Nitrogen-15 nuclear magnetic resonance studies on the tautomerism of 8-hydroxy-2'-deoxyguanosine, 8-hydroxyguanosine, and other C8-substituted guanine nucleosides

Cho, Bongsup P.; Kadlubar, Fred F.; Culp, Sandra J.; Evans, Frederick E.

doi:10.1021/tx00017a010

Cited by 75 publications

(57 citation statements)

References 34 publications

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“…1B). Since, at physiological pH, 8-oxoG exists predominantly in a 6,8-diketo form and is protonated at N7 (2,20), the presence of a hydrogen atom at N7 would disrupt hydrogen bonding at this position because of a steric clash with the N3 hydrogen in thymine, and that could impair the incorporation of T that is normally observed opposite an undamaged G. The incorporation of a C opposite 8-oxoG would also be hindered if the dCTP is protonated in the Pol active site as we have suggested before (14).…”

Section: Resultsmentioning

confidence: 99%

Role of Hoogsteen Edge Hydrogen Bonding at Template Purines in Nucleotide Incorporation by Human DNA Polymerase ι

Johnson

Haracska

Prakash

et al. 2006

Molecular and Cellular Biology

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Human DNA polymerase (Pol ) differs from other DNA polymerases in that it exhibits a marked template specificity, being more efficient and accurate opposite template purines than opposite pyrimidines. The crystal structures of Pol with template A and incoming dTTP and with template G and incoming dCTP have revealed that in the Pol active site, the templating purine adopts a syn conformation and forms a Hoogsteen base pair with the incoming pyrimidine which remains in the anti conformation. By using 2-aminopurine and purine as the templating residues, which retain the normal N7 position but lack the N 6 of an A or the O 6 of a G, here we provide evidence that whereas hydrogen bonding at N 6 is dispensable for the proficient incorporation of a T opposite template A, hydrogen bonding at O 6 is a prerequisite for C incorporation opposite template G. To further analyze the contributions of O 6 and N7 hydrogen bonding to DNA synthesis by Pol , we have examined its proficiency for replicating through the 6 O-methyl guanine and 8-oxoguanine lesions, which affect the O 6 and N7 positions of template G, respectively. We conclude from these studies that for proficient T incorporation opposite template A, only the N7 hydrogen bonding is required, but for proficient C incorporation opposite template G, hydrogen bonding at both the N7 and O 6 is an imperative. The dispensability of N 6 hydrogen bonding for proficient T incorporation opposite template A has important biological implications, as that would endow Pol with the ability to replicate through lesions which impair the Watson-Crick hydrogen bonding potential at both the N1 and N 6 positions of templating A.Human DNA polymerase (Pol ), a member of the Y family of polymerases, differs from other DNA polymerases in that it incorporates nucleotides opposite template purines with a much higher efficiency and fidelity than opposite template pyrimidines (4,6,19,21,26). Pol exhibits the highest efficiency and fidelity opposite template A, where it misincorporates nucleotides with frequencies of ϳ10 Ϫ4 to 10 Ϫ5 ; opposite template G, Pol incorporates a C with an efficiency that is 5-to 10-fold reduced compared to a T opposite template A, and a T is misincorporated opposite template G with an efficiency that is only a fewfold-lowered than that for a C. Pol 's efficiency and fidelity are much reduced opposite pyrimidine templates, particularly opposite template T (4, 6, 19, 21, 26).The ternary crystal structures of Pol with template A and incoming dTTP and with template G and incoming dCTP have shown that the purine template adopts a syn conformation in the Pol active site and forms a Hoogsteen base pair with the incoming nucleotide which remains in the anti conformation (14, 16). The binding of the pyrimidine nucleotide induces a conformational change in the template purine from anti to syn in the Pol active site, and that results because the active site can accommodate only the ϳ8.6-Å C 1 Ј-C 1 Ј distance of sugars in a Hoogsteen base pair but not the C 1 Ј-C 1 Ј distance of ϳ1...

