Developing An Efficient Screening Method For Optimization of Nanobody-Based Fluorescent Biosensors (Master Thesis Vincent 2022)

FACULTY OF SCIENCES
Developing an efficient
screening method for
optimization of
nanobody-based fluorescent
biosensors
Sander VANWING
Supervisor: Prof. Dr. Peter Dedecker Master thesis submitted in fulfillment

Mentor: Dr. Vincent Van Deuren of the requirements for the degree in
Master of Science in Biochemie & Biotechnologie
Academic year 2021-2022

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Acknowledgements
The master thesis is the culmination of 5 years of effort put into one’s education. You
expect to go out with a story of success and great findings. However, throughout the past
year, it became clear to me that research is not just about success or setbacks. Rather,
the thrill of working on innovative concepts, adapting to new situations and converting
knowledge to practice is what makes this field so exciting.
I am thankful for all the people who were able to show this to me this year. The first of
this group is Vincent, who instructed me the whole year, but also gave me enough space
to discover (and stumble) on my own. I would also like to thank Hana and Silke for their
additional assistance within the NanoBlock project, Wim for some crucial insights and
Iris for all the help in the lab. My thanks also goes out to professor Peter Dedecker, for
offering the opportunity to work on this innovative project.
My gratitude extends also to the other master students, internship students and the
other lab members for creating such a pleasant and open working environment. Whether
it was for a lighthearted chat or serious advice, there was always someone who wanted to
take their time for me.
Naast de academische bijval, kon ik na de uren ook op een groep mensen rekenen die
me hebben bijgestaan op andere vlakken. Daarom wil ik nog mijn familie bedanken voor
hun interesse en steun en mijn vrienden die voor de nodige afleiding en plezier konden
zorgen. Als laatste en belangrijkste, geef ik mijn eindeloze dankbaarheid aan Julie, om er
altijd voor mij te zijn en om me aan te steken met je enthousiasme voor onderzoek.
i
Contents
Acknowledgements i
Contents iii
Samenvatting v
Summary vii
Acronyms ix
List of Figures xi
List of Tables xv
1 Introduction 1
1.1 Biosensors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.2 Fluorescent proteins and other fluorescent labels . . . . . . . . . . . . . . . 2
1.3 Examples of biosensors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.4 Universal biosensors? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
1.5 Nanobodies: structure & function . . . . . . . . . . . . . . . . . . . . . . . 7
1.5.1 Applications of nanobodies . . . . . . . . . . . . . . . . . . . . . . . 8
1.6 Developing and optimizing biosensors . . . . . . . . . . . . . . . . . . . . . 9
1.6.1 Mutagenesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
1.6.2 Mutant screening . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
2 Project Description 13
3 Material and Methods 15

3.1 Buffers, media & solutions . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
3.2 Transformation in E. coli . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
3.3 Large scale E. coli culture . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
3.4 Protein purification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
3.5 Titration of purified biosensors . . . . . . . . . . . . . . . . . . . . . . . . . 17
3.6 Library generation: directed mutagenesis . . . . . . . . . . . . . . . . . . . 18
3.7 Library evaluation: Lysate screening . . . . . . . . . . . . . . . . . . . . . 19
3.8 Library evaluation: Colony screening . . . . . . . . . . . . . . . . . . . . . 19
3.9 Primer list . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
iii
iv CONTENTS
4 Results 21
4.1 Random mutagenesis of blocking peptide . . . . . . . . . . . . . . . . . . . 21
4.1.1 SplitFAST-based sensor: cloning efforts . . . . . . . . . . . . . . . . 24
4.2 Increased throughput mutant screening . . . . . . . . . . . . . . . . . . . . 24
4.2.1 Lysate screening improvement . . . . . . . . . . . . . . . . . . . . . 25
4.2.2 Colony screening . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
4.3 Affinity measurements and control experiment . . . . . . . . . . . . . . . . 31
5 Discussion 33
5.1 Improved lysate screen increases throughput . . . . . . . . . . . . . . . . . 33
5.2 Colony screening is promising, but requires additional work . . . . . . . . . 34
5.3 Is the mCherry-targeting NanoBlock worth it? . . . . . . . . . . . . . . . . 36
6 Conclusion and future perspectives 39
Bibliography 41
Appendices 49
A Supplementary figures 51
B Risk analysis 55
Samenvatting
Biosensoren zijn uitstekende analytische middelen die dynamisch intracellulaire doelwitten

kunnen visualiseren. Omdat ze conditionele fluorescentie vertonen, kunnen veranderingen
in de aanwezigheid van het doelwit zowel in vitro als in vivo gevolgd worden in tijd en
ruimte. Verschillende doelwitten hebben reeds hun bijhorende biosensor, in verschillende
structuren. Toch is er niet voor elk doelwit in een cel een bijhorende biosensor en soms
zijn bestaande biosensoren niet toepasbaar in bepaalde omstandigheden. Daarom zou
een universele biosensorstructuur, waarin de componenten snel aangepast kunnen worden
naargelang het doelwit, deze tekortkomingen kunnen tegemoet komen. Met dit in het hoofd,
werd de NanoBlock biosensorstructuur in het leven geroepen. De NanoBlock-structuur
bestaat uit een fluorescent deel dat conformationele veranderingen visualiseert en een
tweeledig doelwitherkennend deel bestaande uit een nanobody en een klein blokkerend
peptide. Wanneer het doelwit er niet is, blokkeert het blokkerend peptide het paratoop
van de nanobody. Wanneer de nanobody het doelwit kan binden, wordt het blokkerend
peptide verplaatst. Deze conformationele verandering wordt door het fluorescente deel
vertaald in een verandering in fluorescentie. Een ontwerp van de NanoBlock-structuur
dat onderzocht wordt, bestaat uit circulair gepermuteerd EGFP, met het blokkerend
peptide aan de N-terminus en het LaM4 nanobody, met een paratoop voor mCherry,
aan de C-terminus. Om de verandering in fluorescentie te vergroten en het bereik van
mCherry-concentratie waarin deze verandering optreedt, aan te passen, zijn er verschillende
mogelijke doelwitten. Een interessant onderdeel hiervoor is het blokkerend peptide. Door
enkele aminozuren aan te passen, kan de affiniteit van de nanobody voor het blokkerend
peptide veranderen, wat bijgevolg een grotere - of kleinere - fluorescentieverandering met
zich meebrengt wanneer het doelwit gebonden wordt. Om zulke gemuteerde varianten te
beoordelen, is een geschikte screening-methode vereist. Deze screening-methode moet een
groot aantal varianten in parallel kunnen karakteriseren, mag niet te arbeidsintensief zijn
en moet uitvoerbaar zijn met het beschikbare labomateriaal.
In deze thesis werd het blokkerend peptide onderworpen aan willekeurige mutagenese
om een bibliotheek te maken. Eerst werden twaalf mutanten uit deze bibliotheek ge-
screend in lysaat. Hiervan werden twee veelbelovende varianten geselecteerd en in vitro
gekarakteriseerd. In een poging om meer varianten tegelijk te kunnen screenen, werden
twee andere screening-methodes uitgetest. Eerst werd een aangepaste lysaat screening
geëvalueerd waarin vele kolonies uit de bibliotheek tegelijk opgegroeid werden in een
deep well 96-well plaat. Dit leverde geen enkele betere NanoBlock-biosensor op. Daarna
werd een kolonie screening-methode getest. Hiervoor moet het doelwit, mCherry, mee
getransformeerd worden met de bibliotheek van blokkerend peptide. Bovendien moet de
transcriptie van het mCherry-gen onder controle van een induceerbare promoter staan.
Op die manier kan de transcriptie van mCherry onderdrukt of geactiveerd worden om de
v
vi CONTENTS
fluorescentie van de NanoBlock-biosensor te meten met en zonder het doelwit. Hoewel de

kolonie screening-methode niet volledig getest kon worden, tonen de bekomen resultaten
toch dat deze methode het meest geschikt zou kunnen zijn voor dit project. Uiteindelijk
werden er nog affiniteitsmetingen gedaan met het blokkerend peptide en de nanobody.
De resultaten van deze experimenten lijken het theoretisch werkingsmechanisme van de
NanoBlock-biosensor voor mCherry in vraag te stellen.
Summary
Biosensors are great analytical tools that can dynamically visualize intracellular targets.
Because of their conditional fluorescence, the changes in presence of a target can be
followed in real time both in vitro and in vivo and can even be pinpointed in space, given
the right microscopy tools. Many different targets already have their own biosensors,
which come in a variety of architectures. However, not all targets have a biosensor and
sometimes, existing ones are not always suited for all experiments. Therefore, a universal
architecture, in which the components can be readily adapted to the target, could address
this shortcoming. To this end, the NanoBlock biosensor architecture was introduced.
It consists of a fluorescent moiety as the reporter domain, a nanobody and a blocking
peptide that act as the sensing domain of the biosensor. Without the target present, the
blocking peptide blocks the antigen binding site of the nanobody. When the nanobody
binds its target, the blocking peptide is displaced which causes a conformational change
that is translated to a change in fluorescence. One design that is currently investigated,
is made up of a circularly permutated enhanced GFP with the blocking peptide fused
N-terminally and the LaM4 nanobody, targeting mCherry, fused C-terminally. To increase
the change in fluorescence and to alter the working range of target concentration of the
current mCherry-targeting NanoBlock biosensor, several sites can be targeted, for example
the blocking peptide. By mutating some amino acids, the affinity for the nanobody can
change which leads to an increase - or decrease - in the change of fluorescence when the
target binds, i.e. the response. To assess these mutated variants, a suitable screening
method must be used, which should be able to screen a great number of variants, is not
labour-intensive and is also executable with the available lab equipment.
In this thesis, the blocking peptide was subjected to random mutagenesis, creating
a blocking peptide library. First, twelve mutants in this library were assessed in a
low throughput lysate screen. From this, two promising candidates were selected and
characterized in vitro. In an attempt to increase the throughput, two other library screening
methods were tested. First, an increased throughput lysate screen was evaluated where
many colonies of the library are grown at the same time in deep-well 96-well plates. This
yielded no NanoBlock biosensor with an improved response. Then, a colony screening
method was tested. For this, the target mCherry must be genetically encoded under
control of an inducible promoter together with the blocking peptide library. This way,
the expression of mCherry can be repressed and induced to measure the fluorescence of
the NanoBlock biosensor with and without mCherry. While the colony screening method
could not be evaluated completely, the obtained results show that this method might be
the most suited for this project. Finally, some affinity measurements were done with the
blocking peptide and the nanobody. The results from these experiments seem to challenge
the theoretical working principle of the mCherry-targeting NanoBlock biosensor.
vii
viii CONTENTS
Acronyms
Ab antibodies.
BLI biolayer interferometry.
CaM calmodulin.
CDR complementarity-determining regions.
FACS Fluorescence-activated Cell Sorting.

FAST Fluorescence-activating and Absorption-Shifting Tag.
FP fluorescent proteins.
FRET Förster Resonance Energy Transfer.
GECI genetically-encoded calcium indicators.

GFP Green Fluorescent Protein.
HBR 4-hydroxybenzylidene-rhodanine.
HCAb heavy chain-only antibodies.
HDR homology-directed repair.
HMBR 4-hydroxy-3-methylbenzylidene-rhodanine.
IgG immunoglobulin G.
Nb nanobodies.
NHEJ non-homologous end joining.
PCR polymerase chain reaction.

PKA Protein Kinase A.
PYP Photoactive Yellow Protein.
SDS-PAGE sodium dodecyl sulphate polyacrylamide gel electrophoresis.

SLE self-labelling enzymes.
SOC Super optimal broth with catabolite repression.
ix
List of Figures
1.1 A. Example of a genetically-encoded biosensor with a sensing domain

(calmodulin, M13-peptide) and a reporter domain (cpavGFP). B. The
sensor undergoes a conformational change when Ca2+ binds. Adapted from
Frommer et al. (2009). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.2 Different types of fluorescent labels (POI = protein of interest, not to
scale). A. Fluorescent protein. B. FRET labels for two interacting proteins.
C. Self-labelling enzymes (SLE’s) using fluorescent dyes. D. FAST-tag
reversibly binding a fluorogen. . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.3 Generalized, common architectures for genetically-encoded biosensors based
on fluorescent proteins. Adapted from Moeyaert and Dedecker (2020). . . . 5
1.4 A. Classical tetrameric antibody. B. Camelid heavy chain-only antibody
(HCAb). Inset: variable domain of the heavy chain (VHH) or nanobody. Fc:
crystallizable fragment, Blue lines: antigen-binding site. Figure adapted
from Muyldermans (2021b). . . . . . . . . . . . . . . . . . . . . . . . . . . 7
1.5 A. Nanobody (orange) can bind the active site of an enzyme through
its flexible, protruding CDR3 (Adapted from Dmitriev et al. (2016)). B.
Nanobodies can be genetically encoded and expressed in bacteria, even as
fusion proteins. C. The fluorescent tag carried by the Nb is in closer prox-
imity to the original target than with regular Ab. TOI = target of interest.
D. Nanobodies can better penetrate cells compared to heterotetrameric
antibodies, even in permeabilized cells. . . . . . . . . . . . . . . . . . . . . 9
1.6 Two types of PCR mutagenesis: site-directed (A) and random by error-
prone PCR (B). Blue: template plasmid, Red: circularized PCR product
containing mutations (*). . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
2.1 Cartoon representation of two different NanoBlock architectures and their

proposed mode of action. A. GCaMP-based design with circularly permuted
enhanced GFP (cpEGFP). B. SplitFAST-based design with splitFAST-
fragments NFAST and CFAST. . . . . . . . . . . . . . . . . . . . . . . . . 13
2.2 Two main project activities. A. Creating a library of random blocking
peptide (Pep3) mutations, followed by low-throughput screening in lysate. B.
Scheme depicting the work flow of the increased througput colony screening
(Explained in Chapter 3). . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
3.1 Scheme of library generation by the QuickLib method with a mutagenic

