Replication of <i>N</i><sup>2</sup>,3‐Ethenoguanine by DNA Polymerases

Zhao, Linlin; Christov, Plamen P.; Kozekov, Ivan D.; Pence, Matthew G.; Pallan, Pradeep S.; Rizzo, Carmelo J.; Egli, Martin; Guengerich, F. Peter

doi:10.1002/ange.201109004

Cited by 10 publications

(28 citation statements)

References 34 publications

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“…Recombinant hpol and hpol were either purchased from Enzymax (Lexington, KY) or expressed and purified as described previously (39,40). T4 polynucleotide kinase (T4-PNK) and E. coli uracil DNA glycosylase (UDG) were obtained from New England Biolabs (Beverly, MA), whereas [␥-32 P]ATP was purchased from PerkinElmer Life Sciences.…”

Section: Methodsmentioning

confidence: 99%

Error-prone Translesion Synthesis Past DNA-Peptide Cross-links Conjugated to the Major Groove of DNA via C5 of Thymidine

Wickramaratne

Boldry²,

Buehler

et al. 2015

Journal of Biological Chemistry

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Background: DNA-protein conjugates can be induced by reactive oxygen species and proteolytically cleaved to the corresponding peptide conjugates. Results: Polymerase bypass past C5-dT peptide conjugates catalyzed by human polymerases and gives rise to base substitutions and deletions. Conclusion: Replication past C5-T peptide conjugates is mutagenic. Significance: This study provides the first evidence for error-prone replication of DPCs cross-linked to pyrimidines in DNA.

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Section: Methodsmentioning

confidence: 99%

Error-prone Translesion Synthesis Past DNA-Peptide Cross-links Conjugated to the Major Groove of DNA via C5 of Thymidine

Wickramaratne

Boldry²,

Buehler

et al. 2015

Journal of Biological Chemistry

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“…2-Amino-9-(2-deoxy-2-fluoro-␤-D-arabinofuranosyl)-guanine was from Metkinen (Kuopio, Finland). Modified oligonucleotides containing 2Ј-F-N 2 ,3-⑀dG were synthesized as described earlier (38) followed by HPLC purification and desalting with Sephadex G-25 (Sigma-Aldrich). The modified 23-mer template used for extension and kinetic assays was 5Ј-TCATXGAATCCTTACGAGCCCCC-3Ј where X ϭ 2Ј-F- (39), and pol (38) were purified following protocols described previously.…”

Section: Methodsmentioning

confidence: 99%

“…Reactions were quenched with 9 l of 20 mM EDTA (pH 9.0) in 95% (v/v) formamide. Products were separated using 20% (w/v) acrylamide electrophoresis gels, and results were visualized using a phosphorimaging system (Bio-Rad, Molecular Imager FX) and analyzed by Quantity One software as described (38).…”

Section: Methodsmentioning

confidence: 99%

“…Catalytic insertions opposite 2Ј-F-N 2 ,3-⑀dG were examined using five DNA polymerases, including Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4), the replicative bacteriophage pol T7 DNA exonuclease Ϫ , (E. coli pol I) Klenow fragment exonuclease Ϫ , yeast pol , and human DNA pol , where a consistent miscoding pattern (2Ј-F-N 2 ,3-⑀dG:T) was found. Crystal structures of Dpo4 with 2Ј-F-N 2 ,3-⑀dG paired with dCTP showed a Watson-Crick-like structure, whereas the complex with 2Ј-F-N 2 ,3-⑀dG:T revealed a "sheared" base pair (38).…”

mentioning

confidence: 99%

“…We recently investigated the miscoding of N 2 ,3-⑀G using a stabilized 2Ј-fluoro-substituted analog, 2Ј-fluoro-N 2 ,3-⑀-2Ј-deoxyarabinoguanosine (2Ј-F-N 2 ,3-⑀dG) (38). The presence of the electronegative fluorine atom destabilizes the transition state leading to an oxocarbenium-like intermediate and hydrolysis of the glycosidic bond.…”

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confidence: 99%

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Basis of Miscoding of the DNA Adduct N2,3-Ethenoguanine by Human Y-family DNA Polymerases

