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Generation of Aptamers Against Natural Toxins and Their Application as Biosensors

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Applied RNA Bioscience
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Abstract

RNA or ssDNA aptamers, which are capable of binding to target molecules with high affinity and specificity, are selected in vitro from large combinatorial nucleic acid libraries by a process known as systematic evolution of ligands by exponential enrichment (SELEX). Using this SELEX technology, many aptamers have been generated against a wide range of target molecules, including proteins, nucleic acids, small molecules, and whole cells. In this chapter, we described various methods for generating aptamers, including methods that do not require target immobilization. Among these aptamers, ones that are specific for natural toxins, such as mycotoxins, are of great interest to the food industry, as they can used in developing tools (biosensors) for ensuring food safety. We also summarized several aptamer-based detection strategies. Lastly, we described biosensor applications of aptamers for natural toxins.

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References

  • Andrade MA, Lancas FM (2017) Determination of Ochratoxin A in wine by packed in-tube solid phase microextraction followed by high performance liquid chromatography coupled to tandem mass spectrometry. J Chromatogr A 1493:41–48

    Article  CAS  Google Scholar 

  • Aquino-Jarquin G, Toscano-Garibay JD (2011) RNA aptamer evolution: two decades of SELEction. Int J Mol Sci 12:9155–9171

    Article  CAS  Google Scholar 

  • Breidbach A (2017) A greener, quick and comprehensive extraction approach for LC-MS of multiple mycotoxins. Toxins 9:E91

    Article  Google Scholar 

  • Bunka DH, Stockley PG (2006) Aptamers come of age – at last. Nat Rev Microbiol 4:588–596

    Article  CAS  Google Scholar 

  • Cerchia L, Duconge F, Pestourie C, Boulay J, Aissouni Y, Gombert K, Tavitian B, de Franciscis V, Libri D (2005) Neutralizing aptamers from whole-cell SELEX inhibit the RET receptor tyrosine kinase. PLoS Biol 3:e123

    Article  Google Scholar 

  • Chang TW, Janardhanan P, Mello CM, Singh BR, Cai S (2016) Selection of RNA aptamers against botulinum neurotoxin type A light chain through a non-radioactive approach. Appl Biochem Biotechnol 180:10–25

    Article  CAS  Google Scholar 

  • Chen X, Huang Y, Duan N, Wu S, Xia Y, Ma X, Zhu C, Jiang Y, Wang Z (2014) Screening and identification of DNA aptamers against T-2 toxin assisted by graphene oxide. J Agric Food Chem 62:10368–10374

    Article  CAS  Google Scholar 

  • Chiuman W, Li Y (2007) Simple fluorescent sensors engineered with catalytic DNA ‘MgZ’ based on a non-classic allosteric design. PLoS One 2:e1224

    Article  Google Scholar 

  • Cho M, Xiao Y, Nie J, Stewart R, Csordas AT, Oh SS, Thomson JA, Soh HT (2010) Quantitative selection of DNA aptamers through microfluidic selection and high-throughput sequencing. Proc Natl Acad Sci USA 107:15373–15378

    Article  CAS  Google Scholar 

  • Crosby NT (1984) Review of current and future analytical methods for the determination of mycotoxins. Food Addit Contam 1:39–44

    Article  CAS  Google Scholar 

  • Cruz-Aguado JA, Penner G (2008) Determination of ochratoxin a with a DNA aptamer. J Agric Food Chem 56:10456–10461

    Article  CAS  Google Scholar 

  • Daniels DA, Chen H, Hicke BJ, Swiderek KM, Gold L (2003) A tenascin-C aptamer identified by tumor cell SELEX: systematic evolution of ligands by exponential enrichment. Proc Natl Acad Sci USA 100:15416–15421

    Article  CAS  Google Scholar 

  • de Silva C, Walter NG (2009) Leakage and slow allostery limit performance of single drug-sensing aptazyme molecules based on the hammerhead ribozyme. RNA 15:76–84

