Team:Berlin diagnostX/Design

Design

The vision of diagnost-x

Developing a low cost, easy-to-handle diagnostic test for infection with the tapeworm Taenia solium

Transcriptome analysis of T.solium

Behind the Bioinformatics

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Basics: RNA toehold switch

Toehold switches are RNA molecules that can regulate the downstream translation (in our case of a reporter protein) depending on the presence or absence of specific trigger RNA.

They consist of:

  1. a specific single-stranded toehold sequence
  2. a ribosome-binding site (RBS)
  3. a coding sequence for the reporter protein.

The reporter protein can only be produced if the toehold domain (recognition site) of the sensor has bound to its specific trigger RNA sequence. In absence of trigger RNA, the toehold switch forms a hairpin structure that prevents the ribosome from binding to the RBS, and thereby the translation (production of the reporter protein) can’t be initiated.

However, an RNA sensor alone is not sufficient for a screening test. Naked RNA cannot produce a protein nor induce a colour change – we thus relied on cell-free expression systems, a synthetic alternative to cell culture providing both easy handling as well as a controlled micro-environment for synthetic biology.

Basics: Cell free expression system

A cell free expression system is a system allowing for the production of protein using biological machinery without the use of living cells. The in vitro protein synthesis environment is highly controllable and more stable in the face of changes in temperature, buffers or similar interfering factors.

In order to establish our diagnostic test we thus needed:

  • An RNA sensor designed to target the tapeworm
  • A cell free expression system able to produce a color change
  • T. solium specific trigger RNA
  • (for field use: a carrier system to make the cell-free expression system storable)

We thus divided the work over three subteams:

  1. In-silico RNA sensor design (Team 0)
  2. Sensor synthesis (Team 1)
  3. Sensor Screening/Cell free expression (Team 2)

Preliminary Data (Bioinformatics)

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Team 0: In-silico RNA sensor design

1. Analysing existing toehold sensors to extract basic switch design

Using recent publications on toehold switches [1, 2], a text editor (Sublime Text Editor) and the “Analysis” function of the NUPACK software, we identified the most promising basic structural units:

  • a 36-nt long recognition site of which the first 25 nucleotides are unpaired (toehold domain)
  • a 11-nt long bottom stem complementary to the toehold domain
  • a 5-nt long top stem complementary to the toehold domain
  • 12-nt long hairpin loop containing the RBS (ribosomal binding site) and connecting the bottom & top stem
  • 3-nt long bulge containing the start-codon for the translation of the reporter protein (located between the top and bottom stem)
  • 22-nt long linking sequence (consisting of a variable & an invariable domain) attaching the reporter protein sequence (LacZ) to the bottom stem thus providing an open reading frame in combination with the 11-nt long bottom stem.

2. Optimizing the switch design

We used the “Multitube-Design” function of the NUPACK software and optimized the secondary structure towards the desired “toehold structure”. In this optimization, we included not only the sequence of the core sensor/toehold switch but also the first 50 nucleotides of the reporter protein mRNA sequence.

3. Automating the switch design

o compute an optimal toehold-sensor for each 36-nt long target RNA sequence, we wrote a Python-Script. In addition to the NUPACK “Multitube-Design” function, the script incorporated a function that checks for in-frame stop codons in order to avoid premature translation arrest.

4. Selecting promising switches for screening

The python script generates almost N possible sensors for a target sequence of length N, a number far too large be entirely synthesized and screened. 
Thus, a selection step prior to in vitro testing of the sensors was introduced: We selected candidates by their normalized ensemble defect (NED). The NED is a parameter used by the NUPACK software and describes the difference between the most probable secondary structure of each sensor candidate and the desired secondary structure (classic toehold structure).

5. Optimizing switch selection

We improved selection step by adding further criteria, adapted from the original publication [1]: we considered not only the normalized ensemble defect (NED) but also the “single-strandedness” of both the toehold region and the target RNA. “Single-strandedness” describes the probabilities of finding unpaired nucleotides in a sequence of a given length. We established a scoring system rating each sensor candidate in terms of

  1. The local single-strandedness of the target mRNA at the binding site.
  2. The local single-strandedness of the toehold of the sensor
  3. The normalized ensemble defect (NED) of the sensor

The score was then used to select the most promising sensors for synthesis and screening.

Team 1: Sensor Synthesis

Zwischenüberschrift

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Zwischenüberschrift

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Team 2: Sensor Screening/Cell free expression system

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Summary

In order to develop a diagnostic tool for the tapeworm infection Taeniasis, we developed a pipeline that allowed for designing, synthesizing and testing any given sensor within 2 days.
Step 1: In silico design

  • Design of a toehold switch sensor specific to T. solium RNA
  • Generating primers necessary for switch synthesis

Step 2: DNA-Switch Synthesis

  • By using extension PCR or nested PCR, the toehold switches were synthesized
  • Reporter gene (Beta-galactosidase) and T7 promoter were added to the sensor

Step 3: Sensor Screening

  • Transcription of DNA sensor into RNA takes place in CFE system
  • Specific binding of RNA sensor to trigger RNA leads to translation of reporter gene in CFE system
  • By measuring absorption at 560 nm, color change was measured and enzymatic reaction quantified

Splitting the work into three teams enabled us to work continuously – trouble shooting in one team did not stall work in the other teams. Alongside the work on the core piece – a CFE system containing a sensitive and specific sensor – we tried to keep the ultimate goal in mind: a test usable in the field.

We thus investigated fixing the system onto cellulose membranes, making it storable, durable and easily transportable. Collaborations with partners in Berlin, Europe and India enabled us to further adapt our system to challenges of real-life application.

References

[1] Pardee, K. et al. Rapid, Low-Cost Detection of Zika Virus Using Programmable Biomolecular Components. Cell 165, 1255–1266 (2016).
[2] Green, A. A., Silver, P. A., Collins, J. J. & Yin, P. Toehold Switches: De-Novo-Designed Regulators of Gene Expression. Cell 159, 925–939 (2014)
[3] Gomez, S. et al. Genome analysis of Excretory/Secretory proteins in Taenia solium reveals their Abundance of Antigenic Regions (AAR). Sci. Rep. 5, 9683 (2015)