N7 methylation alters hydrogen-bonding patterns of guanine in duplex DNA

Abstract

N7-Alkyl-2'-deoxyguanosines are major adducts in DNA that are generated by various alkylating mutagens and drugs. However, the effect of the N7 alkylation on the hydrogen-bonding patterns of the guanine remains poorly understood. We prepared N7-methyl-2'-deoxyguanosine (N7mdG)-containing DNA using a transition-state destabilization strategy, developed a novel polβ-host-guest complex system, and determined eight crystal structures of N7mdG or dG paired with dC, dT, dG, and dA. The structures of N7mdG:dC and N7mdG:dG are very similar to those of dG:dC and dG:dG, respectively, indicating the involvement of the keto tautomeric form of N7mdG in the base pairings with dC and dG. On the other hand, the structure of N7mdG:dT shows that the mispair forms three hydrogen bonds and adopts a Watson-Crick-like geometry rather than a wobble geometry, suggesting that the enol tautomeric form of N7mdG involves in its base pairing with dT. In addition, N7mdG:dA adopts a novel shifted anti:syn base pair presumably via the enol tautomeric form of N7mdG. The polβ-host-guest complex structures reveal that guanine-N7 methylation changes the hydrogen-bonding patterns of the guanine when paired with dT or dA and suggest that N7 alkylation may alter the base pairing patterns of guanine by promoting the formation of the rare enol tautomeric form of guanine.

Figure 1

Structure determination of N7mdG-containing DNA using a transition-state destabilization strategy and polβ host-guest-complex (HGC) system. (A) The keto and enol tautomeric forms of N7-alkyl-dG. (B) Preparation of N7mdG-containing DNA using a 2′-fluorine-mediated transition-state destabilization strategy. (C) Overall structure of N7mdG:dT-containing DNA that is determined by polβ HGC system. The base pairs at the 5′ end of the upstream primer are devoid of protein contact and adopt the B-DNA conformation.

Figure 2

Effect of guanine N7-methylation on base pairing properties of guanine. Hydrogen bonding patterns of: (A) dG:dC, (B) N7mdG:dC, (C) dG:dT, (D) N7mdG:dT, (E) dG:dG, (F) N7mdG:dG, (G) dG:dA and (H) N7mdG:dA. 2F_o-F_c electron density maps contoured at 1σ around the base pairs in polβ-HGC complexes. The base pair geometry including the C1′-C1′ distances and λ angles is shown.

Figure 3

Effect of guanine N7 methylation on the conformation of dG:dT- or dG:dA-containing DNA. (A) Comparison of the dG:dT- and N7mdG:dT-containing DNA. (B) Comparison of base pair conformation of dG:dT and N7mdG:dT. (C) The formation of Watson-Crick-like N7mdG:dT pair via the enol tautomeric form of N7mdG. (D) Comparison of dG:dA- and N7mdG:dA-containing DNA. (E) Comparison of base pair conformation of dG:dA and N7mdG:dA. (F) The formation of the shifted N7mdG:dA base pair via the enol tautomeric form of N7mdG.