Characterization and Inkjet Printing of an RNA Aptamer for Paper-Based Biosensing of Ciprofloxacin

The excessive use of antibiotics in food-producing animals causes a steady rise of multiple antibiotic resistance in foodborne bacteria. Next to sulfonamides, the most common antibiotics groups are fluoroquinolones, aminoglycosides, and ß-lactams. Therefore, there is a need for a quick, efficient, and low-cost detection procedure for antibiotics. In this study, we propose an inkjet-printed aptamer-based biosensor developed for the detection of the fluoroquinolone ciprofloxacin. Due to their extraordinary high affinity and specificity, aptamers are already widely used in various applications. Here we present a ciprofloxacin-binding RNA aptamer developed by systematic evolution of ligands by exponential enrichment (SELEX). We characterized the secondary structure of the aptamer and determined the KD to 36 nM that allow detection of antibiotic contamination in a relevant range. We demonstrate that RNA aptamers can be inkjet-printed, dried, and resolved while keeping their functionality consistently intact. With this proof of concept, we are paving the way for a potential range of additional aptamer-based, printable biosensors.

[1]  J. Jaén-Oltra,et al.  Artificial neural network applied to prediction of fluorquinolone antibacterial activity by topological methods. , 2000, Journal of medicinal chemistry.

[2]  M. Zuker,et al.  Using reliability information to annotate RNA secondary structures. , 1998, RNA.

[3]  Andrea L Edwards,et al.  Riboswitches: structures and mechanisms. , 2011, Cold Spring Harbor perspectives in biology.

[4]  Katsunori Horii,et al.  An Aptamer-Based Biosensor for Direct, Label-Free Detection of Melamine in Raw Milk , 2018, Sensors.

[5]  Yvonne Joseph,et al.  Aptamer-Based Biosensors for Antibiotic Detection: A Review , 2018, Biosensors.

[6]  Kairi Kivirand,et al.  Calibrating Biosensors in Flow-Through Set-Ups: Studies with Glucose Optrodes , 2013 .

[7]  Kay Hamacher,et al.  Riboswitching with ciprofloxacin—development and characterization of a novel RNA regulator , 2018, Nucleic acids research.

[8]  C. Ban,et al.  Gold nanoparticle-based colorimetric detection of kanamycin using a DNA aptamer. , 2011, Analytical biochemistry.

[9]  R. Breaker,et al.  Immobilized RNA switches for the analysis of complex chemical and biological mixtures , 2001, Nature Biotechnology.

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

[11]  Nadia Nikolaus,et al.  Protein Detection with Aptamer Biosensors , 2008, Sensors.

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

[13]  Lei Wang,et al.  Optical aptasensors for quantitative detection of small biomolecules: a review. , 2014, Biosensors & bioelectronics.

[14]  Ángel Maquieira,et al.  Fast screening methods to detect antibiotic residues in food samples , 2010 .

[15]  Shiru Jia,et al.  Fast determination of the tetracyclines in milk samples by the aptamer biosensor. , 2010, The Analyst.

[16]  R. Breaker,et al.  In-line probing analysis of riboswitches. , 2008, Methods in molecular biology.

[17]  Xuewen Lu,et al.  A sensitive lateral flow biosensor for Escherichia coli O157:H7 detection based on aptamer mediated strand displacement amplification. , 2015, Analytica chimica acta.

[18]  James W. Brown,et al.  RNAML: a standard syntax for exchanging RNA information. , 2002, RNA.

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

[20]  John D Brennan,et al.  Patterned paper sensors printed with long-chain DNA aptamers. , 2015, Chemistry.