the helix while its partner on the complementary strand remains stacked. The epsilonC(anti).dG(anti) base pair alignment is sheared and stabilized by the formation of hydrogen bonds. The biological implications of structures of epsilonC-containing DNA duplexes are discussed.

8-(Hydroxymethyl)-3,N4-etheno-C, a Potential Carcinogenic Glycidaldehyde Product, Miscodes In Vitro Using Mammalian DNA Polymerases

“…In addition, the base pairing preferences are similar for both the 8-HM-εC and εC-containing oligonucleotides. The latter compound is closely related structurally to 8-HM-εC and it has been established that it is a mutagenic lesion (24)(25)(26)(27)(28)(29). Moreover, by molecular modeling, we showed that little difference exists in the planarity and sugar conformations of the two derivatives in duplex DNA.…”

The Main Role of Human Thymine-DNA Glycosylase Is Removal of Thymine Produced by Deamination of 5-Methylcytosine and Not Removal of Ethenocytosine

“…Also, the guanine and thymine are stacked well with the adjacent bases in the DNA helix. Although the NMR structure of a G ⅐ ⑀ C base pair reveals a similar wobble geometry, this base pair is much more distorted, and there is only one hydrogen bond between the ethenocytosine and the guanine (42). In addition to this weaker hydrogen bonding, the ethenocytosine base is very poorly stacked with the adjacent bases, suggesting that the G ⅐ ⑀ C base pair is considerably less stable than a G ⅐T mismatch.…”

“…Schematic diagram of the normal Watson-Crick A⅐T base pair and the two mismatches, G ⅐T and G ⅐ ⑀ C. The G ⅐T mismatch is based on the structures found by NMR (41) and crystallographic (40) studies. The G ⅐ ⑀ C base pair is based on a structure determined by NMR (42). Note that in the A⅐T and G ⅐T structures the two bases of each base pair are in the same plane, whereas in the G ⅐ ⑀ C structure the ethenocytosine is distorted out of the plane preventing proper stacking with the flanking bases.…”

Hijacking of the Human Alkyl-N-purine-DNA Glycosylase by 3,N4-Ethenocytosine, a Lipid Peroxidation-induced DNA Adduct

“…Specific binding of ANPG to ⑀C⅐G suggests that the enzyme recognizes ⑀C in the active site pocket; however, in contrast to MUG and hTDG, is not able to excise the adduct. Cullinan et al (53,54) have shown by computer modeling that the ⑀C nucleoside fits neatly into the active site of ANPG. However, these authors proposed that ANPG is not able to extrude the ⑀C residue from duplex DNA.…”