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Scientific Reports Jan 2021Pyrene and chromium (Cr(VI)) are persistent pollutants and cause serious environmental problems because they are toxic to organisms and difficult to remediate. The...
Pyrene and chromium (Cr(VI)) are persistent pollutants and cause serious environmental problems because they are toxic to organisms and difficult to remediate. The toxicity of pyrene and Cr(VI) to three crops (cotton, soybean and maize) was confirmed by the significant decrease in root and shoot biomass during growth in pyrene/Cr(VI) contaminated hydroponic solution. Two bacterial strains capable of simultaneous pyrene biodegradation and Cr(VI) reduction were isolated and identified as Serratia sp. and Arthrobacter sp. A mixture of the isolated strains at a ratio of 1:1 was more efficient for biotreatment of pyrene and Cr(VI) than either strain alone; the mixture effectively carried out bioremediation of contaminated water in a hydroponic system mainly through pyrene biodegradation and Cr(VI) reduction. Application of these isolates shows potential for practical microbial remediation of pyrene and Cr(VI) combined water pollution.
Topics: Arthrobacter; Biodegradation, Environmental; Chromium; Coculture Techniques; Pyrenes; Serratia; Water Pollutants, Chemical; Water Purification
PubMed: 33420172
DOI: 10.1038/s41598-020-80053-2 -
Chembiochem : a European Journal of... Mar 2022In this study, we investigated the photoreaction of U in a pyrene-labeled DNA duplex, RNA duplex, and DNA/RNA hybrids. We found that the photoreactivity of U changed...
In this study, we investigated the photoreaction of U in a pyrene-labeled DNA duplex, RNA duplex, and DNA/RNA hybrids. We found that the photoreactivity of U changed dramatically from hydrogen abstraction to cross-linking by changing the conformation of the duplex from the B-form to the A-form. Among three A-form structures, the largest amount of cross-linked products was observed when U was incorporated into the RNA strand and the pyrene was conjugated to the 5' end of the DNA. These results indicate that the contact manner of pyrene was different between A- and B-form duplexes. This is a rare example of the use of the reactivity of bromouracil to analyze the contact between a small molecule with a weak binding affinity and a nucleic acid.
Topics: Circular Dichroism; DNA; Nucleic Acid Conformation; Pyrenes; RNA
PubMed: 35080796
DOI: 10.1002/cbic.202100626 -
Chemical Society Reviews Dec 2011Pyrene-functionalized oligonucleotides (PFOs) are increasingly explored as tools in fundamental research, diagnostics and nanotechnology. Their popularity is linked to... (Review)
Review
Pyrene-functionalized oligonucleotides (PFOs) are increasingly explored as tools in fundamental research, diagnostics and nanotechnology. Their popularity is linked to the ability of pyrenes to function as polarity-sensitive and quenchable fluorophores, excimer-generating units, aromatic stacking moieties and nucleic acid duplex intercalators. These characteristics have enabled development of PFOs for detection of complementary DNA/RNA targets, discrimination of single nucleotide polymorphisms (SNPs), and generation of π-arrays on nucleic acid scaffolds. This critical review will highlight the physical properties and applications of PFOs that are likely to provide high degree of positional control of the chromophore in nucleic acid complexes. Particular emphasis will be placed on pyrene-functionalized Locked Nucleic Acids (LNAs) since these materials display interesting properties such as fluorescence quantum yields approaching unity and recognition of mixed-sequence double stranded DNA (144 references).
Topics: 3T3-L1 Cells; Animals; Base Sequence; DNA; Humans; Mice; Nanotechnology; Oligonucleotides; Pyrenes
PubMed: 21487621
DOI: 10.1039/c1cs15014f -
International Journal of Molecular... May 2021Newly designed and synthesized diarylethene (DAE) derivatives with aliphatic amine sidearms and one with two pyrenes, revealed excellent photo-switching property of...
