University of Groningen
Novel peptide replicators from dynamic combinatorial libraries
Altay, Yigit
DOI:
10.33612/diss.90041906
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Publication date: 2019
Link to publication in University of Groningen/UMCG research database
Citation for published version (APA):
Altay, Y. (2019). Novel peptide replicators from dynamic combinatorial libraries. University of Groningen. https://doi.org/10.33612/diss.90041906
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Novel Peptide Replicators
from Dynamic Combinatorial Libraries
Cover Design: Yi˘git Altay - www.yigitaltay.com Printed by: Gildeprint - The Netherlands
ISBN: 978-94-034-1803-2 (print) ISBN: 978-94-034-1802-5 (e-book)
The work described in this thesis was carried out at the Stratingh Institute for Chem-istry, University of Groningen, the Netherlands.
This work financially supported by the European Research Council (ERC), the Netherlands Organisation for Scientific Research (NWO) and COST Action 1304 and the Ministry of Education, Culture and Science (Gravity program 024.001.035).
Novel Peptide Replicators
from Dynamic Combinatorial Libraries
PhD Thesis
to obtain the degree of PhD at the University of Groningen
on the authority of the Rector Magnificus Prof. E. Sterken
and in accordance with the decision by the College of Deans. This thesis will be defended in public on
Friday 6 September 2019 at 9.00 hours
by
Yi˘git Altay
born on 2 February 1988 in Altında˘g, Turkey
Cover Design: Yi˘git Altay - www.yigitaltay.com Printed by: Gildeprint - The Netherlands
ISBN: 978-94-034-1803-2 (print) ISBN: 978-94-034-1802-5 (e-book)
The work described in this thesis was carried out at the Stratingh Institute for Chem-istry, University of Groningen, the Netherlands.
This work financially supported by the European Research Council (ERC), the Netherlands Organisation for Scientific Research (NWO) and COST Action 1304 and the Ministry of Education, Culture and Science (Gravity program 024.001.035).
Novel Peptide Replicators
from Dynamic Combinatorial Libraries
PhD Thesis
to obtain the degree of PhD at the University of Groningen
on the authority of the Rector Magnificus Prof. C. Wijmenga
and in accordance with the decision by the College of Deans. This thesis will be defended in public on
Friday 6 September 2019 at 9.00 hours
by
Yi˘git Altay
born on 2 February 1988 in Altında˘g, Turkey
Supervisors Prof. S. Otto Prof. W. R. Browne Assessment Committee Prof. R. Ulijn Prof. J. J. L. M. Cornelissen Prof. W. H. Roos
Contents
1 Introduction 1 1.1 What is life? . . . 2 1.2 Systems Chemistry . . . 21.3 Dynamic Combinatorial Chemistry . . . 3
1.4 Template Induced Self-Assembly . . . 5
1.5 Self-Replication . . . 7
1.6 Out of Equilibrium Systems and Quasi-Speciation . . . 15
1.7 Conclusion and Contents of this Thesis . . . 18
1.8 Acknowledgements . . . 20
1.9 References . . . 21
2 A Structural Survey in the Search for Novel Self-Replicating Pep-tides 25 2.1 Introduction . . . 26
2.2 Results and Discussion . . . 28
2.3 Acknowledgements . . . 44
2.4 Materials and Methods . . . 45
2.5 UPLC, HPLC and LC-MS analyses . . . 49
2.6 Transmission Electron Microscopy Images . . . 103
2.7 Molecular Dynamics Simulations . . . 111
2.8 References . . . 115
3 Emergence of a New Self-Replicator Requires a Specific Pre-Existing Replicator 119 3.1 Introduction . . . 120
3.2 Results and Discussion . . . 122 v
Supervisors Prof. S. Otto Prof. W. R. Browne Assessment Committee Prof. R. Ulijn Prof. J. J. L. M. Cornelissen Prof. W. H. Roos
Contents
1 Introduction 1 1.1 What is life? . . . 2 1.2 Systems Chemistry . . . 21.3 Dynamic Combinatorial Chemistry . . . 3
1.4 Template Induced Self-Assembly . . . 5
1.5 Self-Replication . . . 7
1.6 Out of Equilibrium Systems and Quasi-Speciation . . . 15
1.7 Conclusion and Contents of this Thesis . . . 18
1.8 Acknowledgements . . . 20
1.9 References . . . 21
2 A Structural Survey in the Search for Novel Self-Replicating Pep-tides 25 2.1 Introduction . . . 26
2.2 Results and Discussion . . . 28
2.3 Acknowledgements . . . 44
2.4 Materials and Methods . . . 45
2.5 UPLC, HPLC and LC-MS analyses . . . 49
2.6 Transmission Electron Microscopy Images . . . 103
2.7 Molecular Dynamics Simulations . . . 111
2.8 References . . . 115
3 Emergence of a New Self-Replicator Requires a Specific Pre-Existing Replicator 119 3.1 Introduction . . . 120
3.2 Results and Discussion . . . 122 v
Contents
3.3 Conclusions . . . 126
3.4 Acknowledgements . . . 127
3.5 Materials and Methods . . . 128
3.6 Kinetic Profiles . . . 131
