iGEM 2021 — Team City_of_London_UK

[![](https://static.igem.org/mediawiki/2021/8/8b/HQ_page_logo.jpg)](https://2021.igem.org)

# Team:City of London UK/Notebook

RIBOTOX

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[[![

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* [Project](/Team%3ACity_of_London_UK)
  + [Description](/Team%3ACity_of_London_UK/Description)
  + [Design](/Team%3ACity_of_London_UK/Design)
  + [Parts](/Team%3ACity_of_London_UK/Parts)
  + [Engineering](/Team%3ACity_of_London_UK/Engineering)
  + [Contribution](/Team%3ACity_of_London_UK/Contribution)
  + [Implementation](/Team%3ACity_of_London_UK/Implementation)
  + [Proof of Concept](/Team%3ACity_of_London_UK/Proof_Of_Concept)
  + [Results](/Team%3ACity_of_London_UK/Results)
* [Labwork](/Team%3ACity_of_London_UK/Notebook)
  + [Measurement & Results](/Team%3ACity_of_London_UK/Measurement)
  + [Experiments](/Team%3ACity_of_London_UK/Experiments)
  + [Safety](/Team%3ACity_of_London_UK/Safety)
  + [Notebook](/Team%3ACity_of_London_UK/Notebook)
* [Human Practices](/Team%3ACity_of_London_UK/Human_Practices)
  + [Silver HP](/Team%3ACity_of_London_UK/Human_Practices)
  + [Integrated HP](/Team%3ACity_of_London_UK/Human_Practices)
  + [Communication](/Team%3ACity_of_London_UK/Communication)
  + [Collaborations](/Team%3ACity_of_London_UK/Collaborations)
* [Modelling](/Team%3ACity_of_London_UK/Model)
  + [Mass Action Model](/Team%3ACity_of_London_UK/Model#MAK)
  + [NUPACK model](/Team%3ACity_of_London_UK/Model#NUPACK)
  + [Cost model](/Team%3ACity_of_London_UK/Model#Cost_model)
* [Software](/Team%3ACity_of_London_UK/Software)
  + [ToeholdTools](/Team%3ACity_of_London_UK/Software)
* [Hardware](/Team%3ACity_of_London_UK/Hardware)
  + [Overview](/Team%3ACity_of_London_UK/Hardware)
  + [Luminometer](/Team%3ACity_of_London_UK/Hardware#Luminometer)
  + [Design](/Team%3ACity_of_London_UK/Hardware#Design)
  + [Detection](/Team%3ACity_of_London_UK/Hardware#Detection)
  + [miRNA](/Team%3ACity_of_London_UK/Hardware#miRNA)
* [People](/Team%3ACity_of_London_UK/Team)
  + [Attributions](/Team%3ACity_of_London_UK/Attributions)
  + [Team](/Team%3ACity_of_London_UK/Team)

* [Project](/Team%3ACity_of_London_UK)
  + [Description](/Team%3ACity_of_London_UK/Description)
  + [Design](/Team%3ACity_of_London_UK/Design)
  + [Parts](/Team%3ACity_of_London_UK/Parts)
  + [Engineering](/Team%3ACity_of_London_UK/Engineering)
  + [Contribution](/Team%3ACity_of_London_UK/Contribution)
  + [Implementation](/Team%3ACity_of_London_UK/Implementation)
  + [Proof of Concept](/Team%3ACity_of_London_UK/Proof_Of_Concept)
  + [Results](/Team%3ACity_of_London_UK/Results)
* [Labwork](/Team%3ACity_of_London_UK/Notebook)
  + [Measurement & Results](/Team%3ACity_of_London_UK/Measurement)
  + [Experiments](/Team%3ACity_of_London_UK/Experiments)
  + [Safety](/Team%3ACity_of_London_UK/Safety)
  + [Notebook](/Team%3ACity_of_London_UK/Notebook)
* [Human Practices](/Team%3ACity_of_London_UK/Human_Practices)
  + [Silver HP](/Team%3ACity_of_London_UK/Human_Practices)
  + [Integrated HP](/Team%3ACity_of_London_UK/Human_Practices)
  + [Communication](/Team%3ACity_of_London_UK/Communication)
  + [Collaborations](/Team%3ACity_of_London_UK/Collaborations)
* [Modelling](/Team%3ACity_of_London_UK/Model)
  + [Mass Action Model](/Team%3ACity_of_London_UK/Model#MAK)
  + [NUPACK model](/Team%3ACity_of_London_UK/Model#NUPACK)
  + [Cost model](/Team%3ACity_of_London_UK/Model#Cost_model)
* [Software](/Team%3ACity_of_London_UK/Software)
  + [ToeholdTools](/Team%3ACity_of_London_UK/Software)
* [Hardware](/Team%3ACity_of_London_UK/Hardware)
  + [Overview](/Team%3ACity_of_London_UK/Hardware)
  + [Luminometer](/Team%3ACity_of_London_UK/Hardware#Luminometer)
  + [Design](/Team%3ACity_of_London_UK/Hardware#Design)
  + [Detection](/Team%3ACity_of_London_UK/Hardware#Detection)
  + [miRNA](/Team%3ACity_of_London_UK/Hardware#miRNA)
* [People](/Team%3ACity_of_London_UK/Team)
  + [Attributions](/Team%3ACity_of_London_UK/Attributions)
  + [Team](/Team%3ACity_of_London_UK/Team)

