Difference between revisions of "Part:BBa K3328026:Design"

(→‎Design Notes)
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===References===
 
===References===
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[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
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[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

Revision as of 15:03, 20 October 2020


triggers of NIMPLY gate (NIMPLY2)


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal XbaI site found at 110
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 107
    Illegal XhoI site found at 1
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal XbaI site found at 110
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal XbaI site found at 110
  • 1000
    COMPATIBLE WITH RFC[1000]


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