RNA

Part:BBa_K4811009:Design

Designed by: Kasper Krunderup Jakobsen   Group: iGEM23_DTU-Denmark   (2023-09-25)


TMS(Mn1)


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal XhoI site found at 170
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI.rc site found at 117


Design Notes

The RNA has to fold as a tRNA would.

Multiple versions of a Mn-sensitive TMS were attempted, in this instance, the manganese binding element was inserted into the D-loop along with a small stem, which also is present in the native riboswitch.

Source

The TMS was developed by Avishek Paul during their PhD thesis, see the publication "Modular and Versatile Trans-Encoded Genetic Switches", A. Paul, E. M. Warszawik, M. Loznik, A. J. Boersma, A. Herrmann, Angew. Chem. Int. Ed. 2020, 59, 20328.

The manganese aptamer was adapted from Dambach, M., Sandoval, M., Updegrove, T. B., Anantharaman, V., Aravind, L., Waters, L. S., & Storz, G. (2015). The ubiquitous yybP-ykoY riboswitch is a manganese-responsive regulatory element. Molecular cell, 57(6), 1099–1109. https://doi.org/10.1016/j.molcel.2015.01.035

References