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Section: Resultsmentioning

confidence: 99%

Role of Hoogsteen Edge Hydrogen Bonding at Template Purines in Nucleotide Incorporation by Human DNA Polymerase ι

Johnson

Haracska

Prakash

et al. 2006

Molecular and Cellular Biology

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“…However, in that case, it was not caused by a tautomeric shift, since it appears that this oxidized base exists, under physiological conditions, in a single tautomeric N1-H, N7-H, 6,8-dioxo form [43][44][45]. The formation of the nonmutagenic Watson-Crick-type 8-oxoG : C pair with 8-oxodG in anti conformation and the mutagenic Hoogsteen-type 8-oxoG : A pair with 8-oxodG in syn conformation was proposed on the basis of NMR spectra of designed oligodeoxynucleotide complexes [46,47].…”

Section: Figure 4 Tautomeric Forms Of Igmentioning

confidence: 93%

Neighbouring bases in template influence base-pairing of isoguanine

Maciejewska

Lichota

Kuśmierek

2003

Biochemical Journal

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Assuming that the efficiency of the incorporation of 5-methyl-2h-deoxyisocytosine-5h triphosphate (dMiCTP) and dTTP opposite isoguanine (iG) is a measure of the proportion of the keto and enol tautomers of iG in the Thermus aquaticus DNA polymerase active centre, we studied the influence of temperature and iGneighbouring bases in the template on base-pairing of iG. On the basis of experiments with four sequences (3h-TXT-5h, 3h-GXG-5h, 3h-CXC-5h, 3h-CXT-5h, where X l iG) at 37, 50, 65 and 80 mC, we found that 3h-neighbours decrease the fraction of the keto tautomer in the order C G T, whereas temperature apparently does not influence the tautomeric equilibrium of iG. The variability of the ratio of incorporation of dMiCTP versus dTTP (5-20) primarily reflects the variability of K m values, since

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“…This activity, referred to in this paper as enzyme A, was purified =120-fold from crude extracts prepared from an xth mutant of E. coli K-12. By using standard assay conditions, 0.4 pmol (80%) ofa duplex 23- (2).…”

Section: Methodsmentioning

confidence: 99%

8-oxoguanine (8-hydroxyguanine) DNA glycosylase and its substrate specificity.

Tchou¹,

Kasai²,

Shibutani³

et al. 1991

Proc. Natl. Acad. Sci. U.S.A.

682

433

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Substrate specificities of FPG protein (also known as formamidopyrimidine DNA glycosylase) and 8-hydroxyguanine endonuclease were compared by using defined duplex oligodeoxynucleotides containing single residues of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG), 8-oxo-7,8-dihydro-2'-deoxyadenosine (8-oxodA), and 2,6-diamino-4-hydroxy-5-(N-methyl)formamidopyrimidine (Me-Fapy). Duplexes containing 8-oxodG positioned opposite dC, dG, or dT were cleaved, whereas single-stranded DNA and duplexes containing 8-oxodGdA or 8-oxodA positioned opposite any of the four DNA bases were relatively resistant. Both enzymes cut duplexes containing 8-oxoG-dC 3' and 5' to the modified base but failed to cleave duplex DNA containing synthetic abasic sites, mismatches containing dG, or unmodified DNA. 8-Oxoguanine, identified by HPLC-electrochemical detection techniques, was released during the enzymatic reaction. Apparent Km values for FPG protein acting on duplex substrates containing a single Me-Fapy or 8-oxodG residue positioned opposite dC were 41 and 8 nM, respectively, and those for 8-hydroxyguanine endonuclease were 30 and 13 nM, respectively. Comparison of the properties of the two enzyme activities suggest that they are identical. In view of the widespread distribution of 8-oxodG in cellular DNA, the demonstrated miscoding and mutagenic properties of this lesion, and the existence of a bacterial gene coding for FPG protein, we propose that 8-oxodG DNA is the primary physiological substrate for a constituent glycosylase found in bacteria and mammalian cells.Active oxygen species, generated by ionizing radiation and by endogenous oxidation processes, react with deoxyguanosine (dG) residues in DNA to form 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) (reviewed in ref.

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Nitrogen-15 nuclear magnetic resonance studies on the tautomerism of 8-hydroxy-2'-deoxyguanosine, 8-hydroxyguanosine, and other C8-substituted guanine nucleosides

Cited by 75 publications

References 34 publications

Role of Hoogsteen Edge Hydrogen Bonding at Template Purines in Nucleotide Incorporation by Human DNA Polymerase ι

Role of Hoogsteen Edge Hydrogen Bonding at Template Purines in Nucleotide Incorporation by Human DNA Polymerase ι

Neighbouring bases in template influence base-pairing of isoguanine

8-oxoguanine (8-hydroxyguanine) DNA glycosylase and its substrate specificity.

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