Difference between revisions of "Part:BBa K3328039:Design"

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===Design Notes===
 
===Design Notes===
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We combined the 3WJ switch and toehold switch to realize the IMPLY Boolean calculation. When no trigger expressed, this logic gate just likes a 3WJ switch. When trigger A expressed, the trigger will bind to the switch RNA. The binding allows for a branch migration process, exposing AUG and RBS for translation initiation. When trigger B expressed, the trigger will bind to 3WJ switch RNA. The resulting trigger–switch complex has a stable 3WJ structure that effectively sequesters the RBS and start codon within the loop and stem of the switch RNA, respectively, and strongly represses translation. When trigger A and B both expressed, the binding of trigger RNA to the toehold sequence allow the RNA polymerase binds to the former RBS and break open 3WJ stable hairpin.
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We combined the 3WJ switch and toehold switch to realize the IMPLY Boolean calculation. When no trigger is expressed, this logic gate just likes a 3WJ switch. When trigger A expressed, the trigger will bind to the switch RNA. The binding allows for a branch migration process, exposing AUG and RBS for translation initiation. When trigger B expressed, the trigger will bind to 3WJ switch RNA. The resulting trigger–switch complex has a stable 3WJ structure that effectively sequesters the RBS and the start codon within the loop and stem of the switch RNA, respectively, and strongly represses translation. When both trigger A and B are expressed, the binding of trigger RNA to the toehold sequence allows the RNA polymerase to bind to the former RBS and break open 3WJ stable hairpin.
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https://2020.igem.org/wiki/images/thumb/f/f7/T--OUC-China--design_lunbo_imply.jpg/799px-T--OUC-China--design_lunbo_imply.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,
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Green, A. A., Silver, P. A., Collins, J. J., and Yin, P. (2014) toehold switches: de-novo-
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F. C., … Green, A. A. (2019).  De novo-designed translation-repressing riboregulators for
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multi-input cellular logic. Nature Chemical Biology. doi:10.1038/s41589-019-0388-1
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[2] Green, A. A., Silver, P. A., Collins, J. J., and Yin, P. (2014) toehold switches: de-novo-
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designed regulators of gene expression. Cell 159, 925– 939, DOI: 10.1016/j.cell.2014.10.002
 
designed regulators of gene expression. Cell 159, 925– 939, DOI: 10.1016/j.cell.2014.10.002

Latest revision as of 12:03, 27 October 2020


triggerA of IMPLY gate (IMPLY1)


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
    COMPATIBLE WITH RFC[1000]


Design Notes

We combined the 3WJ switch and toehold switch to realize the IMPLY Boolean calculation. When no trigger is expressed, this logic gate just likes a 3WJ switch. When trigger A expressed, the trigger will bind to the switch RNA. The binding allows for a branch migration process, exposing AUG and RBS for translation initiation. When trigger B expressed, the trigger will bind to 3WJ switch RNA. The resulting trigger–switch complex has a stable 3WJ structure that effectively sequesters the RBS and the start codon within the loop and stem of the switch RNA, respectively, and strongly represses translation. When both trigger A and B are expressed, the binding of trigger RNA to the toehold sequence allows the RNA polymerase to bind to the former RBS and break open 3WJ stable hairpin.

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

Source

synthesize from company


References

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