Newly designed and synthesized diarylethene (DAE) derivatives with aliphatic amine sidearms and one with two pyrenes, revealed excellent photo-switching property of central DAE core in MeOH and water. The only exception was bis-pyrene analogue, its DAE core very readily photochemically closed, but reversible opening completely hampered by aromatic stacking interaction of pyrene(s) with cyclic DAE. In this process, pyrene fluorescence showed to be a reliable monitoring method, an open form characterized by strong emission at 480 nm (typical for pyrene-aggregate), while closed form emitted weakly at 400 nm (typical for pyrene-DAE quenching). Only open DAE-bis-pyrene form interacted measurably with ds-DNA/RNA by flexible insertion in polynucleotide grooves, while self-stacked closed form did not bind to DNA/RNA. For the same steric reasons, flexible open DAE-bis-pyrene form was bound to at least three different binding sites at bovine serum albumin (BSA), while rigid, self-stacked closed form interacted dominantly with only one BSA site. Preliminary screening of antiproliferative activity against human lung carcinoma cell line A549 revealed that all DAE-derivatives are non-toxic. However, bis-pyrene analogue efficiently entered cells and located in the cytoplasm, whereby irradiation by light (315-400 nm) resulted in a strong, photo-induced cytotoxic effect, typical for pyrene-related singlet oxygen species production.
Topics: A549 Cells; Animals; Cattle; Cell Survival; DNA; Electrons; Humans; Light; Molecular Conformation; Nucleic Acid Denaturation; Photochemical Processes; Pyrenes; RNA; Serum Albumin, Bovine; Spectrometry, Fluorescence; Spectrophotometry, Ultraviolet; Temperature
PubMed: 34066402
DOI: 10.3390/ijms22094916 -
The Science of the Total Environment Apr 2023The productive application of motile microorganisms for degrading hydrophobic contaminants in soil is one of the most promising processes in modern remediation due to...
The productive application of motile microorganisms for degrading hydrophobic contaminants in soil is one of the most promising processes in modern remediation due to its sustainability and low cost. However, the incomplete biodegradation of the contaminants and the formation of the intermediary metabolites in the process may increase the toxicity in soil during bioremediation, and motile inoculants may mobilize the pollutants through biosorption. Therefore, controlling these factors should be a fundamental part of soil remediation approaches. The aim of this study was to evaluate the sources of risk associated with the cometabolism-based transformation of C-labeled pyrene by inoculated Pseudomonas putida G7 and identify ways to minimize risk. Our model scenario examined the increase in bioaccessibility to a distant source of contamination facilitated by sunflower (Helianthus annuus L.) roots. A biochar trap for mobilized pollutant metabolites and bacteria has also been employed. The experimental design consisted of pots filled with a layer of sand with C-labeled pyrene (88 mg kg) as a contamination focus located several centimeters from the inoculation point. Half of the pots included a biochar layer at the bottom. The pots were incubated in a greenhouse with sunflower plants and P. putida G7 bacteria. Pots with sunflower plants showed a higher biodegradation of pyrene, its mobilization as metabolites through the percolate and the roots, and bacterial mobilization toward the source of contamination, also resulting in increased pyrene transformation. In addition, the biochar layer efficiently reduced the concentrations of pyrene metabolites collected in the leachates. Therefore, the combination of plants, motile bacteria and biochar safely reduced the risk caused by the biological transformation of pyrene.
Topics: Pyrenes; Biodegradation, Environmental; Plants; Biotransformation; Soil; Bacteria; Soil Pollutants; Polycyclic Aromatic Hydrocarbons; Soil Microbiology
PubMed: 36681341
DOI: 10.1016/j.scitotenv.2023.161600 -
International Journal of Molecular... May 2023Mangrove ecosystems play curial roles in providing many ecological services and alleviating global climate change. However, they are in decline globally, mainly...