    Article  Google Scholar 

  • Dobbelstein M, Shenk T (1995) In vitro selection of RNA ligands for the ribosomal L22 protein associated with Epstein-Barr virus-expressed RNA by using randomized and cDNA-derived RNA libraries. J Virol 69:8027–8034

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ellington AD, Szostak JW (1990) In vitro selection of RNA molecules that bind specific ligands. Nature 346:818–822

    Article  CAS  Google Scholar 

  • El-Moghazy AY, Soliman EA, Ibrahim HZ, Noguer T, Marty JL, Istamboulie G (2016) Ultra-sensitive biosensor based on genetically engineered acetylcholinesterase immobilized in poly (vinyl alcohol)/Fe-Ni alloy nanocomposite for phosmet detection in olive oil. Food Chem 203:73–78

    Article  CAS  Google Scholar 

  • Fang X, Tan W (2010) Aptamers generated from cell-SELEX for molecular medicine: a chemical biology approach. Acc Chem Res 43:48–57

    Article  CAS  Google Scholar 

  • Fedor MJ, Uhlenbeck OC (1992) Kinetics of intermolecular cleavage by hammerhead ribozymes. Biochemistry 31:12042–12054

    Article  CAS  Google Scholar 

  • Feng C, Dai S, Wang L (2014) Optical aptasensors for quantitative detection of small biomolecules: a review. Biosens Bioelectron 59:64–74

    Article  CAS  Google Scholar 

  • Forster AC, Symons RH (1987) Self-cleavage of virusoid RNA is performed by the proposed 55-nucleotide active site. Cell 50:9–16

    Article  CAS  Google Scholar 

  • Frauendorf C, Jaschke A (2001) Detection of small organic analytes by fluorescing molecular switches. Bioorg Med Chem 9:2521–2524

    Article  CAS  Google Scholar 

  • Furukawa K, Gu H, Breaker RR (2014) In vitro selection of allosteric ribozymes that sense the bacterial second messenger c-di-GMP. Methods Mol Biol 1111:209–220

    Article  CAS  Google Scholar 

  • Gu H, Furukawa K, Breaker RR (2012) Engineered allosteric ribozymes that sense the bacterial second messenger cyclic diguanosyl 5′-monophosphate. Anal Chem 84:4935–4941

    Article  CAS  Google Scholar 

  • Gu H, Duan N, Wu S, Hao L, Xia Y, Ma X, Wang Z (2016) Graphene oxide-assisted non-immobilized SELEX of okdaic acid aptamer and the analytical application of aptasensor. Sci Rep 6:21665

    Article  CAS  Google Scholar 

  • Guo X, Wen F, Zheng N, Luo Q, Wang H, Wang H, Li S, Wang J (2014) Development of an ultrasensitive aptasensor for the detection of aflatoxin B1. Biosens Bioelectron 56:340–344

    Article  CAS  Google Scholar 

  • Guo X, Wen F, Zheng N, Li S, Fauconnier ML, Wang J (2016) A qPCR aptasensor for sensitive detection of aflatoxin M1. Anal Bioanal Chem 408:5577–5584

    Article  CAS  Google Scholar 

  • Ha TH (2015) Recent advances for the detection of Ochratoxin A. Toxins 7:5276–5300

    Article  CAS  Google Scholar 

  • He J, Liu Y, Fan M, Liu X (2011) Isolation and identification of the DNA aptamer target to acetamiprid. J Agric Food Chem 59:1582–1586

    Article  CAS  Google Scholar 

  • Hu W, Li X, He G, Zhang Z, Zheng X, Li P, Li CM (2013) Sensitive competitive immunoassay of multiple mycotoxins with non-fouling antigen microarray. Biosens Bioelectron 50:338–344

    Article  CAS  Google Scholar 

  • Huang CJ, Lin HI, Shiesh SC, Lee GB (2010) Integrated microfluidic system for rapid screening of CRP aptamers utilizing systematic evolution of ligands by exponential enrichment (SELEX). Biosens Bioelectron 25:1761–1766

