Binding of pyrene to DNA, base squence specificity and its implication

Chen, Fuming

doi:10.1093/nar/11.20.7231

Cited by 37 publications

(22 citation statements)

References 25 publications

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“…Pyrene is a highly symmetrical PAH containing four fused aromatic rings and is one of 16 PAHs included in the list of 129 priority pollutants compiled by the U.S. Environmental Protection Agency (28). This PAH, encountered regularly in environmental samples (21), is not genotoxic but has a chemical structure found in several carcinogenic PAHs such as benzo[a]pyrene, indeno-(1,2,3-cd)-pyrene, and 1-nitropyrene, and it has been used as a model compound in PAH metabolism studies (8,25).…”

Section: Discussionmentioning

confidence: 99%

Microbial metabolism of polycyclic aromatic hydrocarbons: isolation and characterization of a pyrene-degrading bacterium

Heitkamp

Franklin

Cerniglia

1988

Appl Environ Microbiol

274

120

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Microbiological analyses of sediments located near a point source for petrogenic chemicals resulted in the isolation of a pyrene-mineralizing bacterium. This isolate was identified as a Mycobacterium sp. on the basis of its cellular and colony morphology, gram-positive and strong acid-fast reactions, diagnostic biochemical tests, 66.6% G+C content of the DNA, and high-molecular-weight mycolic acids (C58 to C64). The mycobacterium mineralized pyrene when grown in a mineral salts medium supplemented with nutrients but was unable to utilize pyrene as a sole source of carbon and energy. The mycobacterium grew well at 24 and 30°C and minimally at 35°C. No growth was observed at 5 or 42°C. The mycobacterium grew well at salt concentrations up to 4%. Pyrene-induced Mycobacterium cultures mineralized 5% of the pyrene after 6 h and reached a maximum of 48% mineralization within 72 h. Treatment of induced and noninduced cultures with chloramphenicol showed that pyrene-degrading enzymes were inducible in this Mycobacterium sp. This bacterium could also mineralize other polycyclic aromatic hydrocarbons and alkyl-and nitro-substituted polycyclic aromatic hydrocarbons including naphthalene, phenanthrene, fluoranthene, 3-methylcholanthrene, 1-nitropyrene, and 6-nitrochrysene. This is the first report of a bacterium able to extensively mineralize pyrene and other polycyclic aromatic hydrocarbons containing four aromatic rings.

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Section: Discussionmentioning

confidence: 99%

Microbial metabolism of polycyclic aromatic hydrocarbons: isolation and characterization of a pyrene-degrading bacterium

Heitkamp

Franklin

Cerniglia

1988

Appl Environ Microbiol

274

120

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“…FRET, which is also known as a “spectroscopic ruler”,11–13 is very often used to measure the distance between two sites on a macromolecule 14. As pyrene and its derivatives are known to interact with biological macromolecules,6, 15 FRET can serve as an efficient tool to investigate the biomolecular recognition of these molecules. In an earlier study,16 attempts to use FRET from pyrenes to perylene were made for nucleic acid assays under homogeneous solution conditions by using steady‐state spectroscopy.…”

Section: Introductionmentioning

confidence: 99%

A Potential Carcinogenic Pyrene Derivative under Förster Resonance Energy Transfer to Various Energy Acceptors in Nanoscopic Environments

2013

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Picosecond-resolved Förster resonance energy transfer (FRET) from various vibronic bands in benzo[a]pyrene (BP) shows a strong dependency on the spectral overlap of an energy acceptor in a confined environment. Our study on the dipolar interactions between BP and different acceptors, including ethidium (Et), acridine orange (AO), and crystal violet (CV), at the surface of a model anionic micelle revealed that the Förster distance (R0) and the rate of energy transfer is dependent on the individual spectral overlap of the vibronic bands of BP with the absorption spectra of the different energy acceptors. The differential behavior of the vibronic bands is compared with that of different dyes [quantum dots (QDs)] in a "dye-blend" (mixture) under FRET to an energy acceptor. Comparison of the FRET of the QDs with that of BP confirmed the independent nature of the dipolar interaction of the vibronic bands with other organic molecules, and the use of deconvolution techniques in the interpretation of the donor-acceptor (D-A) distance was also justified. We also showed that the consideration of differential FRET from the vibronic bands of BP and from the QDs in the dye-blend is equally acceptable in theoretical frameworks including the Infelta-Tachiya model and D-A distribution analysis in nanoenvironments.

