Synthesis and Miscoding Specificity of Oligodeoxynucleotide Containing 8-Phenyl-2‘-deoxyguanosine

Kohda, Kohfuku; Tsunomoto, Hirotaka; Kasamatsu, Toshio; Sawamura, Fumiko; Terashima, Isamu; Shibutani, Shinya

doi:10.1021/tx970111k

Cited by 35 publications

(57 citation statements)

References 43 publications

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“…Although various modifications of guanine are known to cause miscoding lesions, during enzymatic replication these result in the generation of transversions; for example, a common product of oxidative degradation, 8-oxoguanine, generates G→T transversions (21), whereas other guanine products such as 8-methyl-2′-deoxyguanosine generate both G→C and G→T transversions (22). Furthermore, the mutagen ethylene dibromide, a once common insecticide, fumigant and anti-knock agent for gasoline has been observed to indirectly cause G→A miscoding lesions in living cells (23).…”

Section: Discussionmentioning

confidence: 99%

Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis

Gilbert¹,

Binladen²,

Miller

et al. 2006

Nucleic Acids Research

172

133

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Although ancient DNA (aDNA) miscoding lesions have been studied since the earliest days of the field, their nature remains a source of debate. A variety of conflicting hypotheses exist about which miscoding lesions constitute true aDNA damage as opposed to PCR polymerase amplification error. Furthermore, considerable disagreement and speculation exists on which specific damage events underlie observed miscoding lesions. The root of the problem is that it has previously been difficult to assemble sufficient data to test the hypotheses, and near-impossible to accurately determine the specific strand of origin of observed damage events. With the advent of emulsion-based clonal amplification (emPCR) and the sequencing-by-synthesis technology this has changed. In this paper we demonstrate how data produced on the Roche GS20 genome sequencer can determine miscoding lesion strands of origin, and subsequently be interpreted to enable characterization of the aDNA damage behind the observed phenotypes. Through comparative analyses on 390 965 bp of modern chloroplast and 131 474 bp of ancient woolly mammoth GS20 sequence data we conclusively demonstrate that in this sample at least, a permafrost preserved specimen, Type 2 (cytosine→thymine/guanine→adenine) miscoding lesions represent the overwhelming majority of damage-derived miscoding lesions. Additionally, we show that an as yet unidentified guanine→adenine analogue modification, not the conventionally argued cytosine→uracil deamination, underpins a significant proportion of Type 2 damage. How widespread these implications are for aDNA will become apparent as future studies analyse data recovered from a wider range of substrates.

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Section: Discussionmentioning

confidence: 99%

Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis

Gilbert¹,

Binladen²,

Miller

et al. 2006

Nucleic Acids Research

172

133

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“…28 Thus, C-and Nlinked adducts have different mutagenic outcomes. For example, in contrast to the nonmutagenic N-linked C8-aniline-dG adduct, 25 the single-ringed C8-phenyl-dG ([Ph]G) adduct induces transversion and frameshift mutations 26,29 and strongly blocks the progress of DNA replication by high-fidelity DNA polymerases: Klenow fragment exo − (Kf − ) 26,29 and DNA pol α. 26 To establish the structural and biochemical impact of an Olinked C8-dG adduct, the unsubstituted C8-phenoxyl-dG adduct ([PhO]G, Figure 1a) was previously incorporated into the G3-position (X) of the NarI sequence (Figure 1a), 11,12 which is a hotspot for frameshift mutations induced by polycyclic N-linked C8-dG adducts in bacterial mutagenesis 30 via a two-base slippage mechanism.…”

Section: ■ Introductionmentioning

confidence: 99%

Chlorine Functionalization of a Model Phenolic C8-Guanine Adduct Increases Conformational Rigidity and Blocks Extension by a Y-Family DNA Polymerase

Witham

Verwey

Sproviero

et al. 2015

Chem. Res. Toxicol.

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Certain phenoxyl radicals can attach covalently to the C8-site of 2'-deoxyguanosine (dG) to afford oxygen-linked C8-dG adducts. Such O-linked adducts can be chemically synthesized through a nucleophilic displacement reaction between a phenolate and a suitably protected 8-Br-dG derivative. This permits the generation of model O-linked C8-dG adducts on scales suitable for insertion into oligonucleotide substrates using solid-phase DNA synthesis. Variation of the C8-aryl moiety provides an opportunity to derive structure-activity relationships on adduct conformation in duplex DNA and replication bypass by DNA polymerases. In the current study, the influence of chlorine C8-dG functionalization on in vitro DNA replication by Klenow fragment exo(-) (Kf(-)) and the Y-family polymerase (Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4)) has been determined. Model O-linked C8-dG adducts derived from the pentachlorophenoxyl radical ([PCP]G) and 2,4,6-trichlorophenoxyl radical ([TCP]G) were inserted into the reiterated G3-position of the NarI sequence (12-mer, NarI(12); and 22-mer, NarI(22)), which is a known hotspot for frameshift mutations mediated by N-linked polycyclic C8-dG adducts in bacterial mutagenesis. Within the NarI(12) duplex, the unsubstituted C8-phenoxy-dG ([PhO]G) adduct adopts a minimally perturbed B-form helix. Chlorination of [PhO]G to afford [PCP]G does not significantly change the adduct conformation within the NarI(12) duplex, as predicted by molecular dynamics simulations. However, when using NarI(22) for DNA synthesis in vitro, the chlorinated [PCP]G and [TCP]G lesions significantly block DNA replication by Kf(-) and Dpo4, whereas [PhO]G is readily bypassed. These findings highlight the impact that chlorine substituents impart to bulky C8-dG lesions.