    Article  CAS  Google Scholar 

  • Janardhanan P, Mello CM, Singh BR, Lou J, Marks JD, Cai S (2013) RNA aptasensor for rapid detection of natively folded type A botulinum neurotoxin. Talanta 117:273–280

    Article  CAS  Google Scholar 

  • Jenison RD, Gill SC, Pardi A, Polisky B (1994) High-resolution molecular discrimination by RNA. Science 263:1425–1429

    Article  CAS  Google Scholar 

  • Jenne A, Hartig JS, Piganeau N, Tauer A, Samarsky DA, Green MR, Davies J, Famulok M (2001) Rapid identification and characterization of hammerhead-ribozyme inhibitors using fluorescence-based technology. Nat Biotechnol 19:56–61

    Article  CAS  Google Scholar 

  • Jensen KB, Atkinson BL, Willis MC, Koch TH, Gold L (1995) Using in vitro selection to direct the covalent attachment of human immunodeficiency virus type 1 Rev protein to high-affinity RNA ligands. Proc Natl Acad Sci USA 92:12220–12224

    Article  CAS  Google Scholar 

  • Kim HK, Liu J, Li J, Nagraj N, Li M, Pavot CM, Lu Y (2007) Metal-dependent global folding and activity of the 8-17 DNAzyme studied by fluorescence resonance energy transfer. J Am Chem Soc 129:6896–6902

    Article  CAS  Google Scholar 

  • Klug SJ, Famulok M (1994) All you wanted to know about SELEX. Mol Biol Rep 20:97–107

    Article  CAS  Google Scholar 

  • Klussmann S, Nolte A, Bald R, Erdmann VA, Furste JP (1996) Mirror-image RNA that binds D-adenosine. Nat Biotechnol 14:1112–1115

    Article  CAS  Google Scholar 

  • Koizumi M, Soukup GA, Kerr JN, Breaker RR (1999) Allosteric selection of ribozymes that respond to the second messengers cGMP and cAMP. Nat Struct Biol 6:1062–1071

    Article  CAS  Google Scholar 

  • Kulbachinskiy AV (2007) Methods for selection of aptamers to protein targets. Biochem Biokhim 72:1505–1518

    Article  CAS  Google Scholar 

  • Lai HC, Wang CH, Liou TM, Lee GB (2014) Influenza A virus-specific aptamers screened by using an integrated microfluidic system. Lab Chip 14:2002–2013

    Article  CAS  Google Scholar 

  • Lipi F, Chen S, Chakravarthy M, Rakesh S, Veedu RN (2016) In vitro evolution of chemically-modified nucleic acid aptamers: pros and cons, and comprehensive selection strategies. RNA Biol 13:1232–1245

    Article  Google Scholar 

  • Liu J, Lu Y (2006) Preparation of aptamer-linked gold nanoparticle purple aggregates for colorimetric sensing of analytes. Nat Protoc 1:246–252

    Article  CAS  Google Scholar 

  • Lou X, Qian J, Xiao Y, Viel L, Gerdon AE, Lagally ET, Atzberger P, Tarasow TM, Heeger AJ, Soh HT (2009) Micromagnetic selection of aptamers in microfluidic channels. Proc Natl Acad Sci USA 106:2989–2994

    Article  CAS  Google Scholar 

  • Luan Y, Chen J, Li C, Xie G, Fu H, Ma Z, Lu A (2015a) Highly sensitive colorimetric detection of Ochratoxin A by a label-free aptamer and gold nanoparticles. Toxins 7:5377–5385

    Article  CAS  Google Scholar 

  • Luan Y, Chen Z, Xie G, Chen J, Lu A, Li C, Fu H, Ma Z, Wang J (2015b) Rapid visual detection of Aflatoxin B1 by label-free aptasensor using unmodified gold nanoparticles. J Nanosci Nanotechnol 15:1357–1361

    Article  CAS  Google Scholar 

  • Malhotra S, Pandey AK, Rajput YS, Sharma R (2014) Selection of aptamers for aflatoxin M1 and their characterization. J Mol Recognit 27:493–500

