Generation and characterization of quinolone-specific DNA aptamers suitable for water monitoring.

Quinolones are antibiotics that are accredited in human and veterinary medicine but are regularly used in high quantities also in industrial livestock farming. Since these compounds are often only incompletely metabolized, significant amounts contaminate the aquatic environment and negatively impact on a variety of different ecosystems. Although there is increasing awareness of problems caused by pharmaceutical pollution, available methods for the detection and elimination of numerous pharmaceutical residues are currently inefficient or expensive. While this also applies to antibiotics that may lead to multi-drug resistance in pathogenic bacteria, aptamer-based technologies potentially offer alternative approaches for sensitive and efficient monitoring of pharmaceutical micropollutants. Using the Capture-SELEX procedure, we here describe the selection of an aptamer pool with enhanced binding qualities for fluoroquinolones, a widely used group of antibiotics in both human and veterinary medicine. The selected aptamers were shown to detect various quinolones with high specificity, while specific binding activities to structurally unrelated drugs were not detectable. The quinolone-specific aptamers bound to ofloxacin, one of the most frequently prescribed fluoroquinolone, with high affinity (KD=0.1-56.9 nM). The functionality of quinolone-specific aptamers in real water samples was demonstrated in local tap water and in effluents of sewage plants. Together, our data suggest that these aptamers may be applicable as molecular receptors in biosensors or as catcher molecules in filter systems for improved monitoring and treatment of polluted water.

[1]  J. Fick,et al.  Occurrence and Abundance of Antibiotics and Resistance Genes in Rivers, Canal and near Drug Formulation Facilities – A Study in Pakistan , 2013, PloS one.

[2]  Rodrigo Lopez,et al.  Clustal W and Clustal X version 2.0 , 2007, Bioinform..

[3]  Mats Tysklind,et al.  Environmental risk assessment of antibiotics in the Swedish environment with emphasis on sewage treatment plants. , 2007, Water research.

[4]  Scott Wallace,et al.  Comparative analysis of constructed wetlands: The design and construction of the ecotechnology research facility in Langenreichenbach, Germany , 2013 .

[5]  T. Ternes Occurrence of drugs in German sewage treatment plants and rivers 1 Dedicated to Professor Dr. Klaus , 1998 .

[6]  Jilin Tang,et al.  Label-free detection of kanamycin using aptamer-based cantilever array sensor. , 2014, Biosensors & bioelectronics.

[7]  Gan Zhang,et al.  Determination of selected antibiotics in the Victoria Harbour and the Pearl River, South China using high-performance liquid chromatography-electrospray ionization tandem mass spectrometry. , 2007, Environmental pollution.

[8]  Yan-Wen Li,et al.  Determination of four fluoroquinolone antibiotics in tap water in Guangzhou and Macao. , 2010, Environmental pollution.

[9]  Shihua Wang,et al.  A signal-on fluorescent aptasensor based on Tb3+ and structure-switching aptamer for label-free detection of Ochratoxin A in wheat. , 2013, Biosensors & bioelectronics.

[10]  T. Ternes,et al.  Pharmaceuticals and personal care products in the environment: agents of subtle change? , 1999, Environmental health perspectives.

[11]  Diana S Aga,et al.  Pharmaceutical metabolites in the environment: Analytical challenges and ecological risks , 2009, Environmental toxicology and chemistry.

[12]  Beate Strehlitz,et al.  Aptamers for pharmaceuticals and their application in environmental analytics , 2011, Bioanalytical reviews.

[13]  Michael Zuker,et al.  Mfold web server for nucleic acid folding and hybridization prediction , 2003, Nucleic Acids Res..

[14]  K. Drlica,et al.  DNA gyrase, topoisomerase IV, and the 4-quinolones , 1997, Microbiology and molecular biology reviews : MMBR.

[15]  Zoltán Konthur,et al.  Probing the SELEX Process with Next-Generation Sequencing , 2011, PloS one.

[16]  D. Fatta-Kassinos,et al.  Chronic ecotoxic effects to Pseudomonas putida and Vibrio fischeri, and cytostatic and genotoxic effects to the hepatoma cell line (HepG2) of ofloxacin photo(cata)lytically treated solutions. , 2013, The Science of the total environment.

[17]  M. Moeder,et al.  Solid-phase microextraction-gas chromatography-mass spectrometry of biologically active substances in water samples. , 2000, Journal of chromatography. A.

[18]  Jaehoon Yu,et al.  In vitro selection of RNA aptamers that selectively bind danofloxacin. , 2014, Biochemical and biophysical research communications.