primer. Red: randomized degenerate nucleotides. Light blue: complemen-
tary primer ends. Based on Galka et al. (2017). . . . . . . . . . . . . . . . 18
xi
xii LIST OF FIGURES
4.1 Titration of dark mCherry (0.04 - 10 µM, y-axis = 0 µM) with Pep3-
cpEGFP-LaM4 sensor (2 µM, n = 3). a.u. = arbitrary units, x-axis is
log2-transformed. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
4.2 Visualisation of the interaction between the LaM4 nanobody (orange) and
mCherry (red). The CDR3-loop from the nanobody is coloured in yellow,
the sequence in mCherry corresponding to the blocking peptide in the sensor
(PDYLKSF) is shown in blue. Inset: interaction between Asn103 of the
nanobody and K84 of mCherry. PDB: 6IR1 (Wang et al., 2021). . . . . . . 22
4.3 Titrations with dmCherry (10-6 - 1 µM) of Pep3 library cell lysates and
corresponding peptide sequences (* = stop codon). As template for the
library generation, an earlier blocking peptide iteration was used, hence the
template blocking peptide sequence is PDYAKSF. . . . . . . . . . . . . . . 23
4.4 Comparison between Pep3 mutants 2 and 6 and the original Pep3 (n=3
each). Titrations of purified protein (2 µM) with dmCherry (0.04 - 10 µM,
y-axis = 0 µM). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
4.5 1 % agarose gels of SplitFAST-based sensor blocking peptide mutagenesis
products. A. PCR product of mutagenesis with QuickLib for the intro-
duction of the Pep3.6 blocking peptide. B. PCR products of mutagenesis
by ’round-the-horn method for the Pep3.6 blocking peptide and blocking
peptide library. C. PCR products with annealing temperature gradient of
mutagenesis by ’round-the-horn method for the Pep3.6 blocking peptide
and blocking peptide library. . . . . . . . . . . . . . . . . . . . . . . . . . . 25
4.6 Lysate screening from colonies grown in a deep-well 96-well plate. A.
Response of Pep3 library (n=42) in lysate upon addition of dmCherry (10
µM), coloured according to the response (increase or decrease in fluorescence).
B. Same data as in A, without colonies with positive response (n=30),
coloured by the value of the response. A darker shade indicates a larger
response, which corresponds with a greater change in fluorescence when
the biosensor target is added. C. Average response to dmCherry (10 µM)
of three Pep3 blocking peptide variants (n=3 each) in lysate, coloured
by change fluorescence. The average was taken after normalization . *:
p < 0.05, **: p < 0.01. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
4.7 Fluorescence of colonies containing the pBAD-eGFP plasmid grown on
either inducing (10 mM L-arabinose, 10 mM D-glucose) or repressing (20
mM D-glucose) LB agar. Left: The average fluorescence intensity of colonies
on the induced plates is not significantly (NS.) different from those on the
repressed plates. Right: Variance between plates of the same condition is
relatively high. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
4.8 Average fluorescence of mCherry in single colonies (n=9) on LB agar
plates containing varying amounts of L-arabinose. Red line indicates the
background fluorescence. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
4.9 Induction of mCherry expression visualized by fluorescence. A. Image of the
plate at 3 h after spraying. B. Image of the plate at 22 h (overnight) after
spraying. C. Data on 9 colonies of the plate shown in A and B. The two
other plates have comparable behaviour. ***: p < 0.001. D. Comparison
of fluorescence between colonies on the inside (n=5) versus the outside of
the plate (n=4). Background traces of each region are shown in grey. . . . 29
LIST OF FIGURES xiii
4.10 1 % agarose gels of PCR products (A, C) and assemblies (B, D). A. PCR
products of the mCherry gene (left) for ligation in the empty pBAD vector.
The mCherry gene appears to have the expected size. B. PCR products
after assembly of the fragments in A. While it is the correct size, the final,
complete plasmid did not contain mCherry according to sequencing. C.
PCR products of different Gibson assembly fragments. All fragments appear
to have the right size. D. Gibson assembly product after restriction with
BaMHI. The desired plasmid has three restriction sites for BaMHI, which
would result in three fragments. The pRSETb-vector only has one, therefore
the product on the gel is (a chimaeric version of) the pRSETb-vector. . . 30
4.11 Affinity of the LaM4 nanobody (320 nM) for the blocking peptide of the
mCherry NanoBlock measured by BLI. First red line: addition of LaM4
nanobody, second red line: start of dissociation of LaM4. Data courtesy of
Ulrich Rothbauer, University of Tübingen. . . . . . . . . . . . . . . . . . . 31
4.12 Titrations with different NanoBlock sensors (n=3 each). While the ALFA-
tag sensor behaves as expected, the mCherry sensor with GGS blocking
peptide (GS-Pep) still shows a decrease in fluorescence upon target addition,
although it starts at the same baseline as ALFA-tag sensor with GS blocking
peptide. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
5.1 Proposed mechanism for difference in fluorescence of mCherry-targeting and

ALFA-tag-targeting NanoBlock biosensor when target is present. Top: dark
mCherry is large, which leads to the “open” state of the NanoBlock biosensor.
Bottom: the ALFA-tag is small, only leading to a small conformational
change or the “partially open” state in the NanoBlock biosensor. . . . . . . 37
6.1 Adapted working mechanism of the GCaMP-based, mCherry-targeting

NanoBlock sensor, based on the observations in Results section 4.3. Without
(dark) mCherry present, the cpEGFP is in a “partially open” state. When
mCherry binds LaM4, the blocking peptide is further displaced due to the
size of mCherry, leading to the “open” state. . . . . . . . . . . . . . . . . . 40
A.1 SDS-PAGE of purified dark mCherry (26.7 kDa). Left: 10 µg protein, right:
5 µg. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
A.2 Comparison of cells containing pBAD-eGFP plasmid on plates with 20
mM D-glucose before (A) and after (B) spraying with a concentrated L-
arabinose solution. Plates were incubated on room temperature for 3 hours
after spraying when image was taken. . . . . . . . . . . . . . . . . . . . . . 51
A.3 Affinity of the ALFA nanobody (320 nM) for different blocking peptide
mutants of the ALFA-tag NanoBlock measured by BLI. First red line:
addition of ALFA nanobody. Second red line: start of dissociation of ALFA
nanobody. Data courtesy of Ulrich Rothbauer, University of Tübingen. . . 52
A.4 Plasmid map of the pRSETb vector containing the GCaMP-based mCherry-
targeting NanoBlock biosensor. . . . . . . . . . . . . . . . . . . . . . . . . 52
A.5 Plasmid map of the pBAD vector containing mCherry (Addgene plasmid
#54630. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
A.6 Plasmid map of the pRSETb vector containing the SplitFAST-based mCherry-
xiv LIST OF FIGURES
A.7 Plasmid map of the pET28b vector containing the GCaMP-based mCherry-
List of Tables
1.1 Assessment of the discussed screening methods. -: bad, +: okay, ++: good,
+++: excellent. *replica plating/spraying . . . . . . . . . . . . . . . . . . 12
3.1 FWD: forward primer, REV: reverse primer, QL: QuickLib, RTH: ’round-
the-horn mutagenesis. Bases in upper case indicate where the mutation or
site of interest is. N = A, T, G or C; K = G or T; M = A or C. . . . . . . 20
4.1 Average volume of spray and amount of L-arabinose applied when spraying
once, when doing the spray pattern once and when doing the spray pattern
4 times. The values for the latter is extrapolated from the data of doing
the spray pattern once. Density of 1 mg/mL was assumed. . . . . . . . . . 28
xv
Chapter 1
Introduction
1.1 Biosensors
Inside living cells, uncountable complex pro-
cesses and dynamic interactions are happening
at every instance. Many different stimuli trig-
ger separate signalling cascades leading to a
change of the equilibrium of the intracellular en-
vironment. While the sheer number of possible
interactions and outcomes is already difficult
to grasp, the whole picture gets even more in-
tricate when these events are also considered
to differ in intracellular localization and time
scale. Decades of research has been able to
elucidate complex signalling pathways and pro-
tein interactions on their own through methods
such as yeast two-hybrid, synthetic genetic anal-
ysis or gene knock-out. In more recent years,
in silico methods were added to this toolbox
to address the shortcomings of the wetlab ex-
periments (Rao et al., 2014). However these
methods largely fail to capture the information
Figure 1.1: A. Example of a genetically-
about the local surroundings and time scale of encoded biosensor with a sensing domain
these processes. This information is nonethe- (calmodulin, M13-peptide) and a reporter
less crucial for a complete understanding of the domain (cpavGFP). B. The sensor under-
function of said processes. To acquire this spa- goes a conformational change when Ca2+
tiotemporal context, a method is required that binds. Adapted from Frommer et al. (2009).
minimally disturbs the intracellular environment
and can report and detect changes both in a small volume and in short periods of time. A
method that seems to accommodate these requirements, is optical microscopy and more
specifically, fluorescence microscopy. By labelling a protein or structure of interest with
a fluorescent moiety, its localization inside the cell can be tracked. With techniques like
Förster Resonance Energy Transfer (FRET), transient protein interactions can even be
visualized while still retaining the spatial information on the interaction. However the
direct labelling of target molecules can sometimes interfere with the system that is to
1
2 CHAPTER 1. INTRODUCTION
be observed or more dramatically, the protein of interest can be incompatible for fusion
to a fluorescent marker. Therefore, an alternative approach is to work with an extrinsic
molecule that can bind the subject under study and contains a reporter that changes
output when the subject is bound. A molecule with these characteristics is then defined as
a biosensor. This labelling method retains the same advantages of high specificity, rapid
read-out and the ability to localize a target while aiming to circumvent incompatibility
and system disrupting issues. Additionally, dynamics of the system under study can be
visualized. Biosensors that make use of a fluorescent protein as a reporter, have the added
value that they are able to be expressed by the host organism and are thus described as
genetically-encoded fluorescent biosensors.
In practice, genetically-encoded biosensors are fusion proteins containing a sensing
domain and a feedback domain (Fig. 1.1). The sensing domain must be able to bind the
target molecule in such a way that it creates a conformational change in the biosensor
that leads to a change in the activity of the feedback domain. For the latter, fluorescent
proteins are used that can undergo a change in fluorescence upon the binding of the sensing
domain.
1.2 Fluorescent proteins and other fluorescent labels

The history of fluorescent proteins (FP) is marked by the discovery of Green Fluorescent
Protein (GFP) by Shimomura et al. (1962) and the observation that GFP can be expressed
in other organisms by Chalfie et al. (1994). This ultimately led to a Nobel Prize in 2008
for the previous two researchers together with Roger Y. Tsien. The FP derived from the
jellyfish Aequorea victoria has been a popular tool for the past twenty years for optically
measuring gene expression, following protein localization (Phillips, 2001) and of course
its use in biosensors (Fig. 1.2A). Many other FP’s were derived from wild-type GFP by
modifying the chromophore, which yielded a range of different emission colours going from
blue to orange (Tsien, 1998). This is not only useful for labelling multiple targets in the
same cell, but it also enables techniques like FRET, (Fig. 1.2B). When illuminating one FP,
the donor, with light with a wavelength corresponding to its absorption spectrum, it can
transfer the energy it gained to a nearby other FP, the acceptor. This can happen given
that their respective emission and absorption spectra overlap and they are in close enough
proximity. A commonly used donor-acceptor FRET pair is Cyan and Yellow Fluorescent
Protein (CFP & YFP) (Frommer et al., 2009). What was still missing from the FP
toolbox, were FP’s that absorbed and emitted in the red light spectrum. This changed
when a number of new FP’s was discovered in several anthozoans, one of which had an
emission maximum of 583 nm (Matz et al., 1999). This red FP was later named DsRed and
now various improved variants exist (e.g. mCherry) with some reaching into the far-red
emission spectrum (Miyawaki et al., 2012). Both the GFP-like and DsRed-like FP can
be categorized as FP with an intrinsic chromophore. This means that their chromophore
is encoded in the DNA sequence and is autocatalyzed, requiring nothing but molecular
oxygen.
In contrast to intrinsically fluorescent proteins, there exist also labelling proteins that
make use of an extrinsic fluorescent moiety (Fig. 1.2C). A popular class of labels are the
self-labelling enzymes (SLE) like the commercially available SNAP-tag (Keppler et al.,
2002), CLIP-tag (Gautier et al., 2008) (NEB) and HaloTag (Los et al., 2008) (Promega).
1.2. FLUORESCENT PROTEINS AND OTHER FLUORESCENT LABELS 3
Figure 1.2: Different types of fluorescent labels (POI = protein of interest, not to scale). A.
Fluorescent protein. B. FRET labels for two interacting proteins. C. Self-labelling enzymes
(SLE’s) using fluorescent dyes. D. FAST-tag reversibly binding a fluorogen.
These types of labels consist of an enzyme that recognizes a certain substrate and cleaves
it while covalently binding one of the leaving groups. When a fluorescent dye is attached
to this substrate, the enzyme can label itself with the dye, hence the name self-labelling
enzyme. The SNAP-tag and CLIP-tag are based on a DNA repair enzyme O6 -alkylguanine-
DNA alkyltransferase (AGT) that transfers an alkyl group attached to a guanine molecule
to a cysteine residue on the enzyme (Keppler et al., 2002). The HaloTag is derived from a
bacterial dehalogenase which is capable of forming stable bonds with a chlorinated alkane
linker (Los et al., 2008). The advantage of SLE’s is that they use fluorescent dyes, which are
generally more bright than FP’s (Toseland, 2013). Brighter probes emit more photons for
the same intensity of the excitation light. This implies on the one hand that a lower light
source power can be used, leading to less photobleaching and on the other hand that fewer
probe molecules are sufficient for visualization. Photobleaching is a degradation process
where the fluorophore loses its fluorescence due to a prolonged exposure to excitation light.
Furthermore, SLE’s can not only be used for fluorescent labelling, but also for purification
(Ohana et al., 2011). One of the drawbacks to these fluorescent dyes is that they are
fluorescent even when they are not bound to the SLE (Schneider and Hackenberger, 2017).
This implies an extra washing step to remove background fluorescence from unbound dye
molecules.
This problem is circumvented by protein tags that use fluorogens instead of chromophores.
The difference between the two is that fluorogens are nonfluorescent until they are activated
by the appropriate protein tag. Furthermore, because the fluorogens are not washed away,
a continuous renewal of fluorogen in the binding site of the protein is possible which
reduces the apparent photobleaching (Pimenta et al., 2017). In other words, photobleached
fluorogen can leave the binding pocket and fresh fluorogen can replace it. An interesting
example makes use of the Photoactive Yellow Protein (PYP) which is natively found in
purple bacteria and uses coumaric acid as a chromophore. Aside from avoiding background
fluorescence from unbound chromophores, the protein is also much smaller in comparison
to the HaloTag and CLIP-tag (14 kDa vs 33 kDa and 20 kDa respectively) which makes it
less likely to interfere with the function of the protein of interest it is coupled to (Schneider
and Hackenberger, 2017). A first attempt at using PYP as a protein tag is reported by
Hori et al. (2009). It features a fluorogen made up of a coumaric acid derivative coupled
to a fluorescein molecule. Intramolecular interactions are thought to prevent fluorescence
of the unbound fluorogen.
A more elegant protein tag based on PYP was later introduced by Plamont et al. (2016)
and named Fluorescence-activating and Absorption-Shifting Tag (FAST) (Fig. 1.2D).
This tag uses simple rhodanine derivatives, 4-hydroxybenzylidene-rhodanine (HBR) and
4-hydroxy-3-methylbenzylidene-rhodanine (HMBR), as a fluorogen. Free HBR and HMBR
absorb light around 400 nm but show little to no fluorescence. Binding to FAST causes
a deprotonation of a hydroxyl group that leads to a redshifted absorption spectrum and
a drastic increase in emission light with maxima at 527 nm and 540 nm for HBR and
HMBR respectively. Interestingly, the fluorogen molecules do not form a covalent bond
with the FAST-tag and can therefore exchange with other fluorogen molecules. This is
advantageous since photobleached fluorogen does not remain attached to the tag and can
be exchanged for fresh fluorogen. In later publications, the group presented additional
fluorogens compatible with FAST to offer a broader colour palette (Li et al., 2017). Further
development of FAST resulted in a split version of the protein tag for studying protein-
protein interactions, named split-FAST (Tebo and Gautier, 2019). The first 114 amino
acids of FAST, NFAST, and the last 11 amino acids, CFAST, can each be fused to two
proteins of interest. When the proteins interact, NFAST and CFAST rapidly dimerize and
show fluorescence in the presence of a fluorogen. The association of the two split-FAST
peptides was shown to be reversible and self-complementation proved to be limited.
1.3 Examples of biosensors