    Article  CAS  Google Scholar 

  • Marton S, Cleto F, Krieger MA, Cardoso J (2016) Isolation of an aptamer that binds specifically to E. coli. PLoS One 11:e0153637

    Article  Google Scholar 

  • Mayer G, Ahmed MS, Dolf A, Endl E, Knolle PA, Famulok M (2010) Fluorescence-activated cell sorting for aptamer SELEX with cell mixtures. Nat Protoc 5:1993–2004

    Article  CAS  Google Scholar 

  • McKeague M, Bradley CR, De Girolamo A, Visconti A, Miller JD, Derosa MC (2010) Screening and initial binding assessment of fumonisin b(1) aptamers. Int J Mol Sci 11:4864–4881

    Article  CAS  Google Scholar 

  • Mendonsa SD, Bowser MT (2004) In vitro selection of high-affinity DNA ligands for human IgE using capillary electrophoresis. Anal Chem 76:5387–5392

    Article  CAS  Google Scholar 

  • Morris KN, Jensen KB, Julin CM, Weil M, Gold L (1998) High affinity ligands from in vitro selection: complex targets. Proc Natl Acad Sci USA 95:2902–2907

    Article  CAS  Google Scholar 

  • Nguyen VT, Kwon YS, Kim JH, Gu MB (2014) Multiple GO-SELEX for efficient screening of flexible aptamers. Chem Commun 50:10513–10516

    Article  CAS  Google Scholar 

  • Nutiu R, Li Y (2003) Structure-switching signaling aptamers. J Am Chem Soc 125:4771–4778

    Article  CAS  Google Scholar 

  • Nutiu R, Li Y (2005a) Aptamers with fluorescence-signaling properties. Methods 37:16–25

    Article  CAS  Google Scholar 

  • Nutiu R, Li Y (2005b) In vitro selection of structure-switching signaling aptamers. Angew Chem Int Ed 44:1061–1065

    Article  CAS  Google Scholar 

  • Ogihara K, Savory N, Abe K, Yoshida W, Asahi M, Kamohara S, Ikebukuro K (2015) DNA aptamers against the Cry j 2 allergen of Japanese cedar pollen for biosensing applications. Biosens Bioelectron 63:159–165

    Article  CAS  Google Scholar 

  • Oh SS, Qian J, Lou X, Zhang Y, Xiao Y, Soh HT (2009) Generation of highly specific aptamers via micromagnetic selection. Anal Chem 81:5490–5495

    Article  CAS  Google Scholar 

  • Park JW, Tatavarty R, Kim DW, Jung HT, Gu MB (2012) Immobilization-free screening of aptamers assisted by graphene oxide. Chem Commun 48:2071–2073

    Article  CAS  Google Scholar 

  • Park JW, Jin Lee S, Choi EJ, Kim J, Song JY, Bock Gu M (2014) An ultra-sensitive detection of a whole virus using dual aptamers developed by immobilization-free screening. Biosens Bioelectron 51:324–329

    Article  CAS  Google Scholar 

  • Pelossof G, Tel-Vered R, Elbaz J, Willner I (2010) Amplified biosensing using the horseradish peroxidase-mimicking DNAzyme as an electrocatalyst. Anal Chem 82:4396–4402

    Article  CAS  Google Scholar 

  • Raddatz MS, Dolf A, Endl E, Knolle P, Famulok M, Mayer G (2008) Enrichment of cell-targeting and population-specific aptamers by fluorescence-activated cell sorting. Angew Chem Int Ed 47:5190–5193

    Article  CAS  Google Scholar 

  • Rhouati A, Yang C, Hayat A, Marty JL (2013) Aptamers: a promising tool for ochratoxin A detection in food analysis. Toxins 5:1988–2008

    Article  CAS  Google Scholar 

  • Richard JL (2007) Some major mycotoxins and their mycotoxicoses – an overview. Int J Food Microbiol 119:3–10

    Article  CAS  Google Scholar 

  • Robertson DL, Joyce GF (1990) Selection in vitro of an RNA enzyme that specifically cleaves single-stranded DNA. Nature 344:467–468