Zhao

Pence

Christov

et al. 2012

Journal of Biological Chemistry

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N2,3-Ethenoguanine (N2,3-ϵG) is one of the exocyclic DNA adducts produced by endogenous processes (e.g. lipid peroxidation) and exposure to bioactivated vinyl monomers such as vinyl chloride, which is a known human carcinogen. Existing studies exploring the miscoding potential of this lesion are quite indirect because of the lability of the glycosidic bond. We utilized a 2′-fluoro isostere approach to stabilize this lesion and synthesized oligonucleotides containing 2′-fluoro-N2,3-ϵ-2′-deoxyarabinoguanosine to investigate the miscoding potential of N2,3-ϵG by Y-family human DNA polymerases (pols). In primer extension assays, pol η and pol κ replicated through N2,3-ϵG, whereas pol ι and REV1 yielded only 1-base incorporation. Steady-state kinetics revealed that dCTP incorporation is preferred opposite N2,3-ϵG with relative efficiencies in the order of pol κ > REV1 > pol η ≈ pol ι, and dTTP misincorporation is the major miscoding event by all four Y-family human DNA pols. Pol ι had the highest dTTP misincorporation frequency (0.71) followed by pol η (0.63). REV1 misincorporated dTTP and dGTP with much lower frequencies. Crystal structures of pol ι with N2,3-ϵG paired to dCTP and dTTP revealed Hoogsteen-like base pairing mechanisms. Two hydrogen bonds were observed in the N2,3-ϵG:dCTP base pair, whereas only one appears to be present in the case of the N2,3-ϵG:dTTP pair. Base pairing mechanisms derived from the crystal structures explain the slightly favored dCTP insertion for pol ι in steady-state kinetic analysis. Taken together, these results provide a basis for the mutagenic potential of N2,3-ϵG.

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Site‐Specific N²‐dG DNA Adducts: Formation, Synthesis, and TLS Polymerase‐Mediated Bypass

Ghodke

Pradeepkumar

2020

Eur J Org Chem

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The N2‐position of deoxyguanosine (dG) in DNA is susceptible to modification by various damaging agents. These modifications (lesions or adducts) can stall the DNA replication by replicative polymerases, and if the common DNA repair pathways do not remove them, it can result in genomic instability. This generally leads to the death or oncogenic transformation of the cell. An important mechanism to deal with this problem is Translesion synthesis (TLS), a bypass mechanism, which involves the tolerance of DNA damage by low‐fidelity DNA polymerases (TLS polymerases). To understand the accuracy of TLS polymerases, a chemical biology approach is required. In this review, we discuss the reliable methods to synthesize specific N2‐dG DNA adducts and how they are tolerated by bacterial TLS polymerase Pol IV and its mammalian orthologue hpol κ. Molecular insights on the accurate bypass of these adducts emerge from the primer extension assays, X‐ray crystallographic, and molecular modeling studies are reviewed here.

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Replication of N²,3‐Ethenoguanine by DNA Polymerases

Cited by 10 publications

References 34 publications

Error-prone Translesion Synthesis Past DNA-Peptide Cross-links Conjugated to the Major Groove of DNA via C5 of Thymidine

Error-prone Translesion Synthesis Past DNA-Peptide Cross-links Conjugated to the Major Groove of DNA via C5 of Thymidine

Basis of Miscoding of the DNA Adduct N2,3-Ethenoguanine by Human Y-family DNA Polymerases

Site‐Specific N²‐dG DNA Adducts: Formation, Synthesis, and TLS Polymerase‐Mediated Bypass

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Replication of N2,3‐Ethenoguanine by DNA Polymerases

Cited by 10 publications

References 34 publications

Error-prone Translesion Synthesis Past DNA-Peptide Cross-links Conjugated to the Major Groove of DNA via C5 of Thymidine

Error-prone Translesion Synthesis Past DNA-Peptide Cross-links Conjugated to the Major Groove of DNA via C5 of Thymidine

Basis of Miscoding of the DNA Adduct N2,3-Ethenoguanine by Human Y-family DNA Polymerases

Site‐Specific N2‐dG DNA Adducts: Formation, Synthesis, and TLS Polymerase‐Mediated Bypass

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Product

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Replication of N²,3‐Ethenoguanine by DNA Polymerases

Site‐Specific N²‐dG DNA Adducts: Formation, Synthesis, and TLS Polymerase‐Mediated Bypass