Notebook

# Notebook

Here is our unedited, downloaded lab notebook, detailing what happened and when in our limited time in the wet lab!

[![](https://static.igem.org/mediawiki/2021/8/8b/HQ_page_logo.jpg)](https://2021.igem.org)

# Team:City of London UK/Engineering

RIBOTOX

[

Your browser does not support the video tag. :(
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[[![

](https://static.igem.org/mediawiki/2021/6/6b/T--City_of_London_UK--white.png)](https://static.igem.org/mediawiki/2021/6/64/T--City_of_London_UK--Logo_enter_animation.mp4)](/Team%3ACity_of_London_UK)

* [Project](/Team%3ACity_of_London_UK)
  + [Description](/Team%3ACity_of_London_UK/Description)
  + [Design](/Team%3ACity_of_London_UK/Design)
  + [Parts](/Team%3ACity_of_London_UK/Parts)
  + [Engineering](/Team%3ACity_of_London_UK/Engineering)
  + [Contribution](/Team%3ACity_of_London_UK/Contribution)
  + [Implementation](/Team%3ACity_of_London_UK/Implementation)
  + [Proof of Concept](/Team%3ACity_of_London_UK/Proof_Of_Concept)
  + [Results](/Team%3ACity_of_London_UK/Results)
* [Labwork](/Team%3ACity_of_London_UK/Notebook)
  + [Measurement & Results](/Team%3ACity_of_London_UK/Measurement)
  + [Experiments](/Team%3ACity_of_London_UK/Experiments)
  + [Safety](/Team%3ACity_of_London_UK/Safety)
  + [Notebook](/Team%3ACity_of_London_UK/Notebook)
* [Human Practices](/Team%3ACity_of_London_UK/Human_Practices)
  + [Silver HP](/Team%3ACity_of_London_UK/Human_Practices)
  + [Integrated HP](/Team%3ACity_of_London_UK/Human_Practices)
  + [Communication](/Team%3ACity_of_London_UK/Communication)
  + [Collaborations](/Team%3ACity_of_London_UK/Collaborations)
* [Modelling](/Team%3ACity_of_London_UK/Model)
  + [Mass Action Model](/Team%3ACity_of_London_UK/Model#MAK)
  + [NUPACK model](/Team%3ACity_of_London_UK/Model#NUPACK)
  + [Cost model](/Team%3ACity_of_London_UK/Model#Cost_model)
* [Software](/Team%3ACity_of_London_UK/Software)
  + [ToeholdTools](/Team%3ACity_of_London_UK/Software)
* [Hardware](/Team%3ACity_of_London_UK/Hardware)
  + [Overview](/Team%3ACity_of_London_UK/Hardware)
  + [Luminometer](/Team%3ACity_of_London_UK/Hardware#Luminometer)
  + [Design](/Team%3ACity_of_London_UK/Hardware#Design)
  + [Detection](/Team%3ACity_of_London_UK/Hardware#Detection)
  + [miRNA](/Team%3ACity_of_London_UK/Hardware#miRNA)
* [People](/Team%3ACity_of_London_UK/Team)
  + [Attributions](/Team%3ACity_of_London_UK/Attributions)
  + [Team](/Team%3ACity_of_London_UK/Team)