    Article  CAS  Google Scholar 

  • Roll R, Matthiaschk G, Korte A (1990) Embryotoxicity and mutagenicity of mycotoxins. J Environ Pathol Toxicol Oncol 10:1–7

    CAS  PubMed  Google Scholar 

  • Sassanfar M, Szostak JW (1993) An RNA motif that binds ATP. Nature 364:550–553

    Article  CAS  Google Scholar 

  • Seok Y, Byun JY, Shim WB, Kim MG (2015) A structure-switchable aptasensor for aflatoxin B1 detection based on assembly of an aptamer/split DNAzyme. Anal Chim Acta 886:182–187

    Article  CAS  Google Scholar 

  • Shangguan D, Li Y, Tang Z, Cao ZC, Chen HW, Mallikaratchy P, Sefah K, Yang CJ, Tan W (2006) Aptamers evolved from live cells as effective molecular probes for cancer study. Proc Natl Acad Sci USA 103:11838–11843

    Article  CAS  Google Scholar 

  • Sharma A, Catanante G, Hayat A, Istamboulie G, Ben Rejeb I, Bhand S, Marty JL (2016) Development of structure switching aptamer assay for detection of aflatoxin M1 in milk sample. Talanta 158:35–41

    Article  CAS  Google Scholar 

  • Singh KK, Parwaresch R, Krupp G (1999) Rapid kinetic characterization of hammerhead ribozymes by real-time monitoring of fluorescence resonance energy transfer (FRET). RNA 5:1348–1356

    Article  CAS  Google Scholar 

  • Soh JH, Lin Y, Rana S, Ying JY, Stevens MM (2015) Colorimetric detection of small molecules in complex matrixes via target-mediated growth of aptamer-functionalized gold nanoparticles. Anal Chem 87:7644–7652

    Article  CAS  Google Scholar 

  • Soukup GA, Breaker RR (1999) Engineering precision RNA molecular switches. Proc Natl Acad Sci USA 96:3584–3589

    Article  CAS  Google Scholar 

  • Soukup GA, Emilsson GA, Breaker RR (2000) Altering molecular recognition of RNA aptamers by allosteric selection. J Mol Biol 298:623–632

    Article  CAS  Google Scholar 

  • Stoltenburg R, Reinemann C, Strehlitz B (2005) FluMag-SELEX as an advantageous method for DNA aptamer selection. Anal Bioanal Chem 383:83–91

    Article  CAS  Google Scholar 

  • Stoltenburg R, Reinemann C, Strehlitz B (2007) SELEX – a (r)evolutionary method to generate high-affinity nucleic acid ligands. Biomol Eng 24:381–403

    Article  CAS  Google Scholar 

  • Tang Z, Shangguan D, Wang K, Shi H, Sefah K, Mallikratchy P, Chen HW, Li Y, Tan W (2007) Selection of aptamers for molecular recognition and characterization of cancer cells. Anal Chem 79:4900–4907

    Article  CAS  Google Scholar 

  • Tomita Y, Morita Y, Suga H, Fujiwara D (2016) DNA module platform for developing colorimetric aptamer sensors. BioTechniques 60:285–292

    Article  Google Scholar 

  • Travascio P, Li Y, Sen D (1998) DNA-enhanced peroxidase activity of a DNA-aptamer-hemin complex. Chem Biol 5:505–517

    Article  CAS  Google Scholar 

  • Tuerk C, Gold L (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249:505–510

    Article  CAS  Google Scholar 

  • Turner NW, Subrahmanyam S, Piletsky SA (2009) Analytical methods for determination of mycotoxins: a review. Anal Chim Acta 632:168–180

    Article  CAS  Google Scholar 

  • Vater A, Klussmann S (2003) Toward third-generation aptamers: Spiegelmers and their therapeutic prospects. Curr Opin Drug Discov Dev 6:253–261

    CAS  Google Scholar 

  • Wang L, Liu X, Zhang Q, Zhang C, Liu Y, Tu K, Tu J (2012) Selection of DNA aptamers that bind to four organophosphorus pesticides. Biotechnol Lett 34:869–874

