Locating Binding Sites for the Carcinogen N-Acetoxy-N-Acetyl-2-Aminofluorene Using Restriction Enzyme Inhibition Assays

Mallamaci, Michael A.; Bascoy, Marta L.; Brown, J. Steven; Combates, Nicholas J.; Winkle, Stephen A.

doi:10.1080/07391102.1992.10508632

Cited by 5 publications

(3 citation statements)

References 21 publications

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“…The inhibition of Mbol activity on B-form BZ-III by actinomycin, ametantrone, and ethidium is expected and is similar to that observed previously with various restriction enzymes and DNA-binding molecules (Hardwick et al, 1984;Ushay et al, 1981; Barton & Paranawithana, 1986; Mallamaci et al, 1991). Inhibition by these agents of Mbol cleavage of BZ-III containing both B and Z conformations is also observed.…”

Section: Discussionsupporting

confidence: 86%

Enhanced reactivity of a B-Z junction for cleavage by the restriction enzyme MboI

Winkle

Aloyo²,

Morales³

et al. 1991

Biochemistry

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We have been investigating the structure, dynamics, and ligand-binding properties of the interface that exists between a right-handed conformation and a left-handed conformation (i.e., a B-Z junction) in synthetic DNA oligomers. Since exo- and endonuclease activity is known to be sensitive to the conformation of the template DNA, we have designed and synthesized a DNA oligonucleotide of 20 base pairs (designated as BZ-III) with an MboI recognition site (GATC) at the location of a potential B-Z junction. The activity of the MboI enzyme toward this molecule and DNA oligomers that contain multiple MboI sites located at B-Z junctions was monitored in the absence and presence of the Z-conformation-inducing reagent cobalt hexaammine. In all cases, the activity of the enzyme was enhanced in the presence of cobalt hexaammine. The activity of MboI toward BZ-III, in the presence and absence of cobalt hexaammine, was also examined when the DNA oligomer is also in the presence of the DNA binding drugs actinomycin D, ametantrone, or ethidium bromide. In all cases, the activity of the enzyme was inhibited in the presence of drug. The results suggest that B-Z junctions are structurally unique and that this uniqueness may alter nuclease activity at sites in or near the junction.

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Section: Discussionsupporting

confidence: 86%

Enhanced reactivity of a B-Z junction for cleavage by the restriction enzyme MboI

Winkle

Aloyo²,

Morales³

et al. 1991

Biochemistry

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“…To probe the plasmid DNA, we first needed to develop an appropriate assay. Our approach was based in part on the experiments of Winkle and Mallamaci, who utilized restriction enzyme mapping to detect binding of carcinogens to pBR322. , Here, our goal was to develop a nonradioactive assay involving the inhibition of restriction enzyme cleavage and to determine if such an assay could be used to probe whether specific sites on the DNA had undergone cross-linking. Figure illustrates that cross-linking of histone with linear pBR322 leads to a decreased mobility that can be mostly restored upon treatment with protease, as seen previously for supercoiled DNA, consistent with oxidative cross-linking.…”

Section: Discussionmentioning

confidence: 99%

Dependence of DNA–Protein Cross-Linking via Guanine Oxidation upon Local DNA Sequence As Studied by Restriction Endonuclease Inhibition

Madison

Perez

et al. 2011

Biochemistry

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Oxidative damage plays a causative role in many diseases, and DNA-protein cross-linking is one important consequence of such damage. It is known that GG and GGG sites are particularly prone to one-electron oxidation, and here we examined how the local DNA sequence influences the formation of DNA-protein cross-links induced by guanine oxidation. Oxidative DNA-protein cross-linking was induced between DNA and histone protein via the flash quench technique, a photochemical method that selectively oxidizes the guanine base in double-stranded DNA. An assay based on restriction enzyme cleavage was developed to detect the cross-linking in plasmid DNA. Following oxidation of pBR322 DNA by flash quench, several restriction enzymes (PpuMI, BamHI, EcoRI) were then used to probe the plasmid surface for the expected damage at guanine sites. These three endonucleases were strongly inhibited by DNA-protein cross-linking, whereas the AT-recognizing enzyme AseI was unaffected in its cleavage. These experiments also reveal the susceptibility of different guanine sites toward oxidative cross-linking. The percent inhibition observed for the endonucleases, and their pBR322 cleavage sites, decreased in the order: PpuMI (5'-GGGTCCT-3' and 5'-AGGACCC-3') > BamHI (5'-GGATCC-3') > EcoRI (5'-GAATTC-3'), a trend consistent with the observed and predicted tendencies for guanine to undergo one-electron oxidation: 5'-GGG-3' > 5'-GG-3' > 5'-GA-3'. Thus, it appears that in mixed DNA sequences the guanine sites most vulnerable to oxidative cross-linking are those that are easiest to oxidize. These results further indicate that equilibration of the electron hole in the plasmid DNA occurs on a time scale faster than that of cross-linking.