Today, there exist numerous different genetically-encoded biosensors against a broad range
of biologically important targets which are summarized in a review of Greenwald et al.
(2018). Probably the most well-known class of biosensors are the genetically-encoded
calcium indicators (GECI). The first notable example of this is Cameleon (Miyawaki et al.,
1997). This FRET-based biosensor introduced the now common architecture of calmodulin
(CaM) together with the small CaM-binding peptide M13 as a sensing domain for Ca2+
(Fig. 1.3A). When Ca2+ is present, it binds to CaM which allows M13 to interact with
CaM. This leads to a large conformational change that brings the fluorescent proteins,
GFP and BFP, in close proximity to allow FRET which changes the emission light to that
of the acceptor protein upon excitation of donor protein. The CaM-M13 sensing domain
was later also used in single fluorescent protein GECIs, such as GCaMP (Nakai et al.,
2001). Aside from being a smaller construct, single fluorescent protein sensors generally
offer a higher absolute signal in comparison to FRET-based sensors (Dedecker et al., 2013).
The GCaMP sensor uses a circularly permutated variant of enhanced GFP (cpEGFP) to
1.4. UNIVERSAL BIOSENSORS? 5
Figure 1.3: Generalized, common architectures for genetically-encoded biosensors based on

fluorescent proteins. Adapted from Moeyaert and Dedecker (2020).
which CaM and M13 are respectively C-terminally and N-terminally fused (Fig. 1.3B,
see also Fig. 1.1). In absence of Ca2+ , the chromophore of cpEGFP is exposed to the
solvent and the sensor is not fluorescent (Akerboom et al., 2009). The conformational
change due to the Ca2+ -CaM-M13 interaction abolishes this solvent exposure and restores
fluorescence. Modern GECIs such as GCaMP6 (Chen et al., 2013) and the GECO family
(Zhao et al., 2011) show a high sensitivity to Ca2+ and have been instrumental to many
findings especially in the field of neurosciences (Piatkevich et al., 2019).
Another interesting class of biosensors are those that detect a certain protein activity.
Protein kinase sensors are a good example of this and are highly relevant in studying
signal transduction pathways. One of the earliest developed kinase sensors was a FRET-
based sensor for Protein Kinase A (PKA) activity called AKAR (Zhang et al., 2001).
The sensing domain consisted of a 14-3-3 protein domain that binds to phosphoserine or
phosphothreonine and a consensus PKA substrate. Phosphorylation of the PKA substrate
allows the 14-3-3 domain to bind it, which causes a conformational change that brings
the two FRET partners in close proximity (Fig. 1.3C). Recently, a single fluorescent
protein biosensor was introduced as successor to AKAR, named ExRai-AKAR2 (Zhang
et al., 2020). It uses cpEGFP derived from GCaMP3, a consensus PKA substrate and a
phosphothreonine binding domain FHA1 (Mehta et al., 2018). The working principle is
again the same as with e.g. GCaMP: a conformational change prevents solvent access to
the chromophore and restores fluorescence upon binding of FHA1 to the phosphorylated
PKA substrate (Fig. 1.3D).
1.4 Universal biosensors?

Despite the long list of biosensors for different targets provided by Greenwald et al. (2018),
not all possible targets have their own biosensors. Furthermore, in some cases the use of
one of the existing biosensors might not be compatible with a certain experiment. For
example, there might be spectral overlap with other biosensors in the same experiment.
It could also be that certain required characteristics, e.g. high brightness, resistance to
photobleaching or low background fluorescence, are not available in existing biosensors.
With these current restrictions in mind, some sort of universal biosensor targeting a
universal epitope could theoretically be an interesting alternative. To this end, small
protein tags are an obvious starting point. Protein or epitope tags like the polyHis-tag
(Hochuli et al., 1987) or the HA-tag (Wilson et al., 1984) have a long history of use in
either protein purification, immunostaining or immunoprecipitation. In the latter, proteins
in solution are precipitated by using monoclonal antibodies (Ab) that bind to these protein
tags. In immunostaining, Ab are washed over a fixated sample and bind to proteins
with the appropriate epitope tag. Often, secondary Ab are used that are fused to a
radioactive, luminescent or fluorescent label to localize the target. Examples of Ab-binding
epitope tags are the myc-tag (Evan et al., 1985), the HA-tag (Wilson et al., 1984) and the
FLAG-tag (Hopp et al., 1988). In theory, these protein tags can be used for labelling an
intracellular protein of interest, but only in fixated and permeabilized cells since Ab cannot
pass the cell membrane. Additionally, because heterotetrameric Ab are not encoded by a
single DNA sequence and are the product of complex gene recombinations, they cannot
be introduced as genetically-encoded sensors in other organisms but must be extracted
exclusively from the serum of immunized host organisms. Moreover, due to their large
size (around 150 kDa), Ab are not compatible with super-resolution microscopy, which is
becoming increasingly more relevant in the field of fluorescence microscopy.
Briefly, super-resolution techniques aim to overcome the diffraction limit inherent to
light microscopy. The diffraction limit can be defined as the smallest distance between
two emitters to discern one from the other. With classical light microscopy, the diffraction
limit lies around 200 nm. With super-resolution techiques such as dSTORM (Heilemann
et al., 2008), this limit can be decreased down to 20 nm, allowing for higher resolution
images and e.g. to localize closely packed single molecules. Ab are around 10 nm in
size (Reth, 2013), therefore when staining with primary and secondary Ab, the distance
between the label and the target becomes significant in super-resolution microscopy and
can give an inaccurate depiction of the true localization of the target. This phenomenon
is sometimes called the linkage error (Früh et al., 2021).
A solution to the problems associated with Ab had become accessible with the discovery
of heavy chain-only antibodies (HCAb) in the serum of certain camelids. These types
of Ab consist of, as the name suggests, only a homodimer of the Ab heavy chain in
contrast to the classical heterotetrameric Ab with two heavy and two light chains (Fig.
1.4) (Hamers-Casterman et al., 1993). This means that HCAb are not only smaller
than classical Ab, but also that the antigen-binding site is now encoded in a single
polypeptide chain. This groundbreaking discovery lead to the further development of
single-domain antigen binding fragments derived from the variable domain of the heavy
chain (VHH) (Fig. 1.4B) (Muyldermans and Lauwereys, 1999), which would later be
called nanobodies (Nb) (Muyldermans, 2013). Recently, an epitope tag was specifically
designed to outperform existing ones, together with a complementary Nb and was called
the ALFA-tag (Götzke et al., 2019), due to its alpha-helical structure. The ALFA-tag was
rationally designed de novo to minimize interference with the tagged protein of interest
and maximize compatibility with modern analytical techniques. Therefore, Götzke et al.
(2019) provide an exhaustive list of criteria for both the tag itself as well as the molecule
that binds the tag.
1.5. NANOBODIES: STRUCTURE & FUNCTION 7
1.5 Nanobodies: structure & function

In contrast with Ab, Nb do seem to be compatible for use in biosensors. As mentioned
earlier, Nb are the product of years of research on the peculiar type of Ab found in members
of the Camelidae family (Hamers-Casterman et al., 1993). These animals produce another
type of immunoglobulin G (IgG) aside from the classical heterotetrameric IgG, which are
HCAb. They are made up of two IgG heavy chains forming a homodimer and have both
a variable and two constant domains (Fig. 1.4B) (Muyldermans and Lauwereys, 1999).
Around the same time, another group discovered similar HCAb in a shark species, called
IgNAR (Greenberg et al., 1995). They differ from the camelid HCAb in that IgNAR Ab
have five constant domains. What makes both Ab unique and relevant for this thesis,
is that all complementarity-determining regions (CDR) lie in one peptide chain. This
makes it easy to genetically encode the antigen-binding properties and thus reproduce
them outside of immunized host animals. To unlock the full potential of this idea, the
camelid HCAb were further developed and eventually, single-domain antibodies or Nb
were introduced (Muyldermans, 2013). Nb comprise the smallest portion of HCAb with
antigen-binding properties, the variable heavy-chain domain (VHH) and are around 15
kDa in size (Fig. 1.4B) (Harmsen and De Haard, 2007).
Figure 1.4: A. Classical tetrameric antibody. B. Camelid heavy chain-only antibody (HCAb).
Inset: variable domain of the heavy chain (VHH) or nanobody. Fc: crystallizable fragment, Blue
lines: antigen-binding site. Figure adapted from Muyldermans (2021b).
Nb can generally be obtained through three different methods (Muyldermans, 2021a).

One way is to repeatedly immunize a few animals with the desired antigen over the course
of two months. Afterwards, mRNA is extracted from the blood, converted to cDNA and
amplified by polymerase chain reaction (PCR). The PCR products are then digested,
ligated in a plasmid and transformed in Escherichia coli (Olichon and de Marco, 2012).
This yields a so-called immune library with clones of the VHH gene. The immune library
can then be screened for the desired Nb. It is also possible to create a naı̈ve library which
omits the immunization step of animals (Sabir et al., 2014). This can be preferred to
avoid side effects from toxic antigens for example. A downside is that the naı̈ve library
must be substantially larger than the immune library to obtain a suitable candidate. The
naı̈ve library is created by taking blood from several unexposed animals. The third type
of library generation method takes a more de novo approach and gives rise to synthetic
libraries (Zimmermann et al., 2018). First, a stable scaffold is selected in which multiple
random mutations will be incorporated. These randomisations are focused in the three
CDRs. The mutations are not completely random since some amino acids are not optimal
for antigen detection in the CDRs, for example hydrophobic or chemically reactive amino
acids. Furthermore, CDR 3 is characterized by a diverse loop of varying length in different
Nb. Therefore it is useful to incorporate various lengths of CDR 3 in the synthetic library
(Muyldermans, 2021a). The high degree of randomisation in the Nb sequence gives an
enormous theoretical library size, which ensures that all screened clones will be unique.
However, this also implies that the quality of the synthetic library is hard to determine.
Furthermore, the extensive randomisation of amino acids can also cause problems for
protein stability, which might need improving in additional steps.
1.5.1 Applications of nanobodies
The utility of nanobodies was first seen in fields where conventional antibodies fell short in
specific circumstances, such as their use as therapeutics or in imaging processes. But soon
after, the potential of their unique properties began to be explored and nanobodies even
found new niches to fill. A property that was quickly appreciated, was the nanobody’s
ability to form an extruded, finger-like interaction site as opposed to the more flat
interaction surface of a conventional Ab (Desmyter et al., 1996). This protruding interaction
site is usually located in the first or third CDR (De Genst et al., 2006) and allows it to
undergo stable interactions with reaction sites in enzymes or binding pockets in receptors
(Fig. 1.5A). Another advantage over large, tetrameric Ab is that nanobodies are suitable for
transformation and expression in unicellular hosts like E. coli or Saccharomyces cerevisae,
which makes very high yields per batch possible (Muyldermans, 2021b). While nanobodies
have a intrinsic low immunogenicity for humans, it is usually still preferable to humanize
the protein when considering their use as a drug (Arbabi-Ghahroudi, 2017).
For research purposes, nanobodies can be easily transfected for intracellular expression,
in which case they are dubbed ”intrabodies” and even fusion proteins with nanobodies can
be expressed this way (Steeland et al., 2016), (Fig. 1.5B). When nanobodies are fused to
fluorescent proteins, they are also sometimes called chromobodies. In this case, their small
size makes them highly suitable for fluorescence microscopy and even super-resolution
microscopy (Beghein and Gettemans, 2017). In immunostaining, multiple Ab are used: a
primary Ab that binds the target, a secondary Ab that binds the constant domain of the
primary Ab and contains a label and sometimes even a tertiary Ab depending on which
labelling method is used. While conventional Ab are already quite bulky, stacking three
of them on each other puts the label at a significant distance (>25 nm) from the target
(de Beer and Giepmans, 2020). This can lead to an incorrect, enlarged image or blurring
of closely packed target molecules. A labelled nanobody however, is only 3 nm in size
and thus offers an image much closer to reality (Mikhaylova et al., 2015), (Fig. 1.5C).
Nanobodies also have improved penetration over conventional Ab, as was demonstrated by
de Beer and Giepmans (2020). They show that while monoclonal antibodies labelled with
an organic dye have difficulty entering the nucleus and display aspecific labelling, labelled
nanobodies have no such difficulties (Fig. 1.5D). Moreover, some nanobodies are even
capable of crossing the blood-brain barrier (Caljon et al., 2012), which opens possibilities
for brain-targeted drugs or in vivo labelling of specific brain regions.
1.6. DEVELOPING AND OPTIMIZING BIOSENSORS 9
Figure 1.5: A. Nanobody (orange) can bind the active site of an enzyme through its flexible,
protruding CDR3 (Adapted from Dmitriev et al. (2016)). B. Nanobodies can be genetically
encoded and expressed in bacteria, even as fusion proteins. C. The fluorescent tag carried by
the Nb is in closer proximity to the original target than with regular Ab. TOI = target of
interest. D. Nanobodies can better penetrate cells compared to heterotetrameric antibodies, even
in permeabilized cells.
1.6 Developing and optimizing biosensors