[19]  P. Dabert,et al.  Effect of land application of manure from enrofloxacin-treated chickens on ciprofloxacin resistance of Enterobacteriaceae in soil. , 2014, The Science of the total environment.

[20]  Tong Zhang,et al.  Biodegradation and adsorption of antibiotics in the activated sludge process. , 2010, Environmental science & technology.

[21]  L. Gold,et al.  Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. , 1990, Science.

[22]  Z. Sosa-Ferrera,et al.  Combination of microwave-assisted micellar extraction with liquid chromatography tandem mass spectrometry for the determination of fluoroquinolone antibiotics in coastal marine sediments and sewage sludges samples. , 2012, Biomedical chromatography : BMC.

[23]  K Kümmerer,et al.  Significance of antibiotics in the environment. , 2003, The Journal of antimicrobial chemotherapy.

[24]  Weihong Tan,et al.  Optimization and Modifications of Aptamers Selected from Live Cancer Cell Lines , 2007, Chembiochem : a European journal of chemical biology.

[25]  Itamar Willner,et al.  Electronic aptamer-based sensors. , 2007, Angewandte Chemie.

[26]  Scott Wallace,et al.  Oxygen transfer and consumption in subsurface flow treatment wetlands , 2013 .

[27]  F. J. Camino-Sánchez,et al.  Analysis of quinolone antibiotic derivatives in sewage sludge samples by liquid chromatography-tandem mass spectrometry: comparison of the efficiency of three extraction techniques. , 2013, Talanta.

[28]  Walter Giger,et al.  Environmental exposure and risk assessment of fluoroquinolone antibacterial agents in wastewater and river water of the Glatt Valley Watershed, Switzerland. , 2002, Environmental science & technology.

[29]  J. Szostak,et al.  In vitro selection of RNA molecules that bind specific ligands , 1990, Nature.

[30]  Diana S. Aga,et al.  Potential Ecological and Human Health Impacts of Antibiotics and Antibiotic-Resistant Bacteria from Wastewater Treatment Plants , 2007, Journal of toxicology and environmental health. Part B, Critical reviews.

[31]  T. A. Larsen,et al.  Soft Paths in Wastewater Management – The Pros and Cons of Urine Source Separation , 2007 .

[32]  Rolf U Halden,et al.  Occurrence and loss over three years of 72 pharmaceuticals and personal care products from biosolids-soil mixtures in outdoor mesocosms. , 2010, Water research.

[33]  Nadia Nikolaus,et al.  Capture-SELEX: Selection of DNA Aptamers for Aminoglycoside Antibiotics , 2012, Journal of analytical methods in chemistry.

[34]  R. Stoltenburg,et al.  SELEX--a (r)evolutionary method to generate high-affinity nucleic acid ligands. , 2007, Biomolecular engineering.

[35]  Chunhai Fan,et al.  Aptamer-based biosensors , 2008 .

[36]  R. Stoltenburg,et al.  FluMag-SELEX as an advantageous method for DNA aptamer selection , 2005, Analytical and bioanalytical chemistry.

[37]  A. Poapolathep,et al.  Dispositions and residue depletion of enrofloxacin and its metabolite ciprofloxacin in muscle tissue of giant freshwater prawns (Macrobrachium rosenbergii). , 2009, Journal of veterinary pharmacology and therapeutics.

[38]  A. Leung,et al.  Residues of fluoroquinolones in marine aquaculture environment of the Pearl River Delta, South China , 2012, Environmental Geochemistry and Health.

[39]  Baldev Singh,et al.  Spectrophotometric Methods for the Determination of Fluoroquinolones: A Review , 2008 .

[40]  Jörg Römbke,et al.  Environmental fate of pharmaceuticals in water/sediment systems. , 2005, Environmental science & technology.

[41]  Kevin W Plaxco,et al.  Structure-switching biosensors: inspired by Nature. , 2010, Current opinion in structural biology.

[42]  J. Vidal,et al.  An electrochemical competitive biosensor for ochratoxin A based on a DNA biotinylated aptamer. , 2011, Biosensors & bioelectronics.

[43]  Xiliang Luo,et al.  Signal amplified strategy based on target-induced strand release coupling cleavage of nicking endonuclease for the ultrasensitive detection of ochratoxin A. , 2013, Biosensors & bioelectronics.

[44]  Nicole Kemper,et al.  Veterinary antibiotics in the aquatic and terrestrial environment , 2008 .

[45]  K. Takakura,et al.  Occurrence of fluoroquinolones and fluoroquinolone-resistance genes in the aquatic environment. , 2013, The Science of the total environment.

[46]  Simon Webb,et al.  Indirect human exposure to pharmaceuticals via drinking water. , 2003, Toxicology letters.