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

Revision as of 14:15, 20 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

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

@@ Line 7: / Line 7: @@
 ===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.
+These sequences were designed using NUPACK and were further screened using RNAfold and RNAstructure.
 ===Source===