* [Project](/Team%3ACity_of_London_UK)
  + [Description](/Team%3ACity_of_London_UK/Description)
  + [Design](/Team%3ACity_of_London_UK/Design)
  + [Parts](/Team%3ACity_of_London_UK/Parts)
  + [Engineering](/Team%3ACity_of_London_UK/Engineering)
  + [Contribution](/Team%3ACity_of_London_UK/Contribution)
  + [Implementation](/Team%3ACity_of_London_UK/Implementation)
  + [Proof of Concept](/Team%3ACity_of_London_UK/Proof_Of_Concept)
  + [Results](/Team%3ACity_of_London_UK/Results)
* [Labwork](/Team%3ACity_of_London_UK/Notebook)
  + [Measurement & Results](/Team%3ACity_of_London_UK/Measurement)
  + [Experiments](/Team%3ACity_of_London_UK/Experiments)
  + [Safety](/Team%3ACity_of_London_UK/Safety)
  + [Notebook](/Team%3ACity_of_London_UK/Notebook)
* [Human Practices](/Team%3ACity_of_London_UK/Human_Practices)
  + [Silver HP](/Team%3ACity_of_London_UK/Human_Practices)
  + [Integrated HP](/Team%3ACity_of_London_UK/Human_Practices)
  + [Communication](/Team%3ACity_of_London_UK/Communication)
  + [Collaborations](/Team%3ACity_of_London_UK/Collaborations)
* [Modelling](/Team%3ACity_of_London_UK/Model)
  + [Mass Action Model](/Team%3ACity_of_London_UK/Model#MAK)
  + [NUPACK model](/Team%3ACity_of_London_UK/Model#NUPACK)
  + [Cost model](/Team%3ACity_of_London_UK/Model#Cost_model)
* [Software](/Team%3ACity_of_London_UK/Software)
  + [ToeholdTools](/Team%3ACity_of_London_UK/Software)
* [Hardware](/Team%3ACity_of_London_UK/Hardware)
  + [Overview](/Team%3ACity_of_London_UK/Hardware)
  + [Luminometer](/Team%3ACity_of_London_UK/Hardware#Luminometer)
  + [Design](/Team%3ACity_of_London_UK/Hardware#Design)
  + [Detection](/Team%3ACity_of_London_UK/Hardware#Detection)
  + [miRNA](/Team%3ACity_of_London_UK/Hardware#miRNA)
* [People](/Team%3ACity_of_London_UK/Team)
  + [Attributions](/Team%3ACity_of_London_UK/Attributions)
  + [Team](/Team%3ACity_of_London_UK/Team)

Engineering

# Engineering

In order to create a working test for Preeclampsia, we designed multiple generations of Toehold switches
and an
isothermal amplification strategy in addition to hardware including a luminometer, magnetic nanoparticle
extraction
strategy and reaction chamber. However, this section will focus on the engineering success of our
toehold switch and
amplification probe design.

While we had access to labs at some points during our project, this came late on in our project, so much
of our testing
was done in Silico. On this page, we will outline two design cycles, the first using in Silico testing
using our
software tool, and the second using wet lab characterisation.

## The First Cycle

Despite its name, this first cycle starts with our second generation (gen2) toehold switches, after we
tested our gen1
switches using Nupack and then, after talking to Dr Alex Green and Dr Bae Wooli, a researchers in the
field, we decided
to create simpler, more specific ‘gen2’ switches. You can read more about this in our [Design page](https://2021.igem.org/Team%3ACity_of_London_UK/Design).

#### Goal

![Relative Expression of miRNAs](https://static.igem.org/mediawiki/2021/thumb/1/10/T--City_of_London_UK--Main_MicroRNA_Biomarkers_graph.png/800px-T--City_of_London_UK--Main_MicroRNA_Biomarkers_graph.png)

Our research identified two miRNAs upregulated roughly 4-fold in patients with Preeclampsia at 10 weeks -
miR-210-3p and
miR-517-5p. So, the aim of the switches was to be able to discriminate between this percentage
difference in
concentration.