    Article  CAS  Google Scholar 

  • Wang B, Chen Y, Wu Y, Weng B, Liu Y, Lu Z, Li CM, Yu C (2016) Aptamer induced assembly of fluorescent nitrogen-doped carbon dots on gold nanoparticles for sensitive detection of AFB1. Biosens Bioelectron 78:23–30

    Article  CAS  Google Scholar 

  • Watanabe M, Shimizu H (2005) Detection of patulin in apple juices marketed in the Tohoku district, Japan. J Food Protect 68:610–612

    Article  CAS  Google Scholar 

  • Wu ZS, Lu H, Liu X, Hu R, Zhou H, Shen G, Yu RQ (2010) Inhibitory effect of target binding on hairpin aptamer sticky-end pairing-induced gold nanoparticle assembly for light-up colorimetric protein assay. Anal Chem 82:3890–3898

    Article  CAS  Google Scholar 

  • Wu S, Duan N, Li X, Tan G, Ma X, Xia Y, Wang Z, Wang H (2013) Homogenous detection of fumonisin B(1) with a molecular beacon based on fluorescence resonance energy transfer between NaYF4: Yb, Ho upconversion nanoparticles and gold nanoparticles. Talanta 116:611–618

    Article  CAS  Google Scholar 

  • Xiang Y, Wang Z, Xing H, Wong NY, Lu Y (2010) Label-free fluorescent functional DNA sensors using unmodified DNA: a vacant site approach. Anal Chem 82:4122–4129

    Article  CAS  Google Scholar 

  • Xu Y, Yang X, Wang E (2010) Review: aptamers in microfluidic chips. Anal Chim Acta 683:12–20

    Article  CAS  Google Scholar 

  • Xu L, Zhang Z, Zhang Q, Li P (2016) Mycotoxin determination in foods using advanced sensors based on antibodies or aptamers. Toxins 8:E239

    Article  Google Scholar 

  • Yang J, Bowser MT (2013) Capillary electrophoresis-SELEX selection of catalytic DNA aptamers for a small-molecule porphyrin target. Anal Chem 85:1525–1530

    Article  CAS  Google Scholar 

  • Yang Y, Yang D, Schluesener HJ, Zhang Z (2007) Advances in SELEX and application of aptamers in the central nervous system. Biomol Eng 24:583–592

    Article  CAS  Google Scholar 

  • Yang C, Wang Y, Marty JL, Yang X (2011) Aptamer-based colorimetric biosensing of Ochratoxin A using unmodified gold nanoparticles indicator. Biosens Bioelectron 26:2724–2727

    Article  CAS  Google Scholar 

  • Zhao W, Chiuman W, Brook MA, Li Y (2007) Simple and rapid colorimetric biosensors based on DNA aptamer and noncrosslinking gold nanoparticle aggregation. Chembiochem 8:727–731

    Article  CAS  Google Scholar 

  • Zhao W, Brook MA, Li Y (2008) Design of gold nanoparticle-based colorimetric biosensing assays. Chembiochem 9:2363–2371

    Article  CAS  Google Scholar 

  • Zivarts M, Liu Y, Breaker RR (2005) Engineered allosteric ribozymes that respond to specific divalent metal ions. Nucleic Acids Res 33:622–631

    Article  CAS  Google Scholar 

  • Zollner P, Mayer-Helm B (2006) Trace mycotoxin analysis in complex biological and food matrices by liquid chromatography-atmospheric pressure ionisation mass spectrometry. J Chromatogr A 1136:123–169

    Article  Google Scholar 

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Acknowledgments

We thank Dr. Yasuyuki Tomita for helpful discussions.

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Correspondence to Yuji Morita .

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Morita, Y., Fujiwara, D. (2018). Generation of Aptamers Against Natural Toxins and Their Application as Biosensors. In: Masuda, S., Izawa, S. (eds) Applied RNA Bioscience. Springer, Singapore. https://doi.org/10.1007/978-981-10-8372-3_5

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