Development of a Biosensor for Ergot Alkaloids
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Thesis Proefschrift voorgelegd tot het behalen van de graad van Doctor in de Wetenschappen aan de Universiteit Antwerpen Dissertation for the degree of Doctor in Sciences at the University of Antwerp Development of a biosensor for ergot alkaloids Te verdedigen door/To be defended by: Elsa Rouah-Martin Promotoren/Supervisors: Dr. Johan Robbens and Prof. Ronny Blust Antwerpen 2016 This study was funded by the Federal Public Service of Health, Food Chain Safety and Environment (FOD) project Ergot RF6204. This PhD thesis was supported by a Dehousse grant and by the Institute for Agricultural and Fisheries Research (ILVO). Acknowledgements Regarding this PhD project, the first person to be acknowledged is Dr. Johan Robbens, who wrote this topic, which was accepted by the Federal Public Service of Health, Food Chain Safety and Environment (FOD). I am very grateful to Dr. Johan Robbens for having initiated projects about biosensing technologies and gathering different skills in his team, which revealed to be a fruitful research. I also thank Prof. Ronny Blust for allowing the realization of this work in the field of biosensing technologies, which was uncommon for a laboratory of physiology and ecotoxicology. Thanks to this support, it was possible to work on a passionating and innovative project, opening new horizons in the very recent context of biotechnologies, and more especially the use of biological ligands in sensors. Regarding my past as a scientist, and more particularly as a chemist, the use of ligands to bind to pollutants was already one of my favorite topics, as I worked on ligands used for the extraction of lanthanides used as models for the extraction of radioactive elements from radioactive effluents during my Master in Chemistry at the University of Burgundy, under the supervision of Prof. Michel Meyer (University of Burgundy, France). There, I had the opportunity to synthesize chemical ligands binding to lanthanides, study the complexes formed and finally graft them onto a silica columns allowing the extraction of lanthanides from solutions. These ligands were then used by the Commission à l'Energie Atomique to remove radioactive elements from radioactive effluents. Although I enjoyed working on this project, I wished this process would serve other applications than supporting nuclear energy industry and would rather be used for environmental purposes such as the decontamination of radioactively polluted sites. This different point of view about the use of the ligands synthesized, and in a more general way about the use of radioactivity, made me renounce doing a PhD there. However, the study was very interesting and I particularly enjoyed working on Europium element. There, I also learnt a lot about ligands and I always thought to come back one day to the synthesis and use of new ligands for environmental purposes. Then, I started my PhD at the University of Antwerp with Dr. Johan Robbens, who brought me towards the very recent use of synthetic DNA ligands, named aptamers, which can be specifically selected for any compound of interest and used as sensing tools in biosensors. As the use of biological ligands was new for me, I had to learn about the techniques of molecular biology, such as DNA selection and amplification, and molecular cloning. Fortunately, Dr. Jaytry Mehta, molecular biologist and mathematician, was there in the team of Dr. Johan Robbens, together with Dr. Bieke Van Dorst, bioengineer, to help me with this part. I am especially thankful to Dr. Jaytry Mehta, who friendly taught me a lot about aptamers and all the practical work in the laboratory. I really appreciated our constructive talks, which helped me to have a better understanding of the phenomenons underlying the results we obtained. It was always a pleasure to work with you, Jaytry. Bieke Van Dorst is also a person I appreciated a lot and I have to thank many times for at least all the I publications we wrote together. Unfortunately, I arrived in the laboratory when Bieke was ending her PhD, and we did not have so much time to spend together in the laboratory, neither to run all the experiments we wished. Throughout this innovative project involving chemistry and biology, I needed the help of quite a few scientists. Along the way, I met interesting people, who have really played an important role in my PhD. First, Prof. Sarah De Saeger is to be thanked for having organized the Ergot FOD project, having allowed me working with ergot alkaloids and having provided me the standards as well as natural ergot contaminated samples. In this same team of the Ergot FOD project, I thank Prof. Peter Dubruel for his interesting suggestions about organic synthesis. Regarding the problems that arised in this project, I am very grateful to