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Pour Sonder La Bioaffinité Et Les Interactions Biocatalytiques De Petits Xénobiotiques

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Pour Sonder La Bioaffinité Et Les Interactions Biocatalytiques De Petits Xénobiotiques d’ordre: 2007-12 Année 2007 THESE EN COCO----TUTELLETUTELLE entre l’Ecole Centrale de Lyon, France (Ecole doctorale Electronique, Electrotechnique, Automatique ) et l’Institut de Biologie Moléculaire et Génétique, Kyiv, Ukraine (Discipline : Biotechnologie) présentée devant Ecole Centrale de Lyon pour obtenir le grade de DOCTEUR d’ECOLE CENTRALE DE LYON soutenue publiquement le 15 juin 2007 par Iryna BENILOVA née SKSKRYSHEVSKARYSHEVSKA AppApprocheroche « biocapteur » pour sonder la bioaffinité et les interactions biocatalytiques de petits xénobiotiques Jury: Dr. Nicole JAFFREZIC-RENAULT Présidente Pr. Roland SALESSE Rapporteur Dr. Alexandr KUKLA Rapporteur Pr. Claude MARTELET Directeur de thèse (France) Pr. Alexey SOLDATKIN Directeur de thèse (Ukraine) Dr. Sergey DZYADEVYCH Examinateur AcknowledAcknowledggggmentsments The present work was carried out in the former laboratory CEGELY (now AMPERE) of Ecole Centrale de Lyon (ECL) in collaboration with the Laboratory of Biomolecular Electronics (LBME) in the Institute of Molecular Biology and Genetics (IMBG) of National Academy of Sciences of Ukraine (NASU). These institutions are gratefully acknowledged. My work in French laboratories was financially supported by EGIDE (France). I wish to thank my French supervisors, Professor Claude Martelet and Professor Nicole Jaffrezic-Renault for accepting me in CEGELY for my “co- tutelle” thesis. I am infinitely grateful for their confidence in me, their priceless help and generosity and, of course, for our fruitful scientific discussions during these years. I warmly thank Academician Anna V. El’skaya, the Director of IMBG NASU, and my Ukrainian supervisor, Professor Alexey P. Soldatkin, the Head of LBME, for giving me the chance to start my research work in the LBME and to continue it in the Ecole Centrale de Lyon. Their constant scientific and moral support has been very precious to me. I am also very grateful to Pr. Roland Salesse, Dr. Alexandr Kukla and Dr. Sergey Dzyadevych for accepting to judge this work and for their opinions. Warm thanks to Pr. Didier Leonard and Dr. Francois Bessueille from Laboratoire de Sciences Analytiques (Université Claude Bernard – Lyon 1) for their gentleness and kind help with some manipulations. I would like to acknowledge Drs. Valentina Arkhypova, Alexandr Rachkov and Yaroslav Korpan (LBE IMBG) for all their priceless help, support and sympathy. I thank Drs. Vladimir Chegel and Yuri Ushenin from the Institute of Semiconductor Physics NASU, for initiating me in optical biosensors, for their professional advices and especially for our fruitful “New-Year collaboration” in December 2006-January 2007 which gave rise to the Part 6 of this thesis. I would like to take the opportunity to thank Dr. Edith Pajot from INRA de Jouy-en-Josas, for her kindness, patience and all priceless help given me during all the time of my work with olfactory receptors. My special thanks to Mmes Monique Lacroix, Anne Zucco, Josiane Chabert, Maryline Bonnefoi and Mr. Philippe Billoux for their precious help in my démarches administratives . I am also very grateful to Mme Nina R. Polischuk for editing my first article in English. I want to warmly thank all my colleagues and friends for the unforgettable time we have had together: i) Ali, Basma, Chaker, Houcine, Imen, Mauricio, Mouna, Rita, Rodicka, Walid-1 (Hassen), Zhichang and all others from AMPERE and UCBL-1; ii) Bedja, Chaiyan, Jean-Hubert, Lamine, Lazar, Le Ha, Lucas, Siméon, Thanh, Walid-2 and all others from H9 of ECL; iii) Alena, Andrusha, Lyuda, Nadia and Dima, Oleg, Pasha, Sanya, Sasha Nikolaich and Yulia, Sasha Yashkin, Vitalik and all others from Taras Shevtchenko University (Kyiv) and IMBG NASU. Special thanks to Sveta for her help in navigating the French capital, and to Anya for our pleasant colocation (April-May 2007). Finally, I would like to thank my parents, my parents-in-law and my husband Arthur for their constant and unconditional support: nothing would have been possible without it. TTTableTable of contents INTRODUCTION GENERALE 1 GENERAL INTRODUCTION 3 BIBLIOGRAPHIC REVIEW 5 1. Definition of a biosensor. 5 2. Transducer vs biorecognition event. Proper choice of detection mode. 6 3. Potent macromolecular targets of xenobiotics. 9 3.1.Biocatalytic recognition elements. 9 3.1.1. Enzymes. 9 3.1.2. Ribozymes. 10 3.2. Bioaffinity recognition elements. 11 3.2.1. Antibodies. 11 3.2.2. Lipocalins and anticalins. 12 3.2.3. Aptamers. 13 3.2.4. G protein-coupled receptors. 14 4. Immobilization of biorecognition element. 15 4.1. Covalent attachment. 16 4.2. Electrochemical attachment. 20 4.3. Physical attachment. 20 4.4. Entrapment. 22 5. Bulk properties of biofilms. 