Using biosensors in research is one thing, but actually developing novel biosensors is a
serious work process on its own. First of all, an architecture needs to be thought out
that reconciles the basic principles of biosensor design with the specific target in mind.
Crucial is the choice for the sensing and reporter domain. Furthermore, the physical
change when the target binds must be envisioned: how will the unbound and bound state
of the biosensor differ conformationally and how can the different states be discerned?
Depending on which target is to be detected, either an existing sensing domain can be
copied or adapted or an entirely new form factor must be designed. When working with a
fluorescent readout as the reporter, existing fluorescent proteins or fluorophore-binding
tags are highly suited to incorporate in fusion proteins such as biosensors. When deciding
on which domains to choose, it is important to bear in mind how they are linked to each
other and in which order. Both can drastically change the efficiency of the biosensor. The
linkers connecting the different domains and the order in which they come are therefore
common targets for optimizing the response of the biosensor later on in the development
process.
The next question that arises is how to obtain the best version of the envisioned
biosensor. For this, two things are needed: a way of producing varying mutants and an
assay to determine which of these mutants work best or in other words, a mutagenesis
and a screening method. These can be seen as steps in a process that are often repeated
multiple times.
1.6.1 Mutagenesis
Mutagenesis is a long standing principle in nature and is the engine required to power
the evolution of a species. By generating variations in their genome, a species can both
positively and negatively affect its phenotype. However, history is written by the victor and
thus mutations that increase a species chance of survival, general fitness or reproduction
will be more likely to be carried over to future generations. Of course, natural selection is
a slow process over the course of dozens or even hundreds of generations. However in a
lab setting, this process can be drastically sped up to generate a wide variety of different
mutants each generation (Durland and Ahmadian-Moghadam, 2021).
Mutations can be introduced either specific and site-directed, random and site-directed
or completely random, perhaps in a defined location. For site-directed mutagenesis, PCR
with mutated primers is most used for its ease of use and large amount of DNA it produces
(Fig. 1.6A). Both random and specific mutations can be introduced with PCR. For random
mutations, a primer mixture can be made with a user-defined chance of each nucleotide
occurring in desired locations. There exist several variations on PCR-based mutagenesis
such as QuikChange (Agilent) or ’Round-the-Horn site-directed mutagenesis (Moore, 2018),
but every method follows the same principle.
An interesting technique of more recent years that can introduce mutations both specific
and random, site-directed and genome-wide, relies on the CRISPR-Cas9 system. Briefly,
this Nobel prize-winning technique uses a short guide RNA strand to target an enzyme,
Cas9, to a piece of DNA with complementary sequence, where the enzyme introduces a
double strand break (DSB) (Jinek et al., 2012). This DSB can then be repaired by the
(eukaryotic) host organism in two ways: either by non-homologous end joining (NHEJ) or
by homology-directed repair (HDR). In the former, the two ends of the DSB are quickly
ligated to each other. However this process is very prone to mistakes and insertions or
deletions (indels) are relatively common. HDR is only possible when a template is available,
in which case the DSB is repaired according to this template. With HDR, large insertions
of entire genes can also be introduced (Hryhorowicz et al., 2017). Very recently, Tong et al.
(2021) have shown that the CRISPR-Cas9 system can be used to introduce controlled
indels and substitutions both as point mutations and as larger fragments. Their system
uses a modified Cas9 enzyme that only nicks one strand rather than introducing a DSB,
allowing its use in bacteria as well since they cannot do DNA repair by NHEJ. While
CRISPR-Cas9 editing is usually directed at the genome, Tong et al. (2021) were also able
to target plasmids, showcasing the tool’s potential in directed evolution experiments.
When there is no need for a specific change in the biosensor but rather an overall
performance enhancement is desired, site-directed mutagenesis is not suited. Instead,
random mutagenesis methods can be used. There exist chemicals that can randomly
modify nucleotides, introduce deletions or cause frameshifts both in vitro and in vivo
(Labrou, 2010). While chemical mutagenesis is simple and economic, it is difficult to
control the mutation rate. Random mutations can also be introduced with PCR methods.
An example is error-prone PCR, which is based on the lack of a proofreading ability of the
Taq DNA polymerase (Fig. 1.6B). To further increase the amount of misincorporated bases
by Taq polymerase, Mg2+ and Mn2+ can be added to the reaction mixture, an unbalanced
dNTP mix can be used and the polymerase concentration can be increased (Labrou, 2010).
Error-prone PCR introduces multiple point mutations in any DNA sequence accessible to
PCR with regular primers.
1.6. DEVELOPING AND OPTIMIZING BIOSENSORS 11
Figure 1.6: Two types of PCR mutagenesis: site-directed (A) and random by error-prone PCR
(B). Blue: template plasmid, Red: circularized PCR product containing mutations (*).
1.6.2 Mutant screening

Screening methods are usually categorized by their throughput, or the amount of mutants
that can be judged with one experiment. While mutants from both a targeted and
a random mutagenesis library need to be assessed in some way, the throughput of a
screening method becomes increasingly important in a random mutagenesis library. For
example, random mutagenesis of just 4 amino acids (or 12 base pairs in the DNA) can
produce 160 000 different peptide sequences and more than 16 million different DNA
sequences. Therefore the throughput is an important characteristic of screening methods.
Other important properties are labour intensity, cost and duration of one experiment. In
Table 1.1, three different screening techniques are assessed based on these properties. For
biosensors that have fluorescent feedback domains, titrations with the target in lysate,
so-called lysate screens, can be done to measure the response. Here, high brightness and
a large change in fluorescence upon target addition are two desirable properties. Lysate
screens are quick and inexpensive, albeit quite low-throughput: they are usually performed
on 96-well plates but are limited by the manual colony picking, inoculating in separate
vials and the mutagenesis efficiency, in other words the amount of single colonies. By
inoculating in deep-well 96-well plates, the throughput can be slightly increased. This way,
one could screen around 1 000 colonies per week. However, because of the labour-intensity,
lysate screens are usually applied after an initial, higher-throughput screen (Zhang et al.,
2020) or in a targeted mutagenesis library (Dippel et al., 2018).
A medium-throughput method screens fluorescent biosensors by colonies on plates,
which is called colony screening. One way to measure biosensor response is by replica
plating (Ibraheem et al., 2011). This way, the fluorescence of each colony can be measured
both with and without target present. While replica plating is quite robust, it is also
labour intensive. A quicker and less labour intensive alternative for colony screening
involves applying the target directly to the plate, for example by spraying (Litzlbauer
et al., 2015). Then the fluorescence can be measured before and after addition of the
target to visualise the response. This eliminates the need for making additional plates,
but also introduces some variability since spraying is not completely homogeneous. Colony
screening is mostly limited by the efficiency of the mutagenesis or in other words, the
amount of colonies per plate. It could in theory handle in the order of 105 colonies per
week, assuming on average 100 colonies per plate.
Because most biosensors use fluorescent feedback domains, an attractive high-throughput
screening method is Fluorescence-activated Cell Sorting (FACS) (Della Corte et al., 2020).
Briefly, a cell mixture containing the library is flowed through a small channel so that
the cells line up in a single file. At one point, fluorescence is measured and downstream,
individual cells are sorted in two lanes based on a chosen fluorescence threshold. This
way, only the brightest - or faintest - cells are selected. For biosensors with a fluorescent
reporter domain, this cell sorting can be done two times per mutation round, once with
and once without the target present. This way, the biosensor can be selected based on the
greatest response or in other words, the greatest difference between the on- and off-states
of the fluorescent moiety. FACS is a high-throughput method that requires little manual
labour, however it requires specialized tools which are expensive. In one FACS experiment,
up to 108 cells can be screened at a time (Yang and Withers, 2009).
Method Cost Labour intensity Duration Throughput

Lysate screening +++ - ++ 96 per plate
Colony screening +++ +/++* +/++* >100 per plate
FACS - ++ +++ 108 /experiment
Table 1.1: Assessment of the discussed screening methods. -: bad, +: okay, ++: good, +++:
excellent. *replica plating/spraying
Chapter 2
Project Description
Biosensors have an impressive track record of elucidating conditional, transient intracellular

states and mechanisms. As briefly mentioned in the previous chapter though, many
important and interesting intracellular targets lack a way of tracking their dynamics in
vivo. This greatly limits what mechanisms can be studied and therefore hampers the
progress towards necessary developments in oncology, neurology and other important fields.
The limiting factor in developing new biosensors is not the fluorescent reporting domain,
but the sensing domain that converts the presence of the target into a conformational
change.
To offer a novel concept for the sensing domain, the NanoBlock architecture was
proposed, aiming to broaden the possibilities for biosensor design and to introduce a
generalized way of building genetically-encoded biosensors. Aside from the fluorescent
moiety, the key feature of the NanoBlock architecture consists of a nanobody with
corresponding block ing peptide. When the target epitope of the nanobody is absent,
the blocking peptide will be bound to the antigen-binding site of the nanobody. Then,
when the target becomes available to the sensor, the blocking peptide will be displaced
which leads to a change in fluorescence. Two main designs were further contrived, one
based on the well-established GCaMP biosensor using circularly permuted enhanced GFP
(cpEGFP) (Fig. 2.1A) (Nakai et al., 2001) and the other based on the recently developed
split fluorogen binding protein splitFAST (Fig. 2.1B) (Tebo and Gautier, 2019). Both
Figure 2.1: Cartoon representation of two different NanoBlock architectures and their proposed
mode of action. A. GCaMP-based design with circularly permuted enhanced GFP (cpEGFP). B.
SplitFAST-based design with splitFAST-fragments NFAST and CFAST.
13
14 CHAPTER 2. PROJECT DESCRIPTION
designs function differently: the GCaMP-based NanoBlock sensor will be fluorescent in

absence of the target (closed conformation) and loses fluorescence upon addition of the
target (open conformation). The splitFAST-based sensor works the other way around: it
gains fluorescence when the target becomes present, of course only when the appropriate
fluorogen is also available. For the development of the NanoBlock biosensors, two different
nanobodies will be used: the LaM4 Nb, which targets mCherry and the ALFA Nb, targeting
the ALFA tag, a newly designed epitope tag (Götzke et al., 2019).
My contribution to the NanoBlock project will be to enhance the response of the
GCaMP-based biosensor targeting mCherry to the presence of the target by modifying
the properties of the blocking peptide. This comes down to lowering the affinity of the
blocking peptide for the nanobody so that the biosensor switches more easily to the open
confomation, which implies lower fluorescence. Modifying the blocking peptide will involve
the random mutagenesis by PCR of the blocking peptide sequence and subsequent screening
of the created mutants (Fig. 2.2A). After a preliminary round of mutagenesis and selecting
a good mutant, I will attempt to set up a screening system that balances ease-of-use with
high-throughput. For this, I will consider on the one hand an increased-throughput lysate
screen and on the other hand a colony screening method (Fig. 2.2B). With this, more
mutants from the random mutagenesis can be screened, which means a greater chance
of identifying a better sequence for the blocking peptide. More general, the method can
improve the workflow of optimizing this biosensor and effectively all future sensors in the
lab.
Figure 2.2: Two main project activities. A. Creating a library of random blocking peptide
(Pep3) mutations, followed by low-throughput screening in lysate. B. Scheme depicting the work
flow of the increased througput colony screening (Explained in Chapter 3).
Chapter 3
Material and Methods
3.1 Buffers, media & solutions

Luria-Bertani (LB) broth: Bacterial growth medium containing 10 g/L tryptone, 5
g/L yeast extract and 10 g/L NaCl.
Terrific Broth (TB) medium: Bacterial growth medium containing 24 g/L yeast
extract, 20 g/L tryptone, 4 mL/L glycerol and phosphate buffer with final concentrations
0.017 M KH2 PO4 and 0.072 M K2 HPO4 .
LB agar plates: Same composition as LB broth, but with 12 g/L agar. Depending on
which plasmids the bacteria carry, 40 µg/mL ampicillin, kanamycin (50 µg/mL) and/or
chloramphenicol (34 µg/mL) was added before pouring the agar. For the colony screening
experiments, a final concentration of 20 mM of D-glucose, 1 mM IPTG and/or 10 mM of
both D-glucose and L-arabinose were also added before pouring the agar.
Super optimal broth with catabolite repression (SOC): Bacterial growth medium
containing 5 g/L yeast extract, 20 g/L tryptone, 0.583 g/L NaCl, 0.186 g/L KCl, 0.952
g/L MgCl2, 1.204 g/L MgSO4 dissolved in deionized water. This is then autoclaved at
121°C. After cooling down, 3.603 g/L filter sterilized glucose is added.
Resolving gel for sodium dodecyl sulphate polyacrylamide gel electrophoresis
(SDS-PAGE) contains 10 % acrylamide, 0.38 M Tris (pH 8.8), 0.4 % tetramethylethylene-
diamine (TEMED), 0.1 % SDS and 0.1 % ammonium persulfate in deionized water.
Stacking gel for SDS-PAGE contains 5 % acrylamide, 0.125 M Tris (pH 6.8), 0.1 %
SDS, 0.1 % ammonium persulfate and 0.1 % TEMED in deionized water.
Tris-NaCl (TN) buffer: 100 mM tris(hydroxymethyl)aminomethane (Tris) and 300 mM

NaCl in H2 O. The pH is adjusted to 7.4 with HCl.
Tris-NaCl-Imidazole (TNI) buffer: Same composition as TN buffer, but with a low
concentration of imidazole (20 mM).
TNI+ buffer: Same composition as TN buffer, but with a high concentration of imidazole
(250 mM).
15
16 CHAPTER 3. MATERIAL AND METHODS
3.2 Transformation in E. coli

