Rodriguez Garcia, Marc (2016) Engineering the transition from non-living to living matter. PhD thesis. https://theses.gla.ac.uk/7605/ Copyright and moral rights for this work are retained by the author A copy can be downloaded for personal non-commercial research or study, without prior permission or charge This work cannot be reproduced or quoted extensively from without first obtaining permission in writing from the author The content must not be changed in any way or sold commercially in any format or medium without the formal permission of the author When referring to this work, full bibliographic details including the author, title, awarding institution and date of the thesis must be given Enlighten: Theses https://theses.gla.ac.uk/ [email protected] Engineering the transition from non-living to living matter Marc Rodríguez Garcia A thesis submitted to the University of Glasgow for the degree of Doctor of Philosophy School of Chemistry College of Science and Engineering August 2016 A tota la meva família, per haver-me ajudat a arribar fins aquí. Però sobretot als meus pares, per estar tant a prop malgrat la distància. I en especial a la Nuria, per ser el motiu que em fa tirar endavant. “The good thing about science is that it's true whether or not you believe in it.” -Neil deGrasse Tyson Acknowledgements 1 Acknowledgements This project was carried out between September 2012 and June 2016 in the group of Prof Leroy Cronin in the School of Chemistry at the University of Glasgow. I have received much help and support from many colleagues and friends. In particular, I would like to express my sincere gratitude to the following people: Prof Leroy Cronin, for taking me on as an Erasmus student, and then giving the opportunity to start a PhD in his research group. For his inspiration, guidance and constant support throughout these years. Dr Andrew Surman, for his invaluable help and guidance during most of my PhD. Also, for teaching me to be rigorous and for teaching me everything I know about analysis. Dr Geoff Cooper and Dr Soichiro Tsuda, for their kind help whenever it was needed, and for being such nice colleagues. Dr Trevor Hinkley, for helping me during the first stages of my PhD. Dr Mike Lee and Zied Hosni, for their help with LabView. Kevin Donkers and Dr Mohammed Hezwani, for their contributions to the last part of this thesis. Jonas Kube, José Maria Planchat and Arielle le Nue, for being amazing students and contributing so much to this work. Dr Rebecca Turk Macleod and David Doran, for their help proofreading part of this thesis and for being such nice colleagues. All the past and present members of the Origins team, for the nice discussions and the biscuits. I would also like to thank the other PhD students who started with me: Luzian Porwol, Qi Zheng, Juan Manuel Parrilla and James Taylor, who helped make the writing process less of a tragic experience (and also Dr Ross Winter). Sergio Martin, for being the best gym partner and a great friend. Irene Suarez, for all her help for the past years and her friendship. I wish her the best in her PhD. Mercè Martin, for the Mercè-facts, of which only 10% are true, but still enjoyable to hear. Acknowledgements 2 Dr Laia-Vila Nadal, for being a great group coordinator and for her friendliness. Stuart Marshall and Amanda McGarvey, for their help anytime I needed it. Jim McIver, for his endless help setting all the platforms, the clean room… It’s been a long way since I started in the attic! Dr Diana Castro, for her technical support and kindness. Also, Dr Andreu Ruiz, Dr Ben Rausch, Dr Rachel Scullion, Dr Andrew Macdonell, Dr Jamie Cameron, Dr Salah Sharabi, Dr Ommid Anamimoghadam, Dr Christophe Busche, Dr Stefan Glatzel for being great colleagues and friends. All the members of the Cronin Group, past and present, who have made this such an enjoyable time, despite the horrendous weather. Finally, Dr Marc Segalés and soon to be Dr Irene Cascallana, whom I shared this experience from the very first day I put my foot in Glasgow, and I wish them the best in their futures. Table of contents 3 Table of Contents Acknowledgements ................................................................................................................... 1 Table of Contents ..................................................................................................................... 3 Publications ............................................................................................................................... 6 Abbreviations ........................................................................................................................... 7 Abstract ..................................................................................................................................... 9 1 Introduction ..................................................................................................................... 11 1.1 The origin of life: an unresolved problem ....................................................... 11 1.1.1 Historical Perspective....................................................................................... 16 1.1.2 The birth of Prebiotic Chemistry...................................................................... 17 1.1.3 Main Theories on the Origin of Life ................................................................ 19 1.2 Synthesis of monomers ........................................................................................ 22 1.2.1 Synthesis of Amino acids ................................................................................. 22 1.2.2 Synthesis of Nucleotides .................................................................................. 25 1.3 Synthesis of biopolymers ..................................................................................... 31 1.3.1 Peptide synthesis .............................................................................................. 31 1.3.2 Nucleic acid synthesis ...................................................................................... 43 1.3.3 RNA-peptide systems ...................................................................................... 47 1.4 Missing link between polymers and self-replicating systems .............................. 48 1.4.1 Top-down approaches ...................................................................................... 49 1.4.2 Prebiotic Systems Chemistry ........................................................................... 50 1.5 Future outlook ...................................................................................................... 52 1.6 Microfluidics ........................................................................................................ 53 2 Aims.................................................................................................................................. 56 3 Results and discussion .................................................................................................... 57 3.1 Microfluidic platform for chemical evolution...................................................... 57 3.1.1 Microfluidics and soft lithographic techniques ................................................ 59 3.1.2 Master fabrication ............................................................................................ 61 3.1.3 PDMS chip fabrication ..................................................................................... 70 3.1.4 Droplet-based microfluidics ............................................................................. 74 3.1.5 Ensemble sorting .............................................................................................. 91 3.1.6 Section summary.................................................................................................. 97 3.2 Abiotic Peptide Synthesis .................................................................................... 99 Table of contents 4 3.2.1 The initial APS platform ................................................................................ 100 3.2.2 The abiotic peptide synthesiser system .......................................................... 114 3.2.3 Exploring environmental conditions .............................................................. 124 3.2.4 Section summary ............................................................................................ 139 3.3 Hetero-oligomer synthesis exploration .............................................................. 141 3.3.1 Heteropolymers and expansion to other amino acids .................................... 141 3.3.2 Exploring the differences between using H2SO4 and H3PO4 in co- oligomerisation reactions. ........................................................................................... 143 3.3.3 Systematic co-oligomerisation exploration. ................................................... 145 3.3.4 Environmental programming of peptide synthesis ........................................ 153 3.3.5 Section summary ............................................................................................ 159 4 Conclusions and future work ....................................................................................... 160 4.1 Microfluidic platform for chemical evolution.................................................... 160 4.2 Abiotic Peptide Synthesis .................................................................................. 161 4.3 Programming the formation of heteropeptides