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“…15 However, the miscoding properties of 8phenylguanine and its effect on stability have been reported. 16 The low levels of mutations in daughter strands found in these studies suggest that the correlation between C8-arylguanine adduct formation and carcinogenicity 11 is not the result of misreading or apurinic site formation.…”

Section: Arenediazonium Ionmentioning

confidence: 81%

“…65 d Samples were prepared in 10 mM sodium cacodylate buffer pH 7.0 with 100mM NaCl and 1 mM EDTA. 67 It is also possible to obtain the thermodynamic properties of a process (∆G, ∆H, ∆S)…”

Section: Thermal Denaturation Profilingmentioning

confidence: 99%

“…Both the enthalpy (∆H) and entropy (∆S) of denaturation have been extracted for various duplex oligonucleotides using thermal denaturation data. 66,67 The van't Hoff equation relates the equilibrium constant to temperature and allows one to extract ∆H and ∆S for the transition and to calculate duplex stability at any temperature using the equations ∆G° = ∆H° -T∆S° and 1/T m = (R/∆H°)ln([C T ]/4) + ∆S°/∆H° where [C T ] is the total concentration of single-strands and the strands are non-self-complementary. 68 Calculations are 20 based on the slope and intercept of a plot of 1/T m vs ln([C T ]/4) and yield the van't Hoff transition enthalpies (∆H°), entropies (∆S°) and free energies (∆G°).…”

Section: Thermal Denaturation Profilingmentioning

confidence: 99%

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Molecular modeling and experimental determination of the structure of C8 -arylguanine modified oligonucleotides that preferentially adopt the Z -DNA conformation

Heavner¹

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Molecular Modeling and Experimental Determination of the Structure of C8-Arylguanine Modified Oligonucleotides that Preferentially Adopt the Z-DNA Conformation Sue Ellen Heavner Thermal denaturation, circular dichroism, and NMR have been used extensively in conformational studies of oligonucleotides. Molecular modeling has become a powerful, if not essential, complement to these experimental techniques. To study the effects of C8-arylated purine adducts caused by carcinogenic aryl hydrazines we combined the two approaches. Two oligonucleotides were prepared, an unmodified oligonucleotide d(5' CGCGCGCGCG 3') and a C8-phenylguanine modified oligonucleotide d(5' CGCGCG*CGCG 3') (G* = 8-phenylguanine). These oligonucleotides were compared using thermal denaturation, circular dichroism, and NMR. The phenyl modification destabilizes the B DNA form and stabilizes the Z DNA form such that the B:Z ratio is near one under physiological conditions. Modeling studies were conducted on the modified sequence with G* = guanine, G* = 8phenylguanine, G* = 8-tolylguanine, and G* = 8-hydroxymethylphenylguanine in the B and Z-DNA conformations. We performed quantum mechanical calculations at the B3LYP level with the standard 6-31G* basis set using Gaussian98, and molecular dynamics simulations and free energy calculations using the suite of programs contained in Amber 6 and 7 with the Cornell 95 force field. New parameters for the modified guanines (G*) have been developed for the Cornell force field. Structural and thermodynamic properties of the DNA molecules are described from the analysis of the trajectories. The phenyl and tolyl-modified DNA's favored the Z form and the B conformation was preferred by the unmodified and hydroxymethylphenyl-modified oligonucleotides. In those cases where experimental data was available, it was in agreement with the theoretical data. The phenyl-modified models were useful in supporting and providing explanation for the experimental results. In light of recent studies, which show a role for Z DNA in gene expression and cell transformation, Z DNA stabilization by C8-arylguanine formation from aryl hydrazines may be relevant to their role in carcinogenesis.

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Synthesis and Miscoding Specificity of Oligodeoxynucleotide Containing 8-Phenyl-2‘-deoxyguanosine

Cited by 35 publications

References 43 publications

Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis

Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis

Chlorine Functionalization of a Model Phenolic C8-Guanine Adduct Increases Conformational Rigidity and Blocks Extension by a Y-Family DNA Polymerase

Molecular modeling and experimental determination of the structure of C8 -arylguanine modified oligonucleotides that preferentially adopt the Z -DNA conformation

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