For high expression the E. coli strain JM109(DE3) (endA1, recA1, gyrA96, thi, hsdR17
(rk- , mk+ ), relA1, supE44, λ- , Δ(lac - proAB), [F’ , traD36, proAB, lacIq ZΔM15], lDE3)
(Promega, Leiden, The Nederlands) was made chemocompetent using the Inoue method
(Inoue et al., 1990) or was made electrocompetent as described in Dower et al. (1988). The
cells are then stored at -80°C in aliquots of 50 µL. As a high copy number strain, the E.
coli strains DH5α (F - Φ80lacZΔM15 Δ(lacZYA - argF) U169, recA1, endA1, hsdR17 (rk-,
mk+) phoA supE44, λ-, thi - 1, gyrA96, relA1) (Promega, Leiden, The Nederlands) or
Turbo (F’ proA+ B+ lacIq ΔlacZ M15/ fhuA2 Δ(lac-proAB) glnV gal R(zgb-210::Tn10)TetS
endA1 thi-1 Δ(hsdS-mcrB)5) (New England Biolabs) were made chemocompetent using
the Inoue method (Inoue et al., 1990). The cells are then stored at -80°C.
Heat shock: The frozen cell suspension is gently thawed on ice. 1 µL of purified
plasmid DNA is added to it and is incubated on ice for 30 minutes. Then, the cells are
rapidly brought to 42 °C for 45 seconds in a preheated water bath or a heat block.
Electroporation: The frozen cell suspension is gently thawed on ice. Then, 1 µL of
purified plasmid DNA is added to it and the suspension is transferred to an electroporation
cuvet. The cuvet is placed in the electroporator and is given an electric pulse of 1700 V
for 4 to 6 ms.
Next, 200 to 450 µL of SOC is added and the mixture is incubated for 1 hour at 37 °C.
When single colonies are required, 50 to 100 µL of the incubated cells in SOC medium
is spread out on an LB agar plate with selection marker (e.g. ampicillin) and incubated
overnight at 37 °C. Single colonies can be picked and further cultured in LB broth.
When sequencing of the transformed plasmid was required, the cells from single colonies
were grown in 4 mL liquid LB overnight at 37 °C. Afterwards, the cells are pelleted by
centrifuging for 2 minutes at 13400 rpm. The plasmid DNA is then extracted using the
GeneJET Plasmid Miniprep kit (ThermoFisher Scientific). The plasmid is finally eluted
in 30 µL deionized water and the concentration is measured using a NanoDrop 2000
spectrophotometer (ThermoFisher Sci.). For sequencing, at least 100 ng of the plasmid in
at least 15 µL deionized water is sent to LGC Genomics (Berlin, Germany).
3.3 Large scale E. coli culture

To create a large stock of dark mCherry for the titration experiments, a pRSETb vector
containing the dark mCherry gene was transformed in chemo-competent E. coli JM109
cells. A starter culture was grown overnight in 25 mL of TB medium with 40 µg/mL
ampicillin at 37 °C. Afterwards, this starter culture was transferred to 1.7 L of TB medium
with 40 µg/mL ampicillin and grown in a preheated LEX bioreactor (Epiphyte Three Inc.,
Canada) at 37 °C up to an optical density (OD600 nm ) of 3 to 4. Also 9 drops of Antifoam
204 (Sigma-Aldrich) is added to prevent excessive foam buildup. The LEX bioreactor uses
a water bath to heat the medium and both mixes and aerates it with filtered, compressed
air provided to each individual culture. As a result, large volumes of culture can be grown
in regular 2 L flasks with a screw cap. When the OD600 nm reaches a maximum of 4, a
final concentration of 250 µM of IPTG is added and the culture is switched to 16 °C to
allow protein expression overnight. Afterwards, the cells are pelleted by centrifuging at
4000 rpm for 30 minutes and protein purification is continued as described below.
3.4. PROTEIN PURIFICATION 17
3.4 Protein purification

E. coli JM109 cells for high expression were transformed with the plasmid containing
the gene for the desired protein with a 6xHis-tag. The cells were grown for overnight
at 37 °C or 72h at 21 °C in a shaking incubator in 200 mL LB medium containing 40
µg/mL ampicillin. Then the cells were harvested by centrifuging at 4000 rpm for 30
minutes. The supernatant was decanted and the pellet resuspended with 20 mL TN buffer.
This mixture was then centrifuged again at 5000 rpm for 15 minutes. The pellet was
resuspended in 20 mL TN buffer and this time, 20 mg of lysozyme was added to break the
cell membrane. Next, the cells were put at -80 °C for 30 min to further break the cells
open. After defreezing, the cells were lysed one final time by sonicating 5 times 1 minute
with 1 minute intervals with a sonicator. Then the cell debris was removed by centrifuging
1h at 8500 rpm.
For further purification, affinity chromatography with Ni2+ -nitriloacetic acid (Ni-NTA)
agarose resin (Protino, Macherey-Nagel) was used. 2 mL of the Ni-NTA resin was added
to the total protein extract and the mixture was then gently shaken for 30 to 60 minutes
at 4 °C to let the protein bind the agarose resin. Next, the mixture was transferred to a
polystyrene column and washed with 10 mL of TN buffer. Then, undesired proteins that
were weakly bound to the column were washed away with 10 mL TNI buffer. Finally, the
His-tagged protein was eluted with excess imidazole in the TNI+ buffer (2.5 mL).
The protein solution now contains a high concentration of imidazole which needs to be
removed. For this, a PD10 desalting column (Cytiva) was first equilibrated with 30 mL
TN buffer. Then the 2.5 mL protein solution was loaded on the column. Since the void
volume of the column is also 2.5 mL, it can safely stop running without losing the protein
fraction. Finally, the protein of interest was eluted by adding another 2.5 mL of TN buffer.
The protein concentration of the eluted fraction was measured with a NanoDrop 2000
spectrophotometer (ThermoFisher Sci.). Additionally, the purity of the eluted fraction
and presence of the protein of interest can be verified with SDS-PAGE. For this, 2 µg
of protein was mixed with a 4/1 2X SDS loading buffer/dithiothreitol (DTT) mixture
in a 1:1 ratio. The resulting mixture was briefly centrifuged, boiled for 3 minutes and
centrifuged again. Then the protein sample was loaded on the stacking gel together with
a protein ladder and electrophoresis was done in two steps: first a voltage of 100 V was
applied for 15 minutes followed by 300 V for 45 minutes. The gel was then rinsed with
H2 O and stained overnight with a Coomassie Brilliant Blue solution.
3.5 Titration of purified biosensors

To assess the performance of the purified NanoBlock biosensors, titrations in 96-well plates
are done. In each well, protein in TN buffer is added as well as a varying amount of dark
mCherry. Final concentrations in 100 µL are 2 µM of biosensor and a two-fold dilution
series with 11 different concentrations of dark mCherry in TN buffer starting from 10 µM
or 20 µM. An additional twelfth point in the dilution series is made with no dark mCherry
(i.e. TN buffer). Each titration is done in triplicate. The fluorescence is measured using
the Varioskan™ LUX plate reader (ThermoFisher Sci.) with excitation wavelength (λex )
488 nm, emission wavelength (λem ) 520 nm and automatic gain control. The performance
of the biosensors is assessed with the response r, defined by the fluorescence without target
divided by the fluorescence with the highest concentration of target r = FF−target

+target
. The data
was analysed and processed with Microsoft Excel and R, graphs were made with R.
3.6 Library generation: directed mutagenesis
To create the blocking peptide library, the QuickLib method is used (Fig. 3.1) (Galka et al.,
2017). A primer pair is created so that the forward primer contains an annealing part of at
least 20 bp at the 3’ end, a 5’ end of at least 15 bp that is the reverse complement to the
reverse primer and between those two ends, the degenerate bases for the desired mutation
(e.g. NNK) (see section 3.9 Primer list). A full plasmid PCR is done with these primers
to create the library of linearized plasmids. Before continuing, the remaining template
DNA is degraded by DpnI digestion. To check if the PCR reaction was successful, 5 µL
of the product together with a loading buffer can be loaded on a 1 % agarose gel for gel
electrophoresis (25 minutes, 125 V). The gel is either stained by adding 10000x GelGreen
before solidifying or by soaking in ethidium bromide for 15 minutes after the electrophoresis.
The linear library is circularized by the action of three enzymes: a 5’ exonuclease, DNA
polymerase and DNA ligase, conceptually similar to the Gibson assembly method (Gibson
et al., 2009). The resulting mixture is then transformed in chemo-competent E. coli JM109
cells and grown on LB agar plates for further screening.
Figure 3.1: Scheme of library generation by the QuickLib method with a mutagenic primer.
Red: randomized degenerate nucleotides. Light blue: complementary primer ends. Based on
Galka et al. (2017).
For the directed mutagenesis of the blocking peptide of the SplitFAST-based NanoBlock
sensor, an alternative method called ’round-the-horn mutagenesis was used (Moore, 2018).
This uses 5’-phosphorylated primers with the intended mutation also on the 5’ end of the
forward primer or of both primer if the intended mutation is large (Section 3.9). For the
phosphorylation reaction in 50 µL, 5 µL of 100 µM of each primer is mixed with a 5µL 10x
kinase reaction buffer, 1 µL 50 mM MgSO4 , 1 µL 100 mM ATP and 1 µL polynucleotide
kinase (PNK) in deionized water. This mixture is incubated for 30-60 minutes at 37 °C
followed by a heat inactivation at 95 °C for 5 minutes. The primers can then be used in
the PCR reaction and ligated afterwards. The PCR product can also be checked by gel
electrophoresis.
3.7. LIBRARY EVALUATION: LYSATE SCREENING 19
3.7 Library evaluation: Lysate screening

E. coli JM109 single colony cells are grown in 4 mL LB (in vials) or 400 µL LB (in
deep-well 96-well plate) with appropriate antibiotics overnight at 37 °C or 72 h at 21 °C.
Then, the cells are centrifuged for 2 minutes at 13000 rpm (in eppendorfs) or 10 minutes
at 4000 rpm (in deep-well 96-well plate). The pellet is resuspended in 1 mL (eppendorfs)
or 200 µL (deep-well 96-well plate) B-PER (ThermoFisher Sci.) and incubated for 15
minutes at room temperature. The cell suspension is then centrifuged again at the same
parameters as above. Of the supernatant from cells grown in vials, eight times 90 µL is
then transferred to different wells in a 96-well plate for subsequent titration with 10 µL
purified dark mCherry (10x dilution series and zero concentration). Of the supernatant
from the cells grown in the deep-well plate, two times 90 µL is transferred to two different
96-well plates and either 10 µL of 100 µM of dark mCherry or 10 µL TN buffer is added.
The fluorescence is measured using the Varioskan™ LUX plate reader (ThermoFisher Sci.)
with excitation wavelength (λex ) 488 nm, emission wavelength (λem ) 520 nm and automatic
gain control. For the screening of lysates from cells grown in the deep-well plates, the
response r is defined by the fluorescence without target divided by the fluorescence with
the highest concentration of target r = FF−target
+target
. Data was analysed and processed in
Microsoft Excel and R, graphs were made in R.
3.8 Library evaluation: Colony screening

Circularized PCR product of the Pep3 blocking peptide library in a pET28b-vector is
transformed together with a PBAD-vector containing mCherry (AddGene plasmid #54630,
Supplementary Fig. A.5) in competent E. coli JM109 cells as described above. 1 µL of each
plasmid in H2 O is used. The cells are spread out on LB plates containing 20 mM glucose,
1mM IPTG, 50 µg/mL kanamycin and 40 µg/mL ampicillin. After incubating the plates
at 21 °C for 48 hours, the plates are imaged a first time (Fbef ore ) (cpEGFP: λex = 480 nm,
λem = 530 nm; mCherry: λex = 555 nm, λem = 600 nm). The excitation light is generated
by a MAX-302 xenon lamp (Asahi Spectra, Tokyo, Japan) and fluorescence was detected
with a Cascade 512B CCD camera (Photometrics, Tuscon, AZ, USA). After imaging, the
plates are sprayed with a concentrated arabinose solution (1 M) using a Macherey-Nagel
glass sprayer (Fisher Scientific) to induce mCherry expression. The arabinose solution is
applied by spraying the plate 5 times evenly from top to bottom. This spray pattern is
repeated 4 times in total. Between each round of spraying, the plate is allowed to dry
(<1 min.) and is rotated 90 degrees. Then, the plates are incubated overnight at 37 °C
before imaging again (Faf ter ). Finally the response r is quantified as the ratio of the
F ore
fluorescence before and after spraying with arabinose r = Fbefaf ter
. The images are analysed
and processed with IgorPro, graphs are made in R.
3.9 Primer list
GCaMP-Pep3-library FWD gataaggatctcggatccatggtcgacCCGNNKNNKNNK

NNKTCCTTTctcgagaacgtctatatcaaggccgac
GCaMP-Pep3-library REV CGGgtcgaccatggatccgagatccttatc
dark-mCherry-Y72N FWD tcccctcagttcatgAacggctccaaggcctac
dark-mCherry-Y72N REV gtaggccttggagccgtTcatgaactgagggga
SplitFAST-Pep3.6-QL FWD catgaccccattgccattgccattaCCGCATATTTTTCA
TTCCTTTccattgccattaggcgac
SplitFAST-Pep3.6-QL REV CGGtaatggcaatggcaatggggtcatg
SplitFAST-Pep3.6-RTH FWD TTTCATTCCTTTccattgccattaggcgac
SplitFAST-Pep3.6-RTH REV AATATGCGGtaatggcaatggcaatgg
SplitFAST-Pep3library-RTH FWD NNKNNKTCCTTTccattgccattaggcgac
SplitFAST-Pep3library-RTH REV MNNMNNCGGtaatggcaatggcaatgg
Table 3.1: FWD: forward primer, REV: reverse primer, QL: QuickLib, RTH: ’round-the-horn
mutagenesis. Bases in upper case indicate where the mutation or site of interest is. N = A, T,
G or C; K = G or T; M = A or C.
Chapter 4
Results
4.1 Random mutagenesis of blocking peptide