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“…Some carcinogens present an adduction selectivity for particular sequences, such as benzo[ a ]pyrene which generates more adducts at the central G of sequences 5′ CGG 3′ , 5′ TGG 3′ , 5′ TGT 3′ and 5′ CGT 3′ 23, 24. Similarly, N ‐acetoxy‐ N ‐acetyl‐2‐aminofluorene (AAAF) is fixed to specific sites of pBR322 plasmid,25, 26 and a metabolite of benzo[ c ]phenanthrene has been described to bind predominantly to the hot spot of the carcinogen (+)‐(7 R, 8 S, 9 S, 10 R )‐isomer of benzo[ a ]pyrene 7,8‐diol 9,10‐epoxide ((+)‐BaP DE‐2) in the Chinese hamster hprt gene 27. In order to obtain more precise information on the flanking bases effect on the adduct formation, Vouros and co‐workers have developed a pseudo‐combinatory method based on a partial digestion of modified DNA followed by a characterization of modified oligomers (mainly trimers) by liquid chromatography coupled to mass spectrometry (LC/MS) 28.…”

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confidence: 99%

Mass spectrometric investigation of the sequence selectivity for adduction of heterocyclic aromatic amines on single‐strand oligonucleotides

Jamin¹,

Arquier²,

Debrauwer³

2008

Rapid Comm Mass Spectrometry

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Heterocyclic aromatic amines (HAAs) generated during the cooking of meats are known to be genotoxic substances able to form covalent bonds with DNA bases after metabolic activation. This work aimed at the investigation of the influence of the local environment of nucleobases along the nucleotidic sequence on its modification induced by two different HAAs, namely 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) and 2-amino-3-methylimidazo[4,5-f]quinoline (IQ), in order to identify possible sequences more susceptible to modification. A systematic study of the neighbouring base effect on the adduction was emphasized. Thus, PhIP and IQ adducts have been synthesized with various T-rich model single-strand oligonucleotides displaying different flanking bases (A, G, C or T) at the 3' or the 5' side of the targeted guanine, which allowed a comparison of the flanking base effects on adduction. Modified oligonucleotides were then analyzed by high-performance liquid chromatography (HPLC) coupled to electrospray ionization mass spectrometry. The localization of the modifications induced by PhIP or IQ along the oligonucleotide sequence was achieved by tandem mass spectrometry, and modification yields of the various model sequences were compared. Results indicate a favouring sequence context effect on the G-C8-IQ adduct formation with the sequence 5'GGG3'. Although higher than IQ, modification yields observed with PhIP showed a less obvious effect of the neighbouring base on the G-C8-PhIP adduct formation, with a preferential sequence 5'GGA/G/T3'.

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Locating Binding Sites for the Carcinogen N-Acetoxy-N-Acetyl-2-Aminofluorene Using Restriction Enzyme Inhibition Assays

Cited by 5 publications

References 21 publications

Enhanced reactivity of a B-Z junction for cleavage by the restriction enzyme MboI

Enhanced reactivity of a B-Z junction for cleavage by the restriction enzyme MboI

Dependence of DNA–Protein Cross-Linking via Guanine Oxidation upon Local DNA Sequence As Studied by Restriction Endonuclease Inhibition

Mass spectrometric investigation of the sequence selectivity for adduction of heterocyclic aromatic amines on single‐strand oligonucleotides

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