## Design

![Diagram of how a toehold switch works](https://static.igem.org/mediawiki/2021/c/c6/T--City_of_London_UK--How_A_Toehold_Switch_Works.png)

Our gen2 toehold switches work such that when few microRNAs are present, the ribosome binding site of an
mRNA coding for
luciferase is folded up, so the ribosome cannot unzip the long stem and move down the strand to the
start codon to
initiate translation.

However, when a microRNA binds to the trigger site, the switch unfolds, decreasing the length of the
stem, and exposing
the start codon, so translation of leuciferase - a reporter protein - can begin.

We used the software package NUPACK to help design our gen2 switches in-silico. NUPACK is able to predict
the
interactions of the secondary structure of one or more nucleic acid strands. And so, we used the
programme to model and
perfect our switches.

At first, we designed our switches base by base, checking the minimum free energy (MFE) structure, using
NUPACK, to
ensure that our switch had a strong hairpin structure in the ‘off’ state and was properly unfolded in
its ‘on’ state.

We were successful in designing multiple switches that had MFE structures fulfilling this criteria, but
multiple bases
had low probabilities of being in their respective positions.

Therefore, we used the NUPACK API to generate a Python program to test a randomly generated list of
one-hundred-thousand
linker regions (which did not contain any stop or start codons) and simulated a thousand probabilistic
secondary
structure samples for each, showing which switch had the highest probability of unfolding in the
presence of our miRNA
triggers, but not in their absence.

(To read more about specific design considerations, see the [Design page](https://2021.igem.org/Team%3ACity_of_London_UK/Design)).

#### The gen2 switch for miR-517-5p

![Part BBa_K3905000, gen1 517-5p Toehold Switch](https://static.igem.org/mediawiki/2021/thumb/c/ce/T--City_of_London_UK--Toehold_Switch2.png/1200px-T--City_of_London_UK--Toehold_Switch2.png)

#### The gen2 switch for miR-210-3p

![Part BBa_K3905000, gen1 517-5p Toehold Switch](https://static.igem.org/mediawiki/2021/thumb/c/ce/T--City_of_London_UK--Toehold_Switch2.png/1200px-T--City_of_London_UK--Toehold_Switch2.png)

### Build

After this design, we ended up with two toehold switches (seen above) which we decided to characterise
using our
software tool, ToeholdTools. The building in this design cycle was for the software tool itself, rather
than the
switches, as we were testing them at first in Silico.

### Test

![Part BBa_K3905000, gen1 517-5p Toehold Switch](https://static.igem.org/mediawiki/2021/4/42/T--City_of_London_UK--Modelling_210-2p_g2.png)

![Part BBa_K3905000, gen1 517-5p Toehold Switch](https://static.igem.org/mediawiki/2021/thumb/a/ac/T--City_of_London_UK--Software_517-g1.png/800px-T--City_of_London_UK--Software_517-g1.png)

The software tool utilises Nupack’s API to test to see if the switches will unfold, or ‘activate’ in the
presence of our
target miRNA, but not in the presence of other miRNAs in the human miRNA database (which we downloaded
from miRBase).
The ideal switch is one that has high activation for our target miRNAs but not for other miRNAs. We
found that both our
switches performed well in silico - with high activation and relatively high specificity for the
miR-210-3p switch, but
less specificity for the miR-517-5p.

### Learn

Based on these results, we decided we should design a protocol to characterise these switches in the lab,
to see how
they would unfold, thereby inducing translation of a luciferase CDS, emitting luminescence when
luciferin is added, in
the presence of our target miRNAs at a concentration, and a quarter of that concentration (to mimic the
ratio in human
serum between those with and without the condition) as well as in the presence of similar miRNAs, or
‘homologs’, that
our software tool had identified as being able to somewhat unfold our switch.

Furthermore, this made us realise that in order to create a specific test, it would be better to be able
to detect
multiple miRNAs with the same switch, such that even if another miRNA homolog was over-expressed in the
serum of a
patient without the condition, it wouldn’t give a positive test unless all target miRNAs are expressed.
To show a proof
of concept for this idea, we got to work designing a novel AND-gate switch. This fed into our next
design cycle.

## The Second Cycle

### Design

Our third generation (gen3) toehold switch uses AND-gate logic to detect the presence of our two target
miRNAs in one
switch.