The NanoBlock sensor available at the start of this project consists of an N-terminal
His-tag, followed by the Pep3 blocking peptide, the circularly permutated eGFP (cpEGFP)
and C-terminally, the LaM4 nanobody for mCherry (Supplementary Fig. A.4). Using the
purified protein, a titration with the target was performed to test the response of this
version (Fig. 4.1). As the target, dark mCherry (dmCherry) is used throughout the whole
thesis. A large batch of this protein was made with by growing a large scale E. coli culture
as described in Material & Methods section 3.3. One culture of 1.7 L yielded around 123
mg of purified protein (Supp. Fig. A.1). Dark mCherry is, as the name suggests, a variant
of the red FP with its fluorophore inactivated through a point mutation (Y72N) and is
therefore non-fluorescent. The dark state variant has the advantage that no emission light
from cpEGFP gets lost due to energy transfer between cpEGFP and mCherry in close
proximity. While there is certainly a response (r = 1.43)1 visible in Fig. 4.1, it is rather
modest and the remaining fluorescence at high dmCherry concentration is high. When
normalized fluorescence is used in graphs, all counts are normalized by dividing by the
largest value in the dataset before averaging.
Figure 4.1: Titration of dark mCherry (0.04 - 10 µM, y-axis = 0 µM) with Pep3-cpEGFP-LaM4
sensor (2 µM, n = 3). a.u. = arbitrary units, x-axis is log2-transformed.
1
r is defined as the fluorescence without target divided by the fluorescence with the highest concentration
F
of target: r = F−target
+target
(see also Material & Methods)
21
22 CHAPTER 4. RESULTS
The sequence of the blocking peptide Pep3, PDYLKSF, is now nearly identical the
environment of one of the main interacting residues on mCherry (K84) that binds to
the protruding CDR3-loop of LaM4 (Fig. 4.2) (Wang et al., 2021). While there are also
other residues of mCherry taking part in the interaction with the nanobody, the affinity of
the nanobody for the blocking peptide could still be of the same magnitude. This might
explain the moderate response and high remaining fluorescence. More specifically, if both
the blocking peptide and mCherry have similar affinity for the nanobody, there is little
driving force for the nanobody to preferentially bind the target over the blocking peptide.
Therefore, introducing random mutations in the blocking peptide to potentially lower the
affinity can be a promising starting point.
To create the blocking peptide library, a PCR-based random mutagenesis method called
QuickLib (Galka et al., 2017) was used as described in Materials & Methods section
3.6. From this library, at first 12 mutants were assessed in cell lysate by titration with
dmCherry (Fig. 4.3). For the assessment of the mutants, two properties were taken into
account: the absolute brightness and the response, i.e. the difference in fluorescence in
high versus low dmCherry concentrations. Furthermore, sequencing of the gene encoding
each of these mutants, revealed that several still contained the template Pep3 gene and two
had large inserts (Fig. 4.3, table). Of these 12, two promising mutants from colony 2 and
colony 6 were chosen for further characterization. They were purified and again titrated
with dmCherry to compare their performance in a more controlled manner. However,
when comparing them with the original Pep3, the mutants show a highly similar response
(r3.2 = 1.37, r3.6 = 1.43, Fig. 4.4). This already showcases an important shortcoming of the
preceding lysate screening: judging the performance of the biosensor based on the absolute
fluorescence can lead to wrong conclusions, since the amount of protein in the sample is
unknown. Higher or lower fluorescence counts can also be caused by a higher or lower
concentration of biosensor in the lysate. Therefore, it is better to compare normalized
fluorescence counts.
Figure 4.2: Visualisation of the interaction between the LaM4 nanobody (orange) and mCherry
(red). The CDR3-loop from the nanobody is coloured in yellow, the sequence in mCherry
corresponding to the blocking peptide in the sensor (PDYLKSF) is shown in blue. Inset: interaction
between Asn103 of the nanobody and K84 of mCherry. PDB: 6IR1 (Wang et al., 2021).
4.1. RANDOM MUTAGENESIS OF BLOCKING PEPTIDE 23
colony 1: PDYAKSF colony 2: PAECRSF colony 3: P*YSLSF

colony 4: PDYAKSF colony 5: PG*FFSF colony 6: PHIFHSF
colony 7: PDYAKSF colony 8: PDYAKSF colony 9: PCAVRSF
colony 10: insert colony 11: PSVPTSF colony 12: insert
Figure 4.3: Titrations with dmCherry (10-6 - 1 µM) of Pep3 library cell lysates and corresponding
peptide sequences (* = stop codon). As template for the library generation, an earlier blocking
peptide iteration was used, hence the template blocking peptide sequence is PDYAKSF.
Figure 4.4: Comparison between Pep3 mutants 2 and 6 and the original Pep3 (n=3 each).
Titrations of purified protein (2 µM) with dmCherry (0.04 - 10 µM, y-axis = 0 µM).
4.1.1 SplitFAST-based sensor: cloning efforts

After the identification of blocking peptide variants, one of the Pep3 mutants, Pep3.6, was
to be introduced in the SplitFAST-based NanoBlock sensor (Supp. Fig. A.6). Additionally,
the goal was to make a Pep3 library in the SplitFAST-based sensor similar to the one
in the cpEGFP-based sensor. Multiple efforts were made for both goals, however each
time, no correct PCR products were obtained. First, the introduction of the Pep3.6
blocking peptide was attempted with the QuickLib method, yielding no correct PCR
product (Fig. 4.5A). Next, both the Pep3.6 and a new blocking peptide library with the
SplitFAST sensor was attempted with ’round-the-horn mutagenesis. Both were done two
times with two different DNA polymerases (Q5 and Phusion), each yielding no desired
PCR product (Fig. 4.5B). Finally, a primer annealing temperature gradient was done to
investigate that parameter, however while there was some PCR product this time, none
of them were the correct size (Fig. 4.5C). This would be the final attempt and the idea
for a SplitFAST-based sensor with modified blocking peptide was not further investigated
within the time constraints of this thesis.
4.2 Increased throughput mutant screening

A glaring shortcoming in the previous results is the low amount of mutants analysed in
comparison to the total amount of possible mutants or in other words, the throughput
was too low. The degenerate primers of the PCR mutagenesis use NNK, which allows all
20 amino acids and 1 stop codon, on four different amino acid positions. This yields a
total of 214 or 194,481 different possible mutated peptide sequences. Choosing only 12
of those is not representative for the range of possibilities, certainly considering 34,481
4.2. INCREASED THROUGHPUT MUTANT SCREENING 25
Figure 4.5: 1 % agarose gels of SplitFAST-based sensor blocking peptide mutagenesis products.
A. PCR product of mutagenesis with QuickLib for the introduction of the Pep3.6 blocking peptide.
B. PCR products of mutagenesis by ’round-the-horn method for the Pep3.6 blocking peptide and
blocking peptide library. C. PCR products with annealing temperature gradient of mutagenesis by
’round-the-horn method for the Pep3.6 blocking peptide and blocking peptide library.
(4×203 +6×202 +4×20+1) of them contain at least one stop codon. Therefore, a screening
method that can analyze much more mutants in a reasonable time span is required. An
additional condition for the most suited method is that it can be performed in-house.
Since the lab does not possess a cell sorting machine, a FACS screening experiment was
not straightforward within the scope of this project. It would also have been potentially
excessive, since up to 108 cells can be screened (Yang and Withers, 2009), while only 105
is required. Two accessible alternatives are to either increase the throughput of the lysate
screen or to introduce a way of screening the library in the colonies on agar plates. Both
methods are described in detail in Material & Methods sections 3.7 and 3.8.
4.2.1 Lysate screening improvement

By transferring single colonies to and growing them in a single deep-well 96-well plate,
roughly 4 times more colonies were screened than was performed above in about the
same time window. While the process of colony picking takes slightly longer, it is not an
immensely time-consuming task and handling all colonies in a single recipient compensates
for this. Adding the lysis buffer and transferring the lysate to the regular 96-well plates
for spectroscopy might actually be less tedious thanks to multichannel pipettes. The
performance of the screening method, however, carries over several issues caused by
working in lysate. First of all, because there is no way of knowing the amount of protein
in the sample, care must be taken when comparing absolute fluorescence counts. High
fluorescence counts can also be caused by a higher concentration of biosensor as opposed
to a better performing one. Secondly, the results of the increased throughput lysate screen
seem to be inconsistent.
In Fig. 4.6A, 12 of the 42 different mutants show an increase in fluorescence upon

addition of dmCherry (indicated in red), opposite of how the biosensor is supposed to
work. Additionally, the response of the mutants in the library with the correct response
(1.01 ≤ r ≤ 1.18), is small in comparison to that of Pep3.2 (r = 1.23), Pep3.6 (r = 1.38)
and Pep3 (r = 1.28) in lysate (Fig. 4.6B & C). The decrease in fluorescence in the Pep3
library varies between 0 and 0.13 (normalized fluorescence), while the average slope of the
three previously obtained blocking peptide variants ranges from 0.15 to 0.23. While the
wide variety of response values in the library is a positive point, there still remains the
issues that (1) the data may not reliably reflect the response of isolated protein because
of the many inverse responses and (2) none come close to the average response observed
with the original blocking peptide in lysate. Based on these observations, the increased
throughput lysate method was not further explored.
Figure 4.6: Lysate screening from colonies grown in a deep-well 96-well plate. A. Response
of Pep3 library (n=42) in lysate upon addition of dmCherry (10 µM), coloured according to the
response (increase or decrease in fluorescence). B. Same data as in A, without colonies with
positive response (n=30), coloured by the value of the response. A darker shade indicates a larger
response, which corresponds with a greater change in fluorescence when the biosensor target is
added. C. Average response to dmCherry (10 µM) of three Pep3 blocking peptide variants (n=3
each) in lysate, coloured by change fluorescence. The average was taken after normalization . *:
p < 0.05, **: p < 0.01.
4.2.2 Colony screening

The second screening method that was assessed, screens single colonies of the library
directly on the agar plates, thus skipping the step of picking colonies and growing them
in liquid medium. It should therefore be faster, less labour-intensive and more mutants
can in theory be screened compared to the lysate screening in the same time frame. The
target, mCherry, is genetically encoded and its expression is controlled by the AraC
inducible promoter. This way, the target can be introduced by simply spraying the inducer,
L-arabinose, over the agar plates, activating transcription. This avoids the need for making
replica plates for conditions with and without expression of mCherry, as this would increase
the labour intensity and slow down the process.
The idea of using a sprayer to apply L-arabinose was found in the work of Ibraheem
et al. (2011) and Belal et al. (2013). The first attempts to test this methodology were
therefore heavily based on those publications. The induction of target expression by
L-arabinose was first tested by comparing the fluorescence in single colonies grown on
plates containing only D-glucose on the one hand and equimolar amounts of D-glucose
and L-arabinose on the other hand. Ibraheem et al. (2011) describe that cells grown on
L-arabinose alone experience a significant metabolic burden and is therefore better avoided.
In these experiments, the L-arabinose induction was tested with an AraC-regulated eGFP
gene, as the pBAD-mCherry plasmid was not yet available at the time. For each condition,
three replicate plates were made, each spotted with nine identical colonies. While there is
a greater fluorescence in colonies on the plate containing L-arabinose, the difference in
fluorescence with the D-glucose plates is not significant (p > 0.05, Fig. 4.7). Furthermore,
when comparing the replicate plates within the same condition, it is striking that there
is still quite some variation on the fluorescence. This is unexpected since all colonies
originate from the same glycerol stock and are thus supposed to be identical in fitness,
expression levels et cetera.
Figure 4.7: Fluorescence of colonies containing the pBAD-eGFP plasmid grown on either
inducing (10 mM L-arabinose, 10 mM D-glucose) or repressing (20 mM D-glucose) LB agar.
Left: The average fluorescence intensity of colonies on the induced plates is not significantly
(NS.) different from those on the repressed plates. Right: Variance between plates of the same
condition is relatively high.
First attempts at inducing mCherry expression by spraying a concentrated L-arabinose

solution were not successful (Supp. Fig. A.2). One apparent explanation was that the
amount of arabinose provided by spraying the plate once was simply not sufficient. To
verify this, multiple plates containing varying amounts of L-arabinose in the agar (0.2 -
0.0002 % w/v) were made and mCherry fluorescence was measured in single colonies
(Fig. 4.8). From this, 0.02 % or 200 µg L-arabinose per mL agar seemed to be sufficient.
Also no growth problems due to only providing L-arabinose were observed. Now, the
amount of L-arabinose that reaches the plate per “puff” of the sprayer needed to be
determined. To do so, empty plates were sprayed with the 1 M L-arabinose solution and
weighed before and after on an analytical scale. When spraying the plate in a horizontal
line 5 times from top to bottom, on average 13 mg L-arabinose reaches the plate (Table 4.1).
Compared to an LB agar plate with 200 µg/mL L-arabinose, this would be sufficient when
taking on average 25 mL LB agar per plate. However, this spray pattern was done the
first, unsuccessful times and thus does not suffice. This might be because a part of the
arabinose evaporates together with the water. To reach the equivalent of 0.2 % L-arabinose
in agar, this spray pattern should be repeated 4 times. In between each application, the
plate would be allowed to dry to prevent the colonies from dissolving and is turned 90
degrees to achieve a greater homogeneity.
Figure 4.8: Average fluorescence of mCherry in single colonies (n=9) on LB agar plates
containing varying amounts of L-arabinose. Red line indicates the background fluorescence.
spray volume (µL) 25.2 ± 2.1 86.8 ± 13.9 347 (est.)

mg L-arabinose 3.78 ± 0.32 13.0 ± 2.1 52 (est.)
Table 4.1: Average volume of spray and amount of L-arabinose applied when spraying once,
when doing the spray pattern once and when doing the spray pattern 4 times. The values for the
latter is extrapolated from the data of doing the spray pattern once. Density of 1 mg/mL was
assumed.
With this spraying pattern, a final test to assess the viability of the colony screening
method was performed with cells containing the pBAD-mCherry plasmid on three plates
containing 20 mM D-glucose. Unlike in the work of Belal et al. (2013), 3 hours of incubation
for fluorescence to appear due to induction with L-arabinose was not sufficient (Fig. 4.9A).
However, after overnight incubation, there was a sharp increase in fluorescence in all
colonies (Fig. 4.9B, C), meaning that induction of mCherry expression by spraying a
concentrated L-arabinose solution was successful. Nonetheless, there are a few remarks
to be made. First, because of the long total incubation time (overnight on 37°C before
and after spraying), the colonies develop a slightly fluorescent halo around them in the
final image (Fig. 4.9B). Second, there seems to be a difference in fluorescence between the
center and the outer region of the plate (Fig. 4.9D). More specifically, the background
fluorescence counts are consistently lower in the periphery of the plate. Two possible
explanations are that illumination with the excitation light is not fully homogeneous or
that the L-arabinose solution is applied non-homogeneously.
Figure 4.9: Induction of mCherry expression visualized by fluorescence. A. Image of the plate
at 3 h after spraying. B. Image of the plate at 22 h (overnight) after spraying. C. Data on 9
colonies of the plate shown in A and B. The two other plates have comparable behaviour. ***:
p < 0.001. D. Comparison of fluorescence between colonies on the inside (n=5) versus the
outside of the plate (n=4). Background traces of each region are shown in grey.
Transformation and cloning efforts