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“…Both the 2-NH2 group of guanine and N-3 of adenine are situated in the minor groove of double-stranded DNAs. (2,3) and will enhance the selectivity in covalent binding of aryloxiranes to adenine in such sequences in double-stranded DNAs.…”

Section: Resultsmentioning

confidence: 99%

Selective alkylation of carcinogenic 9-anthryloxirane at the N-3 position of adenine in DNA.

Yang¹,

Chang²

1985

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

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Carcinogenic 9-anthryloxirane binds covalently to calf thymus DNA and poly(dA-dT). Application of the technique for DNA sequence determination shows that acid cleavage of the modified DNA frees approximately half of the anthryl groups from the DNA. HPLC analysis indicates that an adenine adduct and the glycol derived from 9-anthryloxirane are the major acid-labile products. Spectroscopic analyses establish that the adenine adduct is the N-3 adduct of 9-anthryloxirane to adenine. Similar analyses of modified poly(dA-dT) indicate that the binding of 9-anthryloxirane takes place selectively at the N-3 position of adenine. The significance of this finding is briefly discussed. MATERIALS AND METHODSMaterials. Highly polymerized calf thymus DNA, hyperchromicity 30%, was purchased from Sigma, and poly(dAdT) was from the Pharmacia P-L Biochemicals. Solvents and reagents used were of the highest available purity commercially. 9-AO was synthesized by a known method (6).Instruments. All UV-visible absorption spectra were taken on a Varian-Cary 219 spectrometer; NMR spectra, on a University of Chicago DS-1000 spectrometer operating at 500 MHz; and mass spectra, on a VG-70-250 double-focusing integrated GS-MS-GS mass spectrometer. All HPLC were performed on a custom system from Waters Associates with a RCM-100 radial compression module.Reaction of 9-AO with Calf Thymus DNA. A solution of calf thymus DNA (10 mg) in 10 ml of 5 mM sodium cacodylate buffer (pH 7.1) was divided into two equal 5-ml portions. One portion was denatured by heating at 95°C for 5 min and quenched in an ice-water bath for 10 min. Both portions were then treated with a solution of 5 mg of 9-AO dissolved in 0.25 ml of (CH3)2SO, and the reaction mixtures were incubated at 37°C in the dark for 24 hr. Each solution was extracted 14 times with 5 ml of buffer-saturated ethyl acetate and twice with 5 ml of buffer-saturated ether to remove organic compounds that were not covalently bound to DNA. The solutions were then evaporated at 40 torr (1 torr = 133.3 Pa) and 21°C to remove the dissolved organic solvents and were made up to 5 ml (total volume) with distilled water. Absorption spectra ofthe solutions were then recorded. The binding level of I to DNA was estimated from the absorbance at 385 nm, and the value is given in Table 1. A portion of the modified native DNA was heat-denatured as described, and the resulting solution was extracted with buffer-saturated ethyl acetate (six times) and ether (twice). Absorption spectra of the modified native DNA showed no significant decrease in absorption before and after such a treatment.Each portion of the modified DNA was then hydrolyzed by acidifying 3 ml of the solution with 0.1 ml of 1 M HC1 to pH 1.5 and heating the solution at 60°C for 1 hr. Acid-labile products were removed by extraction with six 3-ml portions of buffer-saturated dichloromethane. The dichloromethane extracts were combined, dried, and evaporated. The residue was dissolved in 1.5 ml of CH30H. Absorption spectra of the Abbreviations: 9-AO, ...

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Binding of pyrene to DNA, base squence specificity and its implication

Cited by 37 publications

References 25 publications

Microbial metabolism of polycyclic aromatic hydrocarbons: isolation and characterization of a pyrene-degrading bacterium

Microbial metabolism of polycyclic aromatic hydrocarbons: isolation and characterization of a pyrene-degrading bacterium

A Potential Carcinogenic Pyrene Derivative under Förster Resonance Energy Transfer to Various Energy Acceptors in Nanoscopic Environments

Selective alkylation of carcinogenic 9-anthryloxirane at the N-3 position of adenine in DNA.

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