This switch employs an anti-miRNA with three regions; two hybridization domains that are complementary to
each of our
trigger RNAs and the anti-miRNA’s own trigger site. This 29 nucleotide long strand has a 13 nucleotide
long binding site
for the miRNA 210-3p and an 11 nucleotide long binding site for miRNA 517-5p. This complex of the 3 RNA
strands is
necessary to bind to the toehold switch’s trigger binding site. We had to ensure that each of these
trigger binding
sites was >10 nucleotides on the advice of Dr Bae Wooli.

![Diagram of how a toehold switch works](https://static.igem.org/mediawiki/2021/thumb/0/03/T--City_of_London_UK--ComplexFormation.png/800px-T--City_of_London_UK--ComplexFormation.png)
![Diagram of how a toehold switch works](https://static.igem.org/mediawiki/2021/thumb/e/e3/T--City_of_London_UK--AndGateTHS.png/800px-T--City_of_London_UK--AndGateTHS.png)

For the AND gate, we were unable to use the NUPACK API as the minimum free energy structure would show
each strand
binding, independent of the position of the other strands. Therefore, we designed the anti-miRNA and the
toehold switch
base by base. To ensure that the switch would unfold, we had to ensure that the difference in MFE
structure between the
‘off’ and ‘on’ state was such that unfolding was energetically favourable when the anti-miRNA-miRNA
complex had formed.
In order to help us achieve this energetically favourable state we replaced an adequate amount of C-G
bonds with U-G
bonds to raise the free energy of the MFE structure of the OFF state.

### Build

We ordered four gBlocks from IDT. The first three contained each of our two gen2 switches and also our
gen3 switch. All
three were downstream of a T7 promoter and upstream of a luciferase coding region. The final gBlock was
for the
anti-miRNA for the gen3 switch, which was also under the control of a T7 promoter. All these were linear
DNA with 250
randomly generated base pairs upstream and downstream of the insert. This was on the advice of the
supplier of the TXTL
cell-free ktis we were using in our characterisation.

### Test

To find out more about the performance of our gen2 switches, go to our [Measurement and Results page](https://2021.igem.org/Team%3ACity_of_London_UK/Measurement).
But, as they are
not part of this design cycle, we don’t anaylse their results here.

The main purpose of testing the AND-Gate Switch was to see whether it could discriminate between a high
concentration of
one miRNA, and a low concentration of another, and a high concentration of both. This was in case a
patient had
increased levels of one miRNA and not the other, which would not be indicative of Preeclampsia. This
would also show
that our concept could potentially be scaled up, in order to create a framework for multiple miRNAs to
be tested for,
increasing the specificity of tests.

![Part BBa_K3905000, gen1 517-5p Toehold Switch](https://static.igem.org/mediawiki/2021/thumb/c/cb/T--City_of_London_UK--Graph_8.png/800px-T--City_of_London_UK--Graph_8.png)

![Part BBa_K3905000, gen1 517-5p Toehold Switch](https://static.igem.org/mediawiki/2021/thumb/d/d1/T--City_of_London_UK--Graph_7.png/800px-T--City_of_London_UK--Graph_7.png)

The graphs show how, compared to the negative control, which shows leaky expression of the toehold
switch, the
luminescence output of the sample with 9M concentration of both miRNA triggers is 92% higher.
Interestingly, the
percentage increase in luminescence of the miR-210-3p at 9M and miR-517-5p at 2.25M is twice more than
twice as high as
the miRNAs at flipped concentrations - 28% compared to 12%. This could be because the miR-210-3p binding
site is further
downstream than the miR-517-5p binding site, so miR-210-3p is able to bind and partially unfold the
switch in the
absence of miR-517-5p, increasing the rate of translation. However, as the miR-517-5p binding site is
further upstream,
it is completely bound up in hydrogen bonds, so it is not accessible to the miRNA unless it binds as the
switch is being
transcribed.

### Learn

We concluded that the gen3 toehold switches do cause a noticeable increase in translation when both
miRNAs are at a high
concentration (9M), compared to when one of both of them is at a low concentration (2.25M), which gives
strong evidence
that our AND-gate design works. However, we realised that, since the 2.25M concentrations only caused a
small amount
more translation of luciferase than the negative control (due to leaky expression), if the
concentrations in human serum
were lower than that, we would not be able to discriminate between patients with or without
preeclampsia, despite there
being a 4-fold increase in patients with the condition. Thus, we decided we needed to redesign our test
as a whole by
incorporating a method of amplifying miRNAs before adding toehold switches to the example.