To continue on the above results, the next step was to transform E. coli JM109 cells with
both the pBAD-mCherry plasmid and a pET28b vector containing the mCherry-targeting
NanoBlock sensor (Supp. Fig. A.7). This way, the response of the vector could be tested
when expression of mCherry was induced on the agar plate. Despite multiple attempts at
this double transformation, each time tweaking a few steps or using fresh plates, not once
were the cells able to form colonies on the plates. This was quite surprising since both
plasmids could be transformed separately without a problem.
Initially though, another way of providing both AraC-regulated mCherry and the
NanoBlock sensor to the cells was opted for. As in the publication of Ibraheem et al.
(2011), a single-plasmid setup was to be constructed. A first attempt did this by stepwise
PCR, followed by a restriction ligation. A first PCR reaction would introduce restriction
sites at the ends of the mCherry gene to insert it in an emtpy pBAD vector. A second PCR
reaction would do the same for the AraC cassette containing the mCherry gene to ligate it
in the pRSETb vector containing the NanoBlock gene. While the PCR products and the
intermediate assembly had the right size (Fig. 4.10A, B), the final pRSETb construct did
not contain the mCherry gene according to sequencing.
A second attempt made use of a more straightforward Gibson Assembly with three
fragments (AraC gene and AraC promoter, mCherry gene and AraC terminator) and
the pRSETb vector. Again, all fragments were successfully made (Fig. 4.10C), however
sequencing of the final assembly product showed no presence of mCherry. To get a better
idea of what the problem might be, a restriction digest with BamHI was done of the
assembly product. If the assembly would be successful, there would be three fragments.
One fragment after gel electrophoresis indicates that only the pRSETb-vector is present and
if two fragments are visible, then only the AraC fragments are present. Gel electrophoresis
of this diagnostic restriction show only one, large fragment (Fig. 4.10D), meaning that only
the pRSETb vector is present, perhaps as a homodimer. After this, the single-plasmid
strategy was sidelined and the double transformation was considered and tested.
Figure 4.10: 1 % agarose gels of PCR products (A, C) and assemblies (B, D). A. PCR products
of the mCherry gene (left) for ligation in the empty pBAD vector. The mCherry gene appears to
have the expected size. B. PCR products after assembly of the fragments in A. While it is the
correct size, the final, complete plasmid did not contain mCherry according to sequencing. C.
PCR products of different Gibson assembly fragments. All fragments appear to have the right
size. D. Gibson assembly product after restriction with BaMHI. The desired plasmid has three
restriction sites for BaMHI, which would result in three fragments. The pRSETb-vector only has
one, therefore the product on the gel is (a chimaeric version of ) the pRSETb-vector.
4.3. AFFINITY MEASUREMENTS AND CONTROL EXPERIMENT 31
4.3 Affinity measurements and control experiment

As part of the larger NanoBlock project, both the mCherry and ALFA-tag nanobodies were
subjected to biolayer interferometry (BLI) to measure their affinity for their respective
blocking peptides. This was performed by the Rothbauer Lab, University of Tübingen.
BLI analyzes the interference pattern of white light reflected from two surfaces. When a
molecule binds to another molecule immobilized on the probe, the interference pattern
changes, which can be measured in real-time. Additionally, the association and dissociation
rate constants can be determined with BLI. The blocking peptide was biotinylated to bind
to the probe, the nanobody was then added. Surprisingly, the LaM4 nanobody showed no
affinity whatsoever for the blocking peptide (Fig. 4.11), even when added in large excess
(10 µM, data not shown). This means that the affinity is so low that it is unlikely that
the nanobody will bind the blocking peptide in realistic situations, which in turn heavily
questions the theoretical working mechanism of the NanoBlock biosensor. However it is
very clearly shown that the sensor does respond to the presence of its target. This new
finding shows that the conceptualized model of how the NanoBlock for mCherry works
(Fig. 2.1, Project Description), needs to be reconsidered. In contrast, the ALFA nanobody
was also tested with BLI and did show binding to its blocking peptide (Supp. Fig. A.3).
Figure 4.11: Affinity of the LaM4 nanobody (320 nM) for the blocking peptide of the mCherry
NanoBlock measured by BLI. First red line: addition of LaM4 nanobody, second red line: start of
dissociation of LaM4. Data courtesy of Ulrich Rothbauer, University of Tübingen.
To verify this finding in the context of the NanoBlock sensors, a control experiment
was conducted to determine whether the identity of the blocking peptide actually matters.
Both ALFA-tag- and mCherry-targeting NanoBlock variants were made and purified by
Silke Denis where the blocking peptide was exchanged with a glycine linker sequence (GGS
repeats). With this aspecific blocking peptide, the sensor is expected to be constantly in
the open state, because the blocking peptide will not bind the nanobody. This corresponds
with the same fluorescence intensity as if the sensor were saturated with target. Titrations
were done with these purified variants (Fig. 4.12), where it is clear that the ALFA-tag
sensor shows exactly the postulated behaviour. The mCherry-sensor on the other hand, still
decreases in fluorescence upon target addition, although it has the expected fluorescence
intensity without target present. This affirms that binding of the LaM4 nanobody to the
blocking peptide does not play a role in the sensor’s mode of action.
Figure 4.12: Titrations with different NanoBlock sensors (n=3 each). While the ALFA-tag
sensor behaves as expected, the mCherry sensor with GGS blocking peptide (GS-Pep) still shows a
decrease in fluorescence upon target addition, although it starts at the same baseline as ALFA-tag
sensor with GS blocking peptide.
Chapter 5
Discussion
5.1 Improved lysate screen increases throughput

In order to increase the response, i.e. the difference in fluorescence between the states
with and without target, of the mCherry-targeting NanoBlock, the blocking peptide
was modified. Instead of opting for a targeted mutation, four of the seven amino acids
in the blocking peptide were randomised. In the first lysate screening iteration, only
twelve mutants were screened. From these, the two most promising ones were further
characterized. They were selected based on their high absolute fluorescence in absence of
target dark mCherry and large response, i.e. a decrease in fluorescence, to the addition
of the same target. However when comparing purified proteins of the two mutants to
the original template, they performed highly similar. With this it became apparent that
screening only twelve colonies in a library with more than 105 different possibilities has a
low chance of yielding a desirable variant.
By growing picked colonies in smaller volumes in a compact deep-well 96-well plate,
the amount of colonies in a library that can be screened simultaneously in the same time
span as the first iteration, is thoroughly increased. In the presented data only 42 colonies
were screened, however this was caused by a lack of colonies in the library itself, rather
than a practical limit in handling capacity. While the increased throughput is positive, a
screening method in lysate appeared to have a fundamental flaw to work with a random
mutagenesis library. Specifically, the varying and unknown quantity of protein in each
lysate makes it difficult to compare different mutants without drawing wrong conclusions.
Absolute fluorescence counts cannot be compared to each other for this reason. Responses
to target addition can also be exaggerated or understated if the biosensor concentration is
respectively high or low. A mutant that shows a large change in fluorescence in lysate can
suddenly be a worse responder than the starting variant when purified. The variability
of the lysate stretches so far that even inverted responses were observed (see Results Fig.
4.6A). Taken together, the lysate screening method was not found suitable for selecting
improved mutants in a random library.
Compared to other studies, it seems that the value in lysate screens lies not in the
initial identification of promising mutants in a random mutagenesis library. For example,
Zhang et al. (2020) use a lysate screen after an initial, more high-throughput screening
step to characterize the most promising ones (369 mutants) in vitro. Dippel et al. (2018)
on the other hand, performed a lysate screen of biosensor mutants containing 92 different
phylogenetic variants of a certain component, which more resembles a targeted mutagenesis
33
34 CHAPTER 5. DISCUSSION
library as opposed to a random one. Nevertheless, in both studies, the researchers were
able to find mutants with much better responses (1.5-fold to 28-fold increase), something
that was not achieved here. Interestingly, both studies also reported inverse responses in
the lysate screen. Finally, to counteract the problem of varying protein concentration, the
total protein concentration can be determined and lysates can be diluted to an equal level
as was done by Meister and Joshi (2013).
5.2 Colony screening is promising, but requires addi-

tional work
The testing of the colony screening unfortunately could not be applied to the actual
mCherry-targeting NanoBlock biosensor. In the results, it was explained that cloning
both the biosensor and mCherry in one plasmid failed and that double transformation
of both genes in different plasmids was not successful. Due to a lack of time, the latter
issue could not be investigated further. One concern that was raised, is the compatibility
of both plasmids’ origin of replication (ori). Briefly, when the copy number of a plasmid
increases inside the cell, more antisense RNA species encoded on the plasmid are created,
which inhibit the replication machinery. These antisense RNA’s or iterons are specific for
each ori. If two plasmids that have identical ori’s are transformed together, they both
will generate the same iterons, causing a lower number of each plasmid than intended. In
other words, the cell cannot distinguish between both plasmids and thinks that there are
already many copies. This leads to the loss of both plasmids over generations (Novick,
1987). Comparing the plasmid maps of both the pET28b vector1 , containing the biosensor
and the pBAD vector2 , containing mCherry, the plasmids indeed seem to share the same
pBR322 ori. The lack of colonies after the double transformation is thus probably caused
by the plasmids being incompatible with each other. If the double transformation is to
be continued, the biosensor must be cloned in another plasmid with a different ori. For
example, the pACYC184 vector3 contains the p15A ori, which should be compatible with
the pBR322 ori from the pBAD vector. Additionally, it contains the chloramphenicol
resistance gene which is also different from the pBAD-mCherry plasmid that contains the
ampicillin resistance gene.
While the exploration of the colony screening method is not complete, the first results
are nonetheless promising to continue testing this method. Expression of mCherry was
both successfully suppressed with D-glucose in the agar and induced by spraying with
a concentrated L-arabinose solution. The extent of the induction also seems consistent
enough to compare different colonies, at least in the center of the plate. The heterogeneity
of fluorescence between the center and the periphery of the plate impedes judging the
library by their absolute fluorescence. This can be caused by multiple factors. A simple
explanation could be that this heterogeneity already occurs when pouring the liquid agar
into the petri dish. A too high temperature of the agar can cause it to form a concave
surface while solidifying. This already leads to a difference in background fluorescence.
Additionally, it can result in smaller colonies and reduced L-arabinose availability after
spraying towards the edge of the plate.
1
https://www.addgene.org/vector-database/2566/, accessed 2022-06-07
2
https://www.addgene.org/browse/sequence/138526/, accessed 2022-06-07
3
https://www.addgene.org/vector-database/1679/, accessed 2022-06-07
5.2. COLONY SCREENING IS PROMISING, BUT REQUIRES ADDITIONAL WORK35
In the experiments from the results shown in Figure 4.9 (Results), the difference in
fluorescence of the colonies could also be caused by the non-uniform application of the
L-arabinose solution. The spraying pattern involves many repeated sprays (20 total) in
different orientations of the plate, and in each set of five sprays (top to bottom), no area
is in theory sprayed more than once. While there will always be some human error and
variability of the spray tool, the spray pattern minimizes this variance. The non-uniform
application of L-arabinose also does not influence the background fluorescence.
Another possible cause is the imaging hardware, most prominently the lamp. The
uniformity of the excitation light across the whole illuminated surface is crucial and slight
deviations can contribute to the problem at hand. The uniformity of the excitation light
also depends on the age of the lamp, which was at the time of the last measurement 746
hours. While this is not yet problematic, it certainly will not perform as when it was
brand new. According to the specification sheet from the manufacturer4 , the lamp retains
around 65 % of its original intensity after this time. The camera can also contribute to a
perceived heterogeneity, for example when some pixels become less sensitive over time.
However, the decrease in sensitivity of a pixel is not something that depends on its position
and is therefore not likely to contribute to the problem at hand.
Luckily, several solutions can circumvent the regional fluorescence diversity. For example,
a simple background subtraction - with different background counts at the periphery and
the center - already brings the fluorescence counts to similar levels. Additionally, in
the final model where both the inducible mCherry gene and the biosensor library are
transformed together, the fluorescence from mCherry can be used to correct for the regional
difference in fluorescence. While mCherry fluorescence was initially avoided by using dark
mCherry for concerns of resonance energy transfer occurring with cpEGFP, it can now be
advantageous to have. Another, more crude solution is to subtract the images before and
after and select mutants based on the response alone.
The current colony screening method also has room left for optimization, especially
during the data processing steps. Now, the fluorescence of each colony was manually
extracted one by one. While one of the original advantages of the colony screening over the
lysate screening method was that colony picking is obsolete, this process now comes back
anyway, albeit virtually. When there are hundreds of colonies on a single plate and the
constructed library has a theoretical maximum size of 105 different mutants, this quickly
becomes extremely tedious. Luckily, because the colony picking happens in silico, there is
now potential to speed up this process. The process of extracting the fluorescence counts
of each colony can be automated by writing a specific program for it, as was done for
example by Litzlbauer et al. (2015). This publication also links the code for the program
they used5 . Briefly, after taking an image, the program first creates a mask to remove
data points from outside of the plate. Next, a new mask is created to only retain pixels
with an intensity three times greater than the standard deviation of the pixel intensity.
This retains only fluorescent colonies. After some cleaning up of the image, the colonies
are labeled and their intensity is saved. This way, the position of the colonies are also
remembered. Additionally, the dataset is saved and plots are generated automatically.
After all conditions have been imaged, the best responders are returned both in plots and
in an image to make colony picking easier. While they use different software to analyze
4
https://www.gmp.ch/htmlarea/pdf/asahi_pdf/max302techinfo.pdf, accessed 2022-05-30.
5
https://github.com/GriesbeckLab/ColonySelection, accessed 2022-05-30
imaging data than the lab for Nanobiology (Python vs. Igor Pro), it serves as a good
example. There is also plenty of expertise in the lab of prof. Dedecker to create such a
program in house.
5.3 Is the mCherry-targeting NanoBlock worth it?

