Difference between revisions of "Part:BBa K3328023:Design"

m (Design Notes)
m (References)
Line 16: Line 16:
  
 
===References===
 
===References===
Green, A., Kim, J., Ma, D. et al. Complex cellular logic computation using ribocomputing devices. Nature 548, 117–121 (2017). https://doi.org/10.1038/nature23271
+
[1] Kim, J., Zhou, Y., Carlson, P. D., Teichmann, M., Chaudhary, S., Simmel,F. C., … Green, A. A. (2019).  De novo-designed translation-repressing riboregulators for multi-input cellular logic. Nature Chemical Biology. doi:10.1038/s41589-019-0388-1
 +
 
 +
[2] 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

Revision as of 14:28, 20 October 2020


switch of NIMPLY gate(NIMPLY1)


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 746


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] Kim, J., Zhou, Y., Carlson, P. D., Teichmann, M., Chaudhary, S., Simmel,F. C., … Green, A. A. (2019). De novo-designed translation-repressing riboregulators for multi-input cellular logic. Nature Chemical Biology. doi:10.1038/s41589-019-0388-1

[2] 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