Difference between revisions of "Part:BBa K3328024:Design"

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===Design Notes===
 
===Design Notes===
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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.
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In the NIMPLY gate, a deactivating RNA (INPUT A) uses direct hybridization or strand displacement to abolish trigger RNA (input B) activity. So when only the correct trigger RNA is expressed, the switch can be turned on.
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These sequences were designed using NUPACK and were further screened using RNAfold and RNAstructure.
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https://2020.igem.org/wiki/images/thumb/8/87/T--OUC-China--design_lunbo_nimply.jpg/799px-T--OUC-China--design_lunbo_nimply.jpg
  
 
===Source===
 
===Source===
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===References===
 
===References===
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[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
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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., 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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Latest revision as of 12:38, 22 October 2020


triggers of NIMPLY gate (NIMPLY1)


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


Design Notes

In the NIMPLY gate, a deactivating RNA (INPUT A) uses direct hybridization or strand displacement to abolish trigger RNA (input B) activity. So when only the correct trigger RNA is expressed, the switch can be turned on.

799px-T--OUC-China--design_lunbo_nimply.jpg

Source

synthesize from company


References

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