Mangrove ecosystems play curial roles in providing many ecological services and alleviating global climate change. However, they are in decline globally, mainly threatened by human activities and global warming, and organic pollutants, especially PAHs, are among the crucial reasons. Microbial remediation is a cost-effective and environmentally friendly way of alleviating PAH contamination. Therefore, understanding the effects of environmental and nutritional parameters on the biodegradation of polycyclic aromatic hydrocarbons (PAHs) is significant for the bioremediation of PAH contamination. In the present study, five bacterial strains, designated as Bp1 (Genus ), Sp8 (Genus ), Sp13 (Genus ), Sp23 (Genus ), and Sp24 (Genus ), have been isolated from mangrove sediment and their ring hydroxylating dioxygenase (RHD) genes have been successfully amplified. Afterward, their degradation abilities were comprehensively evaluated under normal cultural (monoculture and co-culture) and different nutritional (tryptone, yeast extract, peptone, glucose, sucrose, and NPK fertilizer) and environmental (cetyl trimethyl ammonium bromide (CTAB), sodium dodecyl sulfate (SDS)) parameters, as well with different co-contaminants (phenanthrene and naphthalene) and heavy metals (Cd, Cu, Fe, Ni, Mg, Mn, and Co). The results showed that strain Sp24 had the highest pyrene degradation rate (85%) in the monoculture experiment after being cultured for 15 days. Adding nitrogen- and carbon-rich sources, including tryptone, peptone, and yeast extract, generally endorsed pyrene degradation. In contrast, the effects of carbon sources (glucose and sucrose) on pyrene degradation were distinct for different bacterial strains. Furthermore, the addition of NPK fertilizer, SDS, Tween-80, phenanthrene, and naphthalene enhanced the bacterial abilities of pyrene removal significantly ( < 0.05). Heavy metals significantly reduced all bacterial isolates' degradation potentials ( < 0.05). The bacterial consortia containing high bio-surfactant-producing strains showed substantially higher pyrene degradation. Moreover, the consortia of three and five bacterial strains showed more degradation efficiency than those of two bacterial strains. These results provide helpful microbial resources for mangrove ecological remediation and insight into optimized culture strategies for the microbial degradation of PAHs.
Topics: Humans; Ecosystem; Fertilizers; Peptones; Pyrenes; Polycyclic Aromatic Hydrocarbons; Phenanthrenes; Bacteria; Biodegradation, Environmental; Naphthalenes; Metals, Heavy
PubMed: 37175988
DOI: 10.3390/ijms24098282 -
Molecules (Basel, Switzerland) May 2020We synthesized a new amino acid-fluorescent nucleobase derivative (qAN1-AA) and from it two new fluorescent nucleobase-fluorophore (pyrene) conjugates, whereby only the...
We synthesized a new amino acid-fluorescent nucleobase derivative (qAN1-AA) and from it two new fluorescent nucleobase-fluorophore (pyrene) conjugates, whereby only the analogue with the longer and more flexible linker (qAN1-pyr2) self-folded into intramolecularly stacked qAN1/pyrene conformation, yielding characteristic, 100 nm-red-shifted emission (λ = 500 nm). On the contrary, the shorter and more rigid linker resulted in non-stacked conformation (qAN1-pyr1), characterized by the emission of free pyrene at λ = 400 nm. Both fluorescent nucleobase-fluorophore (pyrene) conjugates strongly interacted with ds-DNA/RNA grooves with similar affinity but opposite fluorescence response (due to pre-organization), whereas the amino acid-fluorescent base derivative (qAN1-AA) was inactive. However, only intramolecularly self-folded qAN1-pyr2 showed strong fluorescence selectivity toward poly U (Watson-Crick complementary to qAN1 nucleobase) and poly A (reverse Hoogsteen complementary to qAN1 nucleobase), while an opposite emission change was observed for non-complementary poly G and poly C. Non-folded analogue (qAN1-pyr1) showed no ss-RNA selectivity, demonstrating the importance of nucleobase-fluorophore pre-organization.
Topics: Circular Dichroism; DNA; Fluorescence; Fluorescent Dyes; Hydrogen Bonding; Nucleic Acid Conformation; Poly A; Poly C; Poly G; Poly U; Pyrenes; RNA; RNA, Double-Stranded; Solvents; Spectrometry, Fluorescence; Water
PubMed: 32392853
DOI: 10.3390/molecules25092188 -
Molecules (Basel, Switzerland) Aug 2017A new malonate possessing two pyrene moieties was synthesized as a fluoroionophore, and its structure and fluorescence spectroscopic properties were investigated. When...
