Composite

Part:BBa_K3328025:Design

Designed by: Qi Wu   Group: iGEM20_OUC-China   (2020-10-04)
Revision as of 14:48, 20 October 2020 by Felix Felicis (Talk | contribs) (→‎References)


switch of NIMPLY gate (NIMPLY2)


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
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI.rc site found at 778


Design Notes

The NIMPLY gate consist of a Toehold switch and two input triggers that can pair together. The Toehold and the trigger’s core sequences we used originated from the previous literature. Then we added the nucleotide-binding domains at both end of the trigger’s core sequence. This sequence named as “trigger1”. The other one was designed for completely complementary pairing with trigger1 and not pairing with switch sequence. These sequences were designed using NUPACK and were further screened using RNAfold and RNAstructure.

Source

synthesize from company


References

[1] Green, A. A., Kim, J., Ma, D., Silver, P. A., Collins, J. J., & Yin, P. (2017). Complex cellular logic computation using ribocomputing devices. Nature, 548(7665), 117–121. doi:10.1038/nature23271

[2] Green, A. A., Silver, P. A., Collins, J. J., and Yin, P. (2014) toehold switches: de-novo- designed regulators of gene expression. Cell 159, 925– 939, DOI: 10.1016/j.cell.2014.10.002