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Forcing DNA and RNA Through Artificial Nanopores

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Forcing DNA and RNA Through Artificial Nanopores Forcing DNA and RNA through Artificial Nanopores Proefschrift ter verkrijging van de graad van doctor aan de Technische Universiteit Delft; op gezag van de Rector Magnificus prof. ir. K.C.A.M. Luyben, voorzitter van het College voor Promoties, in het openbaar te verdedigen op donderdag 21 oktober 2010 om 15.00 uur door Michiel VAN DEN HOUT doctorandus in de natuurkunde geboren te Leiderdorp. Dit proefschrift is goedgekeurd door de promotor: Prof. dr. N.H. Dekker Samenstelling van de promotiecommissie: Rector Magnificus Voorzitter Prof. dr. N.H. Dekker Technische Universiteit Delft, promotor Prof. dr. U. Gerland München, Germany Prof. dr. G.T. Barkema Universiteit Leiden Prof. dr. C. Dekker Technische Universiteit Delft Prof. dr. H.W. Zandbergen Technische Universiteit Delft Dr. U.F. Keyser Cambridge University, United Kingdom Dr. D. Stein Brown University, Verenigde Staten Keywords: RNA, DNA, nanopores, optical tweezers, single molecule, nanotechnology, electrophoresis Published by: Michiel van den Hout Cover design: Kasper van den Hout Printed by: Off Page The production of this thesis was financially supported by Delft University of Technology and J. van den Hout Beheer B.V. An electronic version of this dissertation is available at: http://www.library.tudelft.nl/dissertations/ Copyright © 2010 by Michiel van den Hout Casimir PhD series, Delft‐Leiden, 2010‐26 ISBN: 978‐90‐8593‐085‐3 Whatever you do will be insignificant, but it is very important that you do it Mahatma Gandhi Preface This is it. And this it can mean a lot of things. First, it refers to this preface, the only part of this book that most of its owners will actually read. Next, to you, the reader, it is likely to represent the part “where he writes something about me. It better be nice…”. Well.., it just might, you know. For me, it refers to this entire book, as it represents the culmination of more than four and a half years of my working life. It is also the opportunity to express my gratitude to those who participated in making it possible. But before that, I wish to briefly recall some recent history, as I believe it may be of some interest. I received my MSc degree in physics in 2001, after a year of research on carbon nanotubes under the very wise supervision of Serge Lemay and Cees Dekker. In the last months of my time there, Cees embarked on an entirely new scientific quest as he started his own Molecular Biophysics group. I had the privilege to be among the very first students to graduate as master of science in this new group. When I finally rejoined the group, after an intermezzo of four years of “real” work at ASM Europe, the group had flourished immensely and I found myself overwhelmed by the many excellent researchers of such a wide variety of backgrounds. Now, some nine years after my first Delft graduation, I feel again privileged, as I will be the first PhD student to graduate in what has evolved into an entirely new department: the department of Bionanoscience! Perhaps, if ever I might be tempted to return to academia in –say‐ five years, I expect nothing less than to see the birth of a completely new faculty of Bionanoscience, and a Delft University of Bionanoscience by 2025..? But now, let’s get on with it! I have many people to whom I wish to express my gratitude. First and foremost, my thanks go to Nynke, my promoter and supervisor, who made this all possible. Thank you for all your support, Nynke. You have taught me some valuable things, which I will benefit from for the rest of my life. First, you have taught me the importance of being accurate and precise. As my personality is such that I often prefer not to be very serious and accurate, this was sometimes a bit hard for me. Next, you have taught me the importance of obtaining results and the systematic approach that this typically requires. As both of these were not exactly abundantly present during the first couple of years, I am very happy that in the end everything worked out fine and this thesis actually contains a reasonable amount of pages with (to some people) even some quite interesting results. I (and with me, this thesis) have also benefited strongly from your excellent writing skills and scientific insight. Finally, I wish to express my gratitude to have been witness to the rise of the Nynke Dekker lab, which will no doubt (remain to) be very successful indeed. As the first student to be subject to your ius promovendi I wish you all the best in the future, particularly with the exciting new scientific directions you have recently started to