### Design

We wanted to find a solution that would allow amplification to take place isothermally, in a single tube,
increasing the
accessibility of our tests, especially in countries with less access to expensive equipment such as
thermocyclers.

Further research introduced us to miRPA which could convert miRNAs into double stranded DNAs with the
miRNA encoded in
part of one strand in DNA. In order to be left with just the strand with the miRNA encoded in it, we
decided our kit
would use another method on top of this - asymmetric RPA, which works the same as RPA, but with an
excess of the forward
primer, such that an excess of the desired strand is polymerised. To learn more about our design
considerations, and the
python tool we created to help us design probes, visit the Isothermal Amplification section of our  [Design page](https://2021.igem.org/Team%3ACity_of_London_UK/Design).

[![](https://static.igem.org/mediawiki/2021/8/8b/HQ_page_logo.jpg)](https://2021.igem.org)

# Team:City of London UK/Experiments

RIBOTOX

[

Your browser does not support the video tag. :(
](https://static.igem.org/mediawiki/2021/9/98/T--City_of_London_UK--Loading_animation.mp4)

[[![

](https://static.igem.org/mediawiki/2021/6/6b/T--City_of_London_UK--white.png)](https://static.igem.org/mediawiki/2021/6/64/T--City_of_London_UK--Logo_enter_animation.mp4)](/Team%3ACity_of_London_UK)

* [Project](/Team%3ACity_of_London_UK)
  + [Description](/Team%3ACity_of_London_UK/Description)
  + [Design](/Team%3ACity_of_London_UK/Design)
  + [Parts](/Team%3ACity_of_London_UK/Parts)
  + [Engineering](/Team%3ACity_of_London_UK/Engineering)
  + [Contribution](/Team%3ACity_of_London_UK/Contribution)
  + [Implementation](/Team%3ACity_of_London_UK/Implementation)
  + [Proof of Concept](/Team%3ACity_of_London_UK/Proof_Of_Concept)
  + [Results](/Team%3ACity_of_London_UK/Results)
* [Labwork](/Team%3ACity_of_London_UK/Notebook)
  + [Measurement & Results](/Team%3ACity_of_London_UK/Measurement)
  + [Experiments](/Team%3ACity_of_London_UK/Experiments)
  + [Safety](/Team%3ACity_of_London_UK/Safety)
  + [Notebook](/Team%3ACity_of_London_UK/Notebook)
* [Human Practices](/Team%3ACity_of_London_UK/Human_Practices)
  + [Silver HP](/Team%3ACity_of_London_UK/Human_Practices)
  + [Integrated HP](/Team%3ACity_of_London_UK/Human_Practices)
  + [Communication](/Team%3ACity_of_London_UK/Communication)
  + [Collaborations](/Team%3ACity_of_London_UK/Collaborations)
* [Modelling](/Team%3ACity_of_London_UK/Model)
  + [Mass Action Model](/Team%3ACity_of_London_UK/Model#MAK)
  + [NUPACK model](/Team%3ACity_of_London_UK/Model#NUPACK)
  + [Cost model](/Team%3ACity_of_London_UK/Model#Cost_model)
* [Software](/Team%3ACity_of_London_UK/Software)
  + [ToeholdTools](/Team%3ACity_of_London_UK/Software)
* [Hardware](/Team%3ACity_of_London_UK/Hardware)
  + [Overview](/Team%3ACity_of_London_UK/Hardware)
  + [Luminometer](/Team%3ACity_of_London_UK/Hardware#Luminometer)
  + [Design](/Team%3ACity_of_London_UK/Hardware#Design)
  + [Detection](/Team%3ACity_of_London_UK/Hardware#Detection)
  + [miRNA](/Team%3ACity_of_London_UK/Hardware#miRNA)
* [People](/Team%3ACity_of_London_UK/Team)
  + [Attributions](/Team%3ACity_of_London_UK/Attributions)
  + [Team](/Team%3ACity_of_London_UK/Team)