Already from the first results of this thesis, some findings cast doubts about the fundamental
workings of the NanoBlock sensor. For example, the two mutants from the first lysate
screening, Pep3.2 and Pep3.6, are both rather different from the original blocking peptide
in terms of hydrophobicity, size and charges. Yet, their supposed interaction with the
LaM4 nanobody is near identical according to the sensor’s response to dark mCherry.
This is somewhat surprising since nanobodies are expected to be highly specific in their
interactions and small changes in the epitope usually gives rise to a different affinity.
Then in the second, increased throughput lysate screen of the library, all responses are
relatively similar and none are better than the original blocking peptide. On top of that,
some variants in the library showed an inverse response. Although it is unclear if this is
a consequence of working in lysate or actually due to the sensor, it still challenges the
postulated working principle of the sensor.
Eventually, the results from the biolayer interferometry (BLI) experiment became
available, which questioned the feasibility of the mCherry-targeting NanoBlock biosensor
even more. These results showed that the LaM4 nanobody does not bind to the blocking
peptide, even in great excess of 10 µM. This means that it has no or very low affinity for the
peptide. As such, the sensor cannot work as intended. The additional control experiment
with the aspecific blocking peptide further defines this problem, since the construct with
this blocking peptide still responds to the addition of mCherry. This indicates that the
identity of the amino acids in the peptide does not matter, but that there merely needs
to be something to be displaced. There remain thus two questions: (1) why does the
nanobody not bind the blocking peptide and (2) why does the sensor still respond to the
target, given that the presumed intramolecular interaction does not take place?
For the first question, the answer may simply be that the peptide does not contain
enough of the original epitope. As described by Wang et al. (2021), the nanobody interacts
with many more residues on the bottom of the β-barrel of mCherry. The seven amino acids
that make up the current blocking peptide may just be insufficient. A comparison with the
ALFA-tag-targeting NanoBlock sensor can give additional insight. Its blocking peptide is
based on the full epitope and is therefore longer. This is of course more straightforward
for the ALFA-tag since its epitope is just a single α-helix as opposed to a combination
of different amino acids in different parts of a peptide chain that only share a surface.
Nevertheless, the blocking peptide in the mCherry-targeting sensor could end up showing
some affinity to the LaM4 nanobody if it is elongated with relevant residues. Since the
goal is to have a lower affinity than the original epitope anyway, this is not an impossible
task.
To address the second question, the sterical interactions between the sensor and
mCherry need to be investigated. Theoretically, when the blocking peptide does not bind
the nanobody, the latter part should be accessible to bind whatever is in the solvent
without undergoing any further conformational changes. No conformational changes
also mean no change in fluorescence, which should already be at a low level because of
5.3. IS THE MCHERRY-TARGETING NANOBLOCK WORTH IT? 37
the “open” conformation. This is exactly what happens in the ALFA-tag sensor with
the aspecific blocking peptide (see Results Fig. 4.12): the nanobody is free to bind the
ALFA-tag in solution without any additional movement, visualized by a constant, low
fluorescence level of cpEGFP. The distinction with the mCherry-targeting sensor and why
it still loses more fluorescence as it binds the target, probably has to do with the target
itself. More specifically, the size of the target most likely plays a role. In comparison to
the ALFA-tag, mCherry is very large. It is therefore not unthinkable that even in the
“open” conformation of the sensor, the nanobody cannot reach the target without opening
even more. In other words, the sensor would be in a partially open state without mCherry
and a fully open state with mCherry bound to the LaM4 nanobody. This would explain
the decrease in fluorescence in Fig. 4.12 as well as why the ALFA-tag-targeting sensor
does not show this behaviour. The ALFA-tag is small and can therefore probably still
bind to the nanobody in the “partially open” state of the sensor without inducing any
further conformational changes (Fig. 5.1). This can be verified by doing a titration of
the ALFA-tag-targeting sensor with a larger protein carrying the ALFA-tag, for example
ALFA-tagged dark mCherry. If the sensor then behaves similar to the mCherry-targeting
sensor in Fig. 4.12, it becomes clear that the size of the target can influence the response
of the sensor. This is an important finding, because it would mean that larger targets
induce a greater change in fluorescence. This size dependency of the NanoBlock sensor is
crucial to keep in mind throughout its further development.
Figure 5.1: Proposed mechanism for difference in fluorescence of mCherry-targeting and ALFA-
tag-targeting NanoBlock biosensor when target is present. Top: dark mCherry is large, which leads
to the “open” state of the NanoBlock biosensor. Bottom: the ALFA-tag is small, only leading to
a small conformational change or the “partially open” state in the NanoBlock biosensor.
Is it now worthwhile to spend more time and effort to further develop the mCherry-
targeting NanoBlock biosensor? The initial optimization efforts did not markedly improve
its response and even in a slightly larger library, no improvement could be found. Then the
results from the BLI experiment came in, which were a crucial development that showed
that the envisioned working principle was not possible with the current structure of the
biosensor. With the subsequent control experiments, imperative insights were obtained
that can benefit the development of the other NanoBlock constructs, as well as possible
adaptations to get the mCherry-targeting NanoBlock to work as intended. However the
next question is then, what would be gained by doing so? The objective of the NanoBlock
project is to offer a universal biosensor architecture that can be readily deployed for
any possible intracellular target. To start this journey, the mCherry-targeting construct
has proven its worth for its ease-of-use and well-characterized components. However,
keeping in mind the end goal of the project as well as the obtained knowledge about its
actual workings, perhaps it is time for the overall project to move away from this design
and focus more on the one that is more universal, innovative and above all, works as
intended. Concretely, the ALFA-tag-targeting NanoBlock fits these criteria better and
while the GCaMP-based design works fine for now, the SplitFAST-based design offers
more novelty. While new does not simply imply better, the scientific community can
always benefit from innovative designs to potentially build on themselves and broaden
the range of possible scaffolds. Therefore, it seems more worthwhile to not continue
development of the mCherry-targeting, GCaMP-based NanoBlock biosensor in favor of
the other architectures.
Chapter 6
Conclusion and future perspectives
In this thesis, the optimization of a novel type of architecture for biosensors was explored.
The biosensor design is called NanoBlock and contains a nanobody for its sensing domain
and a blocking peptide able to bind it in absence of the biosensor target. A circularly
permuted eGFP acts as the fluorescent reporter domain. The sensor that was worked with,
contains the LaM4 nanobody which targets the red fluorescent protein mCherry. The
goal was to change the affinity of the blocking peptide for the nanobody by introducing
mutations in the blocking peptide. By doing so, an increase of the change in fluorescence
upon target addition, i.e. the response can be achieved and the proposed model can be
verified. This would be carried out by random PCR mutagenesis of four of the seven
amino acids of the blocking peptide. To assess the mutagenesis library, a suitable screening
method had to be used. First, a simple lysate screen was performed where 12 mutants
were evaluated. Two of these were further purified and characterized. In an attempt to
increase the amount of mutants that can be screened simultaneously, two options were
tried out and evaluated. An increased throughput lysate screen, in which colonies are
grown in deep-well 96-well plates, was able to screen more colonies, however it yielded no
improved NanoBlock sensor. It was also concluded that judging solely in a lysate screen is
not representative since the protein concentration in each lysate can vary.
The second screening method that was tried out screens single colonies of an on-
plate library. To measure fluorescence before and after target addition, the biosensor
and mCherry need to be transformed together, with the transcription of the mCherry
gene controlled by the AraC promoter. The plates where the colonies are grown on
contain D-glucose, inhibiting transcription of mCherry and transcription is activated by
spraying the plates with a concentrated L-arabinose solution. Introducing mCherry by
providing L-arabinose in a spray proved to work well. However, due to several cloning
and transformation setbacks, the colony screening method could not be applied to the
NanoBlock blocking peptide library.
It was found that the fluorescence of colonies after induction of mCherry was different
for colonies in the center of the plate versus colonies at the periphery of the plate. Several
solutions were suggested to counteract this problem. Taken together, the colony screening
method has proven to be the most promising and can be implemented in the biosensor
optimization workflow, given that standard cloning experiments are successful.
Finally, control experiments were done to assess the functioning of the mCherry-targeting
NanoBlock. The motivation for this were the results from the biolayer interferometry
(BLI), in which was shown that the LaM4 nanobody has next to no affinity for the Pep3
39
40 CHAPTER 6. CONCLUSION AND FUTURE PERSPECTIVES
blocking peptide. While this explained why mutating the blocking peptide has no effect
on the titration curves, it is first and foremost confusing how the sensor could work all
together. It was reasoned that the size of the target might help in displacing the blocking
peptide even when it is not actually bound to the nanobody. Sterically, it can be thought
of as a “partially open” configuration without mCherry and an “open” configuration with
mCherry (Fig. 6.1). While there are still posssible experiments to improve the functioning
of the mCherry-targeting NanoBlock sensor, it was concluded that there is more to be
gained by focusing on the ALFA-tag-targeting design because it better fits the goal of the
project in terms of innovation, universality and because it seems to work as intended.
Figure 6.1: Adapted working mechanism of the GCaMP-based, mCherry-targeting NanoBlock

sensor, based on the observations in Results section 4.3. Without (dark) mCherry present, the
cpEGFP is in a “partially open” state. When mCherry binds LaM4, the blocking peptide is
further displaced due to the size of mCherry, leading to the “open” state.
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Appendices
49
Appendix A
Supplementary figures
Figure A.1: SDS-PAGE of purified dark mCherry (26.7 kDa). Left: 10 µg protein, right: 5 µg.
Figure A.2: Comparison of cells containing pBAD-eGFP plasmid on plates with 20 mM

D-glucose before (A) and after (B) spraying with a concentrated L-arabinose solution. Plates
were incubated on room temperature for 3 hours after spraying when image was taken.
51
52 APPENDIX A. SUPPLEMENTARY FIGURES
Figure A.3: Affinity of the ALFA nanobody (320 nM) for different blocking peptide mutants of
the ALFA-tag NanoBlock measured by BLI. First red line: addition of ALFA nanobody. Second
red line: start of dissociation of ALFA nanobody. Data courtesy of Ulrich Rothbauer, University
of Tübingen.
Figure A.4: Plasmid map of the pRSETb vector containing the GCaMP-based mCherry-targeting
NanoBlock biosensor.
53
Figure A.5: Plasmid map of the pBAD vector containing mCherry (Addgene plasmid #54630.
Figure A.6: Plasmid map of the pRSETb vector containing the SplitFAST-based mCherry-
targeting NanoBlock biosensor.
54 APPENDIX A. SUPPLEMENTARY FIGURES
Figure A.7: Plasmid map of the pET28b vector containing the GCaMP-based mCherry-targeting
NanoBlock biosensor.
Appendix B
Risk analysis
There are several general safety guidelines that must always be followed when performing
experiments in a lab environment. A lab coat must be worn inside the lab at all times
and should not be worn outside the lab. Wearing gloves is necessary if there is a risk for
either the person performing the experiment (injury, harmful substances etc.) or for the
integrity of the experiment itself (e.g. contamination). The working environment such as
the work bench as well as the used equipment must be kept clean and desinfected before
and after use. Also washing your own hands before and especially after an experiment
is important. Biological waste and worn gloves are collected in the yellow Cordi-boxes.
Chemical waste is disposed in waste bins of the appropriate category.
Some chemicals used in the experiments require additional caution. Ethidium bromide
is used to visualize DNA in 1 % agarose gels. This chemical is harmful when ingested
or inhaled and is thought to be carcinogenic and able to cause damage on a genetic
level. Gloves should be worn when handling this product, which are to be disposed of
afterwards. When preparing an SDS-PAGE gel, some compounds call for extra precautions.
Acrylamide can cause skin irritation, is harmful when ingested, is carcinogenic and can
cause organ damage with prolonged or repeated exposure. Sodium dodecyl sulfate can
cause irritation of the skin, eyes and respiratory system, is flammable, harmful when
ingested and harmful for aquatic organisms. Ammonium persulfate can cause irritation
of the skin, eyes and respiratory system, is harmful when ingested and works oxidizing.
Tetramethylethylenediamine (TEMED) is flammable, toxic when ingested or inhaled and
can cause topical burn wounds. Therefore, making an SDS-PAGE gel must be done in
a fume hood and gloves must be worn. During protein purification, ethanol and nickel
nitrilotriacetic acid (Ni-NTA) resin are used. Both chemicals are flammable and cause
serious irritation of the skin and eyes. The GeneJET Plasmid Miniprep kit (ThermoFisher
Sci.) contains buffers with additional hazards, which can be checked on the manual of the
product.
Some experiments have a risk for physical damage. To visualize DNA in agarose gels
stained with ethidium bromide or GelGreen, the gel is placed on under UV light. Prolonged,
direct exposure can cause damage to the eyes. To measure the fluorescence on LB-agar
plates, strong excitation light sources are used. Never look directly into these light sources
to prevent eye damage. The sonicator used to break open cells prior to protein purification,
produces high-pitched sound waves. To prevent hearing damage, the sonicator is placed in
a sound-insulating cabinet. Additional ear protection can be used.
55
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FACULTY OF SCIENCES

Supervisor: Prof. Dr. Peter Dedecker Master thesis submitted in fulfillment

Academic year 2021-2022

3 Material and Methods 15

6 Conclusion and future perspectives 39

Biosensoren zijn uitstekende analytische middelen die dynamisch intracellulaire doelwitten

fluorescentie van de NanoBlock-biosensor te meten met en zonder het doelwit. Hoewel de

BLI biolayer interferometry.

FACS Fluorescence-activated Cell Sorting.

GECI genetically-encoded calcium indicators.

PCR polymerase chain reaction.

SDS-PAGE sodium dodecyl sulphate polyacrylamide gel electrophoresis.

1.1 A. Example of a genetically-encoded biosensor with a sensing domain

2.1 Cartoon representation of two different NanoBlock architectures and their

3.1 Scheme of library generation by the QuickLib method with a mutagenic

5.1 Proposed mechanism for difference in fluorescence of mCherry-targeting and

6.1 Adapted working mechanism of the GCaMP-based, mCherry-targeting

1.2 Fluorescent proteins and other fluorescent labels

1.3 Examples of biosensors

Figure 1.3: Generalized, common architectures for genetically-encoded biosensors based on

1.4 Universal biosensors?

1.5 Nanobodies: structure & function

Nb can generally be obtained through three different methods (Muyldermans, 2021a).

1.5.1 Applications of nanobodies

1.6 Developing and optimizing biosensors

1.6.2 Mutant screening

Method Cost Labour intensity Duration Throughput

Biosensors have an impressive track record of elucidating conditional, transient intracellular

designs function differently: the GCaMP-based NanoBlock sensor will be fluorescent in

Material and Methods

3.1 Buffers, media & solutions

Tris-NaCl (TN) buffer: 100 mM tris(hydroxymethyl)aminomethane (Tris) and 300 mM

3.2 Transformation in E. coli

3.3 Large scale E. coli culture

3.4 Protein purification

3.5 Titration of purified biosensors

divided by the fluorescence with the highest concentration of target r = FF−target

3.6 Library generation: directed mutagenesis

3.7 Library evaluation: Lysate screening

3.8 Library evaluation: Colony screening

3.9 Primer list

GCaMP-Pep3-library FWD gataaggatctcggatccatggtcgacCCGNNKNNKNNK

4.1 Random mutagenesis of blocking peptide

colony 1: PDYAKSF colony 2: PAECRSF colony 3: P*YSLSF

4.1.1 SplitFAST-based sensor: cloning efforts

4.2 Increased throughput mutant screening

4.2.1 Lysate screening improvement

In Fig. 4.6A, 12 of the 42 different mutants show an increase in fluorescence upon

4.2.2 Colony screening

First attempts at inducing mCherry expression by spraying a concentrated L-arabinose

spray volume (µL) 25.2 ± 2.1 86.8 ± 13.9 347 (est.)

Transformation and cloning efforts

4.3 Affinity measurements and control experiment

5.1 Improved lysate screen increases throughput

5.2 Colony screening is promising, but requires addi-

5.3 Is the mCherry-targeting NanoBlock worth it?

Conclusion and future perspectives

Figure 6.1: Adapted working mechanism of the GCaMP-based, mCherry-targeting NanoBlock

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