A new malonate possessing two pyrene moieties was synthesized as a fluoroionophore, and its structure and fluorescence spectroscopic properties were investigated. When excited at 344 nm in acetonitrile/chloroform (9:1, /), the synthesized bispyrenyl malonate has the fluorescence of intramolecular excimer (λ = 467 nm) emissions and not a pyrene monomer emission (λ = 394 nm). A large absolute fluorescence quantum yield was obtained in the solid state (Φ = 0.65) rather than in solution (Φ = 0.13). X-ray crystallography analysis clarified the molecular structure and alignment of the bispyrenyl malonate in the crystal phase, elucidating its fluorescence spectroscopic properties. Such analysis also suggests there are intramolecular C-H···π interactions and intermolecular π···π interactions between the pyrenyl rings. Interestingly, the synthesized bispyrenyl malonate exhibits excellent fluorescence sensing for the Cu ion. Remarkable fluorescence intensity enhancement was only observed with the addition of the Cu ion.
Topics: Cations, Divalent; Coordination Complexes; Copper; Crystallography, X-Ray; Ionophores; Malonates; Pyrenes; Spectrometry, Fluorescence
PubMed: 28841193
DOI: 10.3390/molecules22091415 -
The Journal of Physical Chemistry. B May 2017Bioactive apelin peptide forms ranging in length from 12 to 55 amino acids bind to and activate the apelin receptor (AR or APJ), a class A G-protein coupled receptor....
Bioactive apelin peptide forms ranging in length from 12 to 55 amino acids bind to and activate the apelin receptor (AR or APJ), a class A G-protein coupled receptor. Apelin-12, -17, and -36 isoforms, named according to length, with an additional N-terminal cysteine residue allowed for regiospecific and efficient conjugation of pyrene maleimide. Through steady-state fluorescence spectroscopy, the emission properties of pyrene in aqueous buffer were compared to those of the pyrene-apelin conjugates both without and with zwitterionic or anionic micelles. Pyrene photophysics are consistent with an expected partitioning into the hydrophobic micellar cores, while pyrene-apelin conjugation prevented this partitioning. Apelin, conversely, is expected to preferentially interact with anionic micelles; pyrene-apelin conjugates appear to lose preferential interaction. Finally, Förster resonance energy transfer between pyrene and tryptophan residues in the N-terminal tail and first transmembrane segment (the AR55 construct, comprising residues 1-55 of the AR) was consistent with efficient nonspecific pyrene-apelin conjugate binding to micelles rather than direct, specific apelin-AR55 binding. This approach provides a versatile fluorophore conjugation strategy for apelin, particularly valuable given that even a highly hydrophobic fluorophore is not deleterious to peptide behavior in membrane-mimetic micellar systems.
Topics: Apelin; Fluorescence Resonance Energy Transfer; Micelles; Molecular Structure; Pyrenes; Spectrometry, Fluorescence
PubMed: 28414462
DOI: 10.1021/acs.jpcb.7b02376 -
Chemistry (Weinheim An Der Bergstrasse,... Mar 2015Two new pyrene-polychlorotriphenylmethyl (PTM) dyads and triads have been synthesized and characterized by optical, magnetic, and electrochemical methods. The interplay...
Two new pyrene-polychlorotriphenylmethyl (PTM) dyads and triads have been synthesized and characterized by optical, magnetic, and electrochemical methods. The interplay between the different electronic states of the PTM moiety in the dyads and triads and the optical and magnetic properties of the molecules have been studied. The electronic spectra of the radicals 5(.) and 6(.) show the intramolecular charge-transfer transition at around 700 nm due to the acceptor character of the PTM radical. In the diamagnetic protonated derivatives 3 and 4 the fluorescence due to the pyrene is maintained, whereas in the radicals 5(.) and 6(.) and the corresponding anions 5(-) and 6(-) there is a clear quenching of the fluorescence, which is more efficient in the case of radicals. The redox activity of PTM radicals that are easily reduced to the corresponding carbanion has been exploited to fabricate electrochemical switches with optical and magnetic response.
Topics: Electrochemical Techniques; Electrons; Fluorescence; Halogenation; Magnetics; Methylation; Oxidation-Reduction; Pyrenes
PubMed: 25694181
DOI: 10.1002/chem.201405993