TRAPS, as a team of committed students from the TU Dresden, we felt the need to advance science and contribute to the work of future iGEM teams, by sharing any tools, insights, and resources we have developed throughout our project. Our condensate based RNA detection platform, TRAPS, improves the synthetic biology toolbox with a novel approach to visualize RNA in living cells without fixation or PCR, opening up opportunities for dynamic and sensitive RNA analysis.
In thewet labwe developed new biological parts and protocols (e.g. a yeast transformation protocol, our TRAPS construct and more) which can be used by future researchers and iGEM teams. Additionally we documented our experimental design and results in our digital labbook, provided by the CMCB, making our procedures accessible and reproducible.
On the dry lab site we contributed with our software "SEA-STAR" (Site-Effect Aware Sequence TArgeting & Ranking). SEA-STAR systematically analyzes the transcriptome to find unique RNA binding sites (loci), suitable for guide RNA targeting. The computational advancements will be made available for researchers and iGEM teams to use.
Beyond lab activities, TRAPS vividly brought synthetic biology, RNA detection and science in general closer to society within education and human practices. We participated in events like the UniStem Day
and the Long Night of Science, making biology and our system fun and easy to understand for all ages. Moreover we also focused on sustainability and equal opportunities, addressing both resource friendly consumption and gender representation within iGEM. Another sidequest of ours was to research why there are far less iGEM teams in east Germany, compared to the west.
Through these efforts, the TU-Dresden iGEM team not only contributes to scientific parts and tools, but also fosters awareness, inclusivity and long-term growth within scientific and iGEM communities.
Sorbitol yeast Transformation protocol
Here we present an optimized Lithium-Acetat-PEG yeast transformation protocol. By adding sorbitol solution as an osmo-protectant during the heat shock the efficiency of the transformation is highly increased. This is a newly discovered methodological improvement presented just this year (Kadouch et al., 2025) that we tested and adapted to our own transformation protocol. We compared the traditional Lithium-Acetat transformation method to this new optimized method and noticed a huge difference in transformation success. Future iGEM teams can use this yeast transformation protocol for highly optimized transformation success. This makes working with yeast much easier and faster.
Bio Parts
During the project we used a variety of biological components. We found and reused some of them from the iGEM parts registry, but some parts we found elsewhere in literature. Although the end product is specific to our project, the individual modules certainly are not. In the iGEM spirit of 'Get and Give', we compiled the modular components we used during our project and categorized the components. We hope that the parts contribute to future iGEM teams or scientists to help them in their projects!
Cas13
Cas13-related parts which should aid future teams working with Cas13 design their constructs in combination with our software (SEA-STAR).
| Part | Short Description |
|---|---|
| BBa_2549OBIE | ymCherry binding gRNA1 |
| BBa_253JOLSN | ymCherry binding gRNA2 |
| BBa_25D8GA86 | ymCherry binding gRNA3 |
| BBa_25BPE772 | ymCherry binding gRNA4 |
| BBa_25ASG5KQ | NES-dRfxCas13-Im2 expression cassette |
| BBa_25RQMQO3 | mGFP-E9-1AIE expression cassette |
| BBa_25A5HAEW | dRfxCas13d |
| BBa_2584SWLL | SNR52 Transcription terminator |
| BBa_2528DO4W | HDV ribozyme for 5' RNA cleavage |
| BBa_25CBHJTG | Tyr tRNA promoter |
| BBa_25C4HGPL | Nuclear export signal |
| BBa_25Z48D11 | Im2 anti-toxin subunit |
| BBa_25T331X0 | E9 DNAse subunit |
Pumby
The Pumby parts are useful as a genomically integratable RNA-binding modality.
| Part | Short Description |
|---|---|
| BBa_25CXVK8S | Pumby module (A) |
| BBa_25VIOJ02 | Pumby module (C) |
| BBa_2554SQ99 | Pumby module (U) |
| BBa_25SS5GOB | Pumby module (G) |
| BBa_25CDLGH2 | ymCherry targeting pumby1 protein |
| BBa_253BCAA7 | ymCherry targeting pumby2 protein |
| BBa_25BP7SZW | ymCherry targeting pumby3 protein |
| BBa_259FIVRO | ymCherry targeting pumby4 protein |
| BBa_257ES53X | mGFP_Pum2_Pum4 cassette |
| BBa_25M5Y226 | mGFP_Pum1_Pum3 cassette |
General Parts
The general parts are used for protein tags, designing efficient gene cassettes in yeast and other miscellaneous functions
| Part | Short Description |
|---|---|
| BBa_25522YEH | 12 nt Kozak Sequence |
| BBa_25QJ5R84 | GAP promoter |
| BBa_25T0EQSY | mGFP |
| BBa_25ZGDHCRG | GGSGG linker |
| BBa_25PLWI8Y | Myc-tag |
| BBa_25CQ7A16 | HA-tag |
| BBa_25TUJGWE | FLAG-tag |
| BBa_250KPV9Q | GAL-ymCherry plasmid |
| BBa_253RJ77K | 1AIE tetramerization domain |
| BBa_25ZL5PMG | 4LTB dimerization domain |
In addition to our submitted parts, we contributed documentation to the existing ymCherry part we used from the iGEM registry, BBa_E2060
Last but not least, we also created a part collection! https://registry.igem.org/collections/346b8e13-37b7-4e5b-a3ce-dc110046afd1 This showcases a concise overview of the parts we had designed to work together for the TRAPS-Cas13 system. It provides extensive collective documentation on their design, implementation, and characterization.
Software
SEA-STAR (Side Effect Aware TArget Site Ranking) is our tool that we developed to identify RNA target sites with minimal off-target interactions. It compares potential binding sites on a target RNA to a transcriptome using a Boltzmann-based affinity model, ranking them by specificity. Designed for sequence-based probes such as Cas13 sgRNAs or Pumilio RBPs, SEA-STAR helps researchers select highly specific targets and reduce unintended side effects specific for our TRAPS-system or for any RNA-targeting application.
iGEM in East Germany
Our TRAPS team has identified a striking regional imbalance in iGEM participation:
Universities in Eastern Germany are significantly underrepresented relative to those in the West,
despite comparable student enrollment and institutional numbers.
Structural barriers such as limited funding, lack of faculty support,
or insufficient awareness of iGEM within faculties are cited by respondents from institutions as primary obstacles.
To address this, we have initiated outreach efforts including a survey to understand these challenges, collabortation with nearby universities HPI Potsdam, joined regional meetup and hosted one.
Our objectives are to enhance visibility of iGEM in East Germany,
foster institutional support for student research, and build sustainable networks among emerging teams.
We are sure that by reducing financial and administrative burdens and improving access to information,
East German universities can be helped to contribute more consistently and robustly to student-led synthetic biology innovation.
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