22 6. “Apparent” and “true” affinity. 24 7. Concluding remarks. 29 CHAPTER 1. Glycoalkaloids and cholinesterases 31 PART 1. Potato glycoalkaloids: true safety or false sense of security? 35 1. Introduction. 36 2. Potato glycoalkaloids and health. 37 3. Detection of potato GAs in foodstuffs and biological fluids. 39 4. Biotechnological aspects of potato breeding. 40 5. Concluding remarks. 43 PART 2. Cholinesterases inhibition by glycoalkaloidsglycoalkaloids:::: probing with potentiometric biosensorbiosensor.... 45 1. Introduction. 46 2. Experimental. 48 2.1. Materials. 48 2.2. pH-FETs. 49 2.3. Enzyme immobilization. 49 2.4. Measurements. 49 3. Results and discussion. 50 3.1. Optimal pH. 50 3.2. Specificity towards substrates. 51 3.3. Specificity towards inhibitors. 54 4. Conclusion and perspectives. 60 PART 333.3... Impedimetric study of glycoalkaloids binding to cholinesterase. 61 1. Introduction. 62 2. Experimental. 63 2.1. Materials. 63 2.2. Working electrodes. 64 2.2.1. Construction. 64 2.2.2. Surface cleaning. 64 2.2.3. Biofunctionalization. 64 2.3. Impedance measurements. 65 3. Results and discussion. 65 3.1. Biofilm stability. 65 3.2. Electrochemical characteristics of protein layers. 66 3.3. Impedimetry of glycoalkaloids. 67 3.4. Calibration curves. 70 4. Conclusion and perspectives. 72 CHAPTER 2. Odorants and olfactory receptors 73 PART 4. Natural, electronic and bioelectronic olfaction. 77 1. Introduction. 78 2. Detection of odorants. 79 3. From electronic to bioelectronic noses. 80 4. Concluding remarks. 83 PART 5. Electrochemical studstudyy of human olfactory receptor OR 1717----4040 stimulation by some odorantsodorants.... 85 1. Introduction. 86 2. Experimental. 87 2.1. Biomaterials and chemicals. 87 2.2. Single channel SPR spectrometer and gold coated substrates. 88 2.3. Pretreatment of sensor surface. 88 2.4. Self-assembly of the mixed layer on gold. 88 2.5. Blocking step and formation of the upper supporting layers. 89 2.6. Preparation and immobilization of OR 17-40. 89 2.7. Electrochemical probing. 90 2.8. Preparation of odorant solutions. 91 2.9. Monte-Carlo simulation. 91 3. Results and discussion. 92 3.1. Optical and electrochemical monitoring of biofilm assembly. 92 3.1.1. SPR monitoring. 92 3.1.2. Impedance monitoring. 95 3.2. Impedance study of already biofunctionalized SPR chips. 96 3.3. Impedance measurements in the presence of odorants at 20ºC. 98 3.4. Impedance measurements at 4ºC in the presence of odorants and GTP-K-S. 100 3.5. Impedimetric screening unrelated odorants. 104 3.6. Modeling the impact of nanosomes size on their anchoring. 105 4. Conclusion and perspectives. 107 PART 66.. Response pattern of human olfactory rreceptoreceptor OR 1717----4040 ppprobedprobed by surface plasmon resonanceresonance.... 109 1. Introduction. 110 2. Experimental. 110 2.1. Biomaterials and chemicals. 110 2.2. Sensor substrates and SPR spectrometer. 111 2.3. Pretreatment of sensor surface. 111 2.4. Two architectures of biofilms. 111 2.5. Preparation and immobilization of OR 17-40. 111 2.6. Preparation of odorants. 112 2.7. Cyclic voltammetry. 112 2.8. AFM. 113 3. Results. 113 3.1. Orientated and random immobilization of Ab. 113 3.2. Electrochemical properties of biofilms. 117 3.3. AFM study of biofilms. 118 3.4. Detection of odorant molecules. 120 4. Discussion. 123 5. Conclusion and perspectives. 125 CONCLUSION GENERALE ET PERSPECTIVES 127 GENERAL CONCLUSION AND PERSPECTIVES 129 ANNEX A. Potentiometry based on ISFETs (pH-FETs). 131 ANNEX B. Electrochemical impedance spectroscopy (EIS). 133 ANNEX C. CCC-C---1.1.1.1. Single channel SPR spectrometer and gold coated chips. 137 CCC-C---2.2.2.2. Double channel SPR spectrometer and gold coated chips. 140 ANNEX D. Plasmids designed for the heterologous expression of human olfactory receptor 17-40 and protein GM olf in yeast Saccharomyces cerevisiae (strain MC 18). 141 ANNEX E. EEE-E---1111. Preparation of helional, heptanal and blank probes for screening in the double channel SPR spectrometer. 143 EEE-E---2.2.2.2. Protocol of odorant screening in the double channel SPR spectrometer in differential mode. 144 EEE-E---3.3.3.3. Preparation of octanal, nonanal and vanillin. 144 BIBLIOGRAPHY 145 Publications et communications scientifiques 167 List of abbreviations Ab(s) antibody(-ies) AcChE acetyl cholinesterase AcChCl acetylcholine chloride AEAEAE auxiliary electrode AFAFAFMAF MMM atomic force microscopy Biotinyl PEA biotinylated phosphoethanol amine BSA bovine serum albumin BuChE butyryl cholinesterase BuChCl butyrylcholine chloride cAMP cyclic adenosine monophosphate CPE constant phase element CVCVCV cyclic voltammetry DMSO dimethylsulfoxide DNA desoxyribonucleic acid eBuChE equine butyryl cholinesterase EDC 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide EIS electrochemical impedance spectroscopy EST2 carboxyl esterase FRFRFR flow rate GA(s) glycoalkaloid(s)
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