* [Project](/Team%3ACity_of_London_UK)
  + [Description](/Team%3ACity_of_London_UK/Description)
  + [Design](/Team%3ACity_of_London_UK/Design)
  + [Parts](/Team%3ACity_of_London_UK/Parts)
  + [Engineering](/Team%3ACity_of_London_UK/Engineering)
  + [Contribution](/Team%3ACity_of_London_UK/Contribution)
  + [Implementation](/Team%3ACity_of_London_UK/Implementation)
  + [Proof of Concept](/Team%3ACity_of_London_UK/Proof_Of_Concept)
  + [Results](/Team%3ACity_of_London_UK/Results)
* [Labwork](/Team%3ACity_of_London_UK/Notebook)
  + [Measurement & Results](/Team%3ACity_of_London_UK/Measurement)
  + [Experiments](/Team%3ACity_of_London_UK/Experiments)
  + [Safety](/Team%3ACity_of_London_UK/Safety)
  + [Notebook](/Team%3ACity_of_London_UK/Notebook)
* [Human Practices](/Team%3ACity_of_London_UK/Human_Practices)
  + [Silver HP](/Team%3ACity_of_London_UK/Human_Practices)
  + [Integrated HP](/Team%3ACity_of_London_UK/Human_Practices)
  + [Communication](/Team%3ACity_of_London_UK/Communication)
  + [Collaborations](/Team%3ACity_of_London_UK/Collaborations)
* [Modelling](/Team%3ACity_of_London_UK/Model)
  + [Mass Action Model](/Team%3ACity_of_London_UK/Model#MAK)
  + [NUPACK model](/Team%3ACity_of_London_UK/Model#NUPACK)
  + [Cost model](/Team%3ACity_of_London_UK/Model#Cost_model)
* [Software](/Team%3ACity_of_London_UK/Software)
  + [ToeholdTools](/Team%3ACity_of_London_UK/Software)
* [Hardware](/Team%3ACity_of_London_UK/Hardware)
  + [Overview](/Team%3ACity_of_London_UK/Hardware)
  + [Luminometer](/Team%3ACity_of_London_UK/Hardware#Luminometer)
  + [Design](/Team%3ACity_of_London_UK/Hardware#Design)
  + [Detection](/Team%3ACity_of_London_UK/Hardware#Detection)
  + [miRNA](/Team%3ACity_of_London_UK/Hardware#miRNA)
* [People](/Team%3ACity_of_London_UK/Team)
  + [Attributions](/Team%3ACity_of_London_UK/Attributions)
  + [Team](/Team%3ACity_of_London_UK/Team)

Experiments

# Experiments

We have outlined all our experiments in a handy to print out PDF, so that iGEM teams in the future can
print off our
protocols with ease.

[![](https://static.igem.org/mediawiki/2021/8/8b/HQ_page_logo.jpg)](https://2021.igem.org)

# Team:City of London UK/Results

RIBOTOX

[

Your browser does not support the video tag. :(
](https://static.igem.org/mediawiki/2021/9/98/T--City_of_London_UK--Loading_animation.mp4)

[[![

](https://static.igem.org/mediawiki/2021/6/6b/T--City_of_London_UK--white.png)](https://static.igem.org/mediawiki/2021/6/64/T--City_of_London_UK--Logo_enter_animation.mp4)](/Team%3ACity_of_London_UK)