explore. v Next, I want to thank Cees, who has been a source of great inspiration to me. Cees, it was you who made me enthusiastic about carbon nanotubes, some ten years ago. Five years later, it was again through you that I started on this project and I have always very much appreciated your close involvement. I have deep respect for your incredible energy, your quick mind, and your friendly and open attitude. Especially this last thing has made the group (and now the department) such a great place to work. You have the ability to gather a very interesting breed of people around you: intelligent, talented, but also very communicative and willing to have fun in other areas than science such as sports, music or just going out and having a drink. Most importantly, I have always very much appreciated your enthusiasm, which has helped me through some of the more difficult periods during my PhD. Then there are of course many other people who were directly involved in my research. Diego, you were the first person I had the pleasure of working with when I arrived. I realized I had forgotten everything about physics in my four years at ASM and you were a great help in getting me back on track. I enjoyed your impatient and often chaotic approach, and enthusiasm. Ulrich, I regret we had less interaction, but you were definitely always available for questions. In building (and using) my version of your setup, I have continuously been amazed at the level of complexity and subtlety in its design. You are brilliant! Stijn, you too, I trust you´ll do very well in your current research. Serge Lemay, unfortunately we haven’t had much interaction, but I happen to have experienced during my MSc project that you are the perfect teacher, and the best scientific speaker I know. After talking to you I always feel I have learned something new. Igor, thanks for all the help with the RNA and in the bio‐lab: you, Susanne and Andrea (“oi bellooooo, come andiomo?”) made life there a lot more bearable. It was both daunting (and I must admit: encouraging) to see the amount incredible bad luck you faced (and managed to overcome!) before your P2 experiment finally worked. And thanks for all the parties! Wiecher, thanks for skilfully exterminating the RNA ghost, it hasn’t been spotted since. Gary, my good sir knight, you were my saviour when nothing worked: after your short initial stay the experiments finally started rolling. Thanks for your inexhaustible optimism. The Adam, thanks for everything: the Tuesday beers, the Friday squash, the many discussions about our experiments, the fact that your luck with the experiments was usually at least as bad as mine, the dinners together, for inventing the word cinequotefortzone (with Gary), and for being always willing to help. You must be the kindest person I know, you’re a great scientist and I’m sure you’ll be an awesome professor, I am proud to have you as a friend and honoured that you are my paranimf. Ralph, I have always very much enjoyed your company, and the pleasant human angle in most of our conversations. Meng Yue, thanks for all your help with the pores, and good luck with your company. Susanne, so many thanks for all your help with the experiments! Thanks for being always willing to help and putting in the extra hours. Serge, you too, thanks for being such a great help in the bio‐lab. Aart‐Jan, I can’t vi Preface believe you pulled it off, and managed to make that most elusive of biological constructs, the RNA hairpin (even though it was only once..). Great work, hopefully you and others will be able to use it for some cool experiments. Stefan, thanks for being a great room‐mate, and for our nice discussions about nanopores. Dimitri, and Jaap, thanks for your help on my setup. Xander, good luck with the intended further complications to my setup, I thought it was already difficult enough, but I guess I was wrong. And last, but certainly not least, I want to thank Onno, Vincent and Sven (and Alfred). Onno, your coming was (as J.R.R. Tolkien wrote) “..like the falling of small stones that starts an avalanche..”: your work set off the first RNA‐ nanopore publication. Thanks for your drive and enthusiasm. Vincent, always happy, thanks for all your efforts! And Sven, thanks for some of the latest data in this boekje. Jelle, jij krijgt een aparte plaats: bedankt voor al je inzet en hulp (ik hoefde maar te vragen, en jij had het al gemaakt voor ik uitgesproken was) en de vele uren dat we geouwehoerd hebben. Maar bovenal heb jij mijn eeuwige dank voor het mooiste kado dat ik ooit gekregen heb en waar ik nog mijn hele leven lang plezier van zal hebben (en waar ik al zovelen mee heb lastiggevallen in de avonduurtjes): de vleugel.
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