University of Groningen
tRNA mimicking structures to control and monitor biological processes Paul, Avishek
DOI:
10.33612/diss.166342562
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Publication date: 2021
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Paul, A. (2021). tRNA mimicking structures to control and monitor biological processes. University of Groningen. https://doi.org/10.33612/diss.166342562
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tRNA mimicking structures to control and monitor
biological processes
tRNA mimicking structures to control and monitor biological processes Avishek Paul
PhD thesis
University of Groningen
Zernike Institute PhD thesis series 2021-09 ISSN: 1570-1530
ISBN: ISBN:
The research described in thesis was performed in Polymer Chemistry and Bioengineering group at Zernike Institute for Advanced Materials, University of Groningen, the Netherlands and DWI—Leibniz Institute for Interactive Materials, Aachen, Germany. This work was financially supported by European Research Council (ERC).
Cover design by: Avishek Paul Printed by: RIDDERPRINT
tRNA mimicking structures to
control and monitor biological
processes
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 23 April 2021 at 11.00 hours
by
Avishek Paul
born on 13 October 1985 in
Supervisor
Prof. A. Herrmann
Co-supervisor
Prof. P. van Rijn
Assessment Committee
Prof. A. Guskov Prof. F. Simmel Prof. W. Weber
CONTENTS
Chapter 1: General introduction
1.1. Introduction………...2
1.2 . Functional units of a genetic switch………..3
1.3. Bacterial sensor with embedded read out system: a different form of RNA switch………....8
1.4. Optimizing switch response……….11
1.5. Importance of different regulators, other than riboswitch, with different regulatory mechanisms………...14
1.6. Genetic switches v 2.0……….17
1.7. Applications of synthetic genetic switches………..20
1.8. Thesis motivation and overview………...21
Chapter 2: Modular and versatile trans-encoded genetic switches 2.1. Introduction………..37
2.2. Results and discussion………..38
2.3. Conclusion………...46
2.4. Experimental section………47
Chapter 3: Photochemical control of bacterial gene expression based on trans encoded genetic switches 3.1. Introduction………..85
3.2. Results and discussion………..88
3.3. Conclusion……….100
Chapter 4: A DNA based trans-encoded genetic switch
4.1. Introduction………121
4.2. Results and discussion………122
4.3. Conclusion……….129
4.4. Experimental section………..129
Chapter 5: Modularity from RNA aptamers combined with the green fluorescent protein provides versatile genetically encoded fluorescent sensors in bacteria 5.1. Introduction………141
5.2. Results and discussion………142
5.3. Conclusion……….152
5.4. Experimental section………..152
Chapter 6: Outlook and future perspectives………165
Chapter 7: Summary………..168
