RNA

Part:BBa_K4432207

Designed by: Paul Weimer   Group: iGEM22_Evry_Paris-Saclay   (2022-09-26)


PANTR1 Toehold Switch Trigger 07a

This part is a trigger for sequence-based detection of PANTR1 v3, a long non coding (lnc) RNA overexpressed in different types of cancer cells.

Usage and Biology

A toehold switch [1] (Figure 1) is an RNA-based device is composed of several parts which are essential for the efficient functioning of our biosensor :

- a Trigger Binding Site (TBS) which is a sequence complementary to the RNA target to be detected

- a Ribosome Binding Site (RBS) which allows the start of the translation only when the toehold switch is unfolded

- a start codon AUG which constitutes the start of the translation

- a linker which constitutes a bridge between the Start codon and our gene of interest

- a repressed gene of interest that is translated into a protein only when the hairpin is unfolded and the RBS exposed

T--Evry Paris-Saclay--PANTR1 Toehold.jpg

Figure 1. Principle of the toehold switch (inspired from iGEM Evry Paris-Saclay 2020).

The functioning comes as follows :

The binding between the RNA biomarker and the toehold switch unfolds the hairpin structure. The RBS becomes accessible now so that the translation can take place, and the initially repressed gene of interest can then be translated into a protein.


This part is a trigger for the PANTR1 Toehold Switch Sensor n°7 (BBa_K4432007) and was designed using the web tool developed by To et al. [2].

The functionality of this part was tested under controlled of the T7 promoter (BBa_K2150031) and the strong SBa_000587 synthetic terminator (BBa_K3453000) in the composite part BBa_K4432307.

This part proved not to be functional: the transcribed PANTR1 lncRNA fragment was not able to bind to the corresponding toehold switches and no readable output was generated.

Full results are available on the BBa_K4432107 and BBa_K4432307 pages in the registry.

References

[1] Green AA, Silver PA, Collins JJ, Yin P. Toehold switches: de-novo-designed regulators of gene expression. Cell (2014) 159, 925-939.

[2] To AC, Chu DH, Wang AR, Li FC, Chiu AW, Gao DY, Choi CHJ, Kong SK, Chan TF, Chan KM, Yip KY. A comprehensive web tool for toehold switch design. Bioinformatics (2018) 34, 2862-2864.

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


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Parameters
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