* [Project](/Team%3ACity_of_London_UK)
  + [Description](/Team%3ACity_of_London_UK/Description)
  + [Design](/Team%3ACity_of_London_UK/Design)
  + [Parts](/Team%3ACity_of_London_UK/Parts)
  + [Engineering](/Team%3ACity_of_London_UK/Engineering)
  + [Contribution](/Team%3ACity_of_London_UK/Contribution)
  + [Implementation](/Team%3ACity_of_London_UK/Implementation)
  + [Proof of Concept](/Team%3ACity_of_London_UK/Proof_Of_Concept)
  + [Results](/Team%3ACity_of_London_UK/Results)
* [Labwork](/Team%3ACity_of_London_UK/Notebook)
  + [Measurement & Results](/Team%3ACity_of_London_UK/Measurement)
  + [Experiments](/Team%3ACity_of_London_UK/Experiments)
  + [Safety](/Team%3ACity_of_London_UK/Safety)
  + [Notebook](/Team%3ACity_of_London_UK/Notebook)
* [Human Practices](/Team%3ACity_of_London_UK/Human_Practices)
  + [Silver HP](/Team%3ACity_of_London_UK/Human_Practices)
  + [Integrated HP](/Team%3ACity_of_London_UK/Human_Practices)
  + [Communication](/Team%3ACity_of_London_UK/Communication)
  + [Collaborations](/Team%3ACity_of_London_UK/Collaborations)
* [Modelling](/Team%3ACity_of_London_UK/Model)
  + [Mass Action Model](/Team%3ACity_of_London_UK/Model#MAK)
  + [NUPACK model](/Team%3ACity_of_London_UK/Model#NUPACK)
  + [Cost model](/Team%3ACity_of_London_UK/Model#Cost_model)
* [Software](/Team%3ACity_of_London_UK/Software)
  + [ToeholdTools](/Team%3ACity_of_London_UK/Software)
* [Hardware](/Team%3ACity_of_London_UK/Hardware)
  + [Overview](/Team%3ACity_of_London_UK/Hardware)
  + [Luminometer](/Team%3ACity_of_London_UK/Hardware#Luminometer)
  + [Design](/Team%3ACity_of_London_UK/Hardware#Design)
  + [Detection](/Team%3ACity_of_London_UK/Hardware#Detection)
  + [miRNA](/Team%3ACity_of_London_UK/Hardware#miRNA)
* [People](/Team%3ACity_of_London_UK/Team)
  + [Attributions](/Team%3ACity_of_London_UK/Attributions)
  + [Team](/Team%3ACity_of_London_UK/Team)

* [Project](/Team%3ACity_of_London_UK)
  + [Description](/Team%3ACity_of_London_UK/Description)
  + [Design](/Team%3ACity_of_London_UK/Design)
  + [Parts](/Team%3ACity_of_London_UK/Parts)
  + [Engineering](/Team%3ACity_of_London_UK/Engineering)
  + [Contribution](/Team%3ACity_of_London_UK/Contribution)
  + [Implementation](/Team%3ACity_of_London_UK/Implementation)
  + [Proof of Concept](/Team%3ACity_of_London_UK/Proof_Of_Concept)
  + [Results](/Team%3ACity_of_London_UK/Results)
* [Labwork](/Team%3ACity_of_London_UK/Notebook)
  + [Measurement & Results](/Team%3ACity_of_London_UK/Measurement)
  + [Experiments](/Team%3ACity_of_London_UK/Experiments)
  + [Safety](/Team%3ACity_of_London_UK/Safety)
  + [Notebook](/Team%3ACity_of_London_UK/Notebook)
* [Human Practices](/Team%3ACity_of_London_UK/Human_Practices)
  + [Silver HP](/Team%3ACity_of_London_UK/Human_Practices)
  + [Integrated HP](/Team%3ACity_of_London_UK/Human_Practices)
  + [Communication](/Team%3ACity_of_London_UK/Communication)
  + [Collaborations](/Team%3ACity_of_London_UK/Collaborations)
* [Modelling](/Team%3ACity_of_London_UK/Model)
  + [Mass Action Model](/Team%3ACity_of_London_UK/Model#MAK)
  + [NUPACK model](/Team%3ACity_of_London_UK/Model#NUPACK)
  + [Cost model](/Team%3ACity_of_London_UK/Model#Cost_model)
* [Software](/Team%3ACity_of_London_UK/Software)
  + [ToeholdTools](/Team%3ACity_of_London_UK/Software)
* [Hardware](/Team%3ACity_of_London_UK/Hardware)
  + [Overview](/Team%3ACity_of_London_UK/Hardware)
  + [Luminometer](/Team%3ACity_of_London_UK/Hardware#Luminometer)
  + [Design](/Team%3ACity_of_London_UK/Hardware#Design)
  + [Detection](/Team%3ACity_of_London_UK/Hardware#Detection)
  + [miRNA](/Team%3ACity_of_London_UK/Hardware#miRNA)
* [People](/Team%3ACity_of_London_UK/Team)
  + [Attributions](/Team%3ACity_of_London_UK/Attributions)
  + [Team](/Team%3ACity_of_London_UK/Team)

# Results

### Project RIBOTOX was awarded a gold medal!

### We were also nominated for Best new basic part for the High school category!

![BEST NEW BASIC PART](https://static.igem.org/mediawiki/2021/e/ea/T--City_of_London_UK--basic_part.gif)