3.7 UPLC and LC-MS analyses . . . 134
3.8 UV-Vis spectra of different sized macrocycles of peptide 1 . . . 156
3.9 Complete CD spectra of DCLs . . . 157
3.10 ThT Assay Results . . . 157
3.11 Transmission Electron Microscopy Images . . . 158
3.12 References . . . 159
4 Existing Self-Replicators Can Direct the Emergence of New Ones 163 4.1 Introduction . . . 164
4.2 Results and Discussion . . . 166
4.3 Conclusions . . . 172
4.4 Acknowledgements . . . 172
4.5 Materials and Methods . . . 173
4.6 Kinetic Profiles . . . 176
4.7 UPLC and LC-MS analyses . . . 177
4.8 Complete CD spectra of DCLs . . . 218
4.9 ThT Assay Results . . . 219
4.10 Transmission Electron Microscopy Images . . . 220
4.11 References . . . 223
5 Sustaining a Distribution of Replicators Out of Equilibrium 227 5.1 Introduction . . . 228
5.2 Results and Discussion . . . 229
5.3 Conclusions . . . 239
5.4 Acknowledgements . . . 239
5.5 Materials and Methods . . . 240
5.6 UPLC and LC-MS analyses . . . 242
5.7 Kinetic Profiles . . . 244
5.8 References . . . 295
6 Optical Identification of Self-Replicating Molecules 297 6.1 Introduction . . . 298
6.2 Results and Discussion . . . 300
6.3 Conclusions . . . 303
6.4 Acknowledgements . . . 304
6.5 Materials and Methods . . . 305
vi Contents 6.6 Determination of the Sensor Concentration . . . 305
6.7 Fluorescence Assays . . . 305
6.8 UPLC and LC-MS analyses . . . 306
6.9 References . . . 309
7 Conclusion and Perspectives 311 7.1 References . . . 315 Summary 317 Samenvatting 319 Acknowledgements 321 Index 323 vii Contents 6.6 Determination of the Sensor Concentration . . . 305
6.7 Fluorescence Assays . . . 305
6.8 UPLC and LC-MS analyses . . . 306
6.9 References . . . 309
7 Conclusion and Perspectives 311 7.1 References . . . 315 Summary 317 Samenvatting 319 Acknowledgements 321 Index 323 vii
Contents
3.3 Conclusions . . . 126
3.4 Acknowledgements . . . 127
3.5 Materials and Methods . . . 128
3.6 Kinetic Profiles . . . 131
3.7 UPLC and LC-MS analyses . . . 134
3.8 UV-Vis spectra of different sized macrocycles of peptide 1 . . . 156
3.9 Complete CD spectra of DCLs . . . 157
3.10 ThT Assay Results . . . 157
3.11 Transmission Electron Microscopy Images . . . 158
3.12 References . . . 159
4 Existing Self-Replicators Can Direct the Emergence of New Ones 163 4.1 Introduction . . . 164
4.2 Results and Discussion . . . 166
4.3 Conclusions . . . 172
4.4 Acknowledgements . . . 172
4.5 Materials and Methods . . . 173
4.6 Kinetic Profiles . . . 176
4.7 UPLC and LC-MS analyses . . . 177
4.8 Complete CD spectra of DCLs . . . 218
4.9 ThT Assay Results . . . 219
4.10 Transmission Electron Microscopy Images . . . 220
4.11 References . . . 223
5 Sustaining a Distribution of Replicators Out of Equilibrium 227 5.1 Introduction . . . 228
5.2 Results and Discussion . . . 229
5.3 Conclusions . . . 239
5.4 Acknowledgements . . . 239
5.5 Materials and Methods . . . 240
5.6 UPLC and LC-MS analyses . . . 242
5.7 Kinetic Profiles . . . 244
5.8 References . . . 295
6 Optical Identification of Self-Replicating Molecules 297 6.1 Introduction . . . 298
6.2 Results and Discussion . . . 300
6.3 Conclusions . . . 303
6.4 Acknowledgements . . . 304
6.5 Materials and Methods . . . 305
vi Contents 6.6 Determination of the Sensor Concentration . . . 305
6.7 Fluorescence Assays . . . 305
6.8 UPLC and LC-MS analyses . . . 306
6.9 References . . . 309
7 Conclusion and Perspectives 311 7.1 References . . . 315 Summary 317 Samenvatting 319 Acknowledgements 321 Index 323 vii Contents 6.6 Determination of the Sensor Concentration . . . 305
6.7 Fluorescence Assays . . . 305
6.8 UPLC and LC-MS analyses . . . 306
6.9 References . . . 309
7 Conclusion and Perspectives 311 7.1 References . . . 315 Summary 317 Samenvatting 319 Acknowledgements 321 Index 323 vii
Chapter 1
Introduction
“Sane sicut lux seipsam et tenebras manifestat, sic veritas norma sui et falsi est”1
Spinoza
Abstract
How we define life is fundamental to the process of understanding it. Since an-cient times, it has been a puzzling subject to philosophers, writers and san-cientists. In the last 150 years, the number of available tools in the hands of scientists to probe this question increased almost exponentially. Now we are on the edge of understanding the mechanisms of life and possibly creation of an alternative lifelike form by our hands.
This chapter introduces systems chemistry and dynamic combinatorial chem-istry as useful tools to shed light on the complex molecular systems that exhibit emergent properties that are analogous to those found in nature.