Prof. Bert Maes, who nicely guided me to find a way to obtain the ergot alkaloid template, on which the study was based. Dr. Tom Raws is to be thanked for having done the little-risky chemical cleavage of metergoline. Then, I thank Prof. Erik Goormaghtigh, who helped me with the infrared analysis of ergot-coated material. Also, I thank Prof. Wouter Herrebout for having made possible the infrared analysis in his laboratory. I also thank the team of Prof. Lemiere and Norbert Hancke for having analyzed by mass spectrometry my synthesis products. Prof. François Van Hove is acknowledged for his interest in this topic and for having evaluated the results obtained as a jury member of the FOD project. I especially thank Prof. François Van Hove for having elucidated the mechanism underlying the results obtained with the surface plasmon resonance analysis, and improving the quality of the article that was published about the selection of aptamers for ergot alkaloids. I have to thank Dr. Larysa Darchuck for having done a Raman analysis of the complexes of DNA and ergot alkaloids. Unfortunately, due to the complexity of the results, this analysis could not be completed as Larysa's contract was already ending. I really wished we could proceed further with this analysis, and maybe write an article about it. Then, I thank Prof. Adrian Covaci and Lic. Walid Maho for having done the mass spectrometry analysis of the samples in the study of extraction of ergot alkaloids from naturally ergot contaminated samples by DNA-supported silica. I also thank all the jury members for the reviewing of this thesis and their comments and suggestions in the redaction of this thesis. Then, I thank the members of the SPHERE (Laboratory of Systemic Physiological and Ecotoxicological Research) laboratory, alias EBT, who made it a good working atmosphere. The SPHERE laboratory, of what it became in a more personnal view, "my sphere of innovation in sensing technology and extraction systems", was a pleasant environment for the realization of this PhD project. I sincerely hope that this present thesis will be representative of the work accomplished and informative enough for the reader to enter the huge world of small molecules. And finally, I have to thank my great family for always having supported me in my projects. II Table of Content List of abbreviations p. 1 Introduction 3 1. Definition and history of ergot 2. Fungi and plant species producing ergot alkaloids 4 2.1. Main species of the genus Claviceps 2.2. Superior plants producing ergot alkaloids 9 3. Economic impact of ergot 10 4. Regulations concerning ergot 11 5. Analytical and chemical techniques for the identification of ergot 12 alkaloids 5.1. Thin-layer chromatography (TLC) 5.2. High-pressure liquid chromatography (HPLC) 5.3. Mass spectrometry techniques 13 5.4. Capillary zone electrophoresis (CZE) 6. Conclusion 14 Chapter I: Aim and outline of this PhD study 23 1. Problem 2. Production of recognition elements for ergot alkaloids 2.1. Ligands used in sensing and extraction systems 2.1.1. Chemical ligands 24 2.1.2. Biological ligands 27 III 2.2. Selection of DNA aptamers for ergot alkaloids 32 2.3. Monitoring the formation of complexes between ergot alkaloids and 33 DNA aptamers 3. Production of an aptamer-based optical test for ergot alkaloids 34 4. Other applications with the aptamers selected for ergot alkaloids 35 Chapter II: Chemistry of Ergot alkaloids 43 1. Introduction 2. Classification of ergot alkaloids 44 2.1. Lysergic acid and its simple amides 2.2. Clavines 45 2.3. Peptide ergot alkaloids 46 2.4. Synthetic ergot alkaloids 48 3. Experimental part I: Synthesis of a template ergot alkaloid 49 3.1. Materials and Method 50 3.2. Mass spectrometry analysis of the product of the reaction 4. Experimental Part II: Coating of magnetic beads with ergot 51 alkaloids 4.1. Materials and method 4.2. Results and Discussion 53 5. Conclusion 56 Chapter III: Selection of DNA aptamers for ergot alkaloids 61 1. Introduction 2. Chemical structures of nucleic acids 62 2.1. RNA IV 2.2. DNA 2.3. Other types of synthetic nucleic acids 63 3. Hybridization assays with nucleic acids 64 4. Nucleic acid aptamers 65 4.1. Systematic Evolution of Ligands by EXponential enrichment (SELEX) 4.2. Polymerase Chain Reaction (PCR) 68 4.3. Gel electrophoresis 69 4.4. Cloning and sequencing of aptamers 70 5. Experimental Part: Selection of DNA aptamers for ergot alkaloids 71 5.1. Materials and Methods 5.2. Results and Discussion 76 6. Conclusion 84 Chapter IV: Study of the complexes formed by ergot 91 alkaloids and DNA aptamers 1. Introduction 2. Binding parameters of a complex 3. Techniques for the determination of the binding parameters of a 92 complex 3.1. Quartz Crystal Microbalance (QCM) 93 3.2. Surface Plasmon Resonance (SPR) 3.3. Isothermal Titration Calorimetry (ITC) 96 3.4. Fluorescence techniques 97 3.5.