Difference between revisions of "Part:BBa K3328004:Design"

(→‎Design Notes)
(→‎Design Notes)
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===Design Notes===
 
===Design Notes===
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As a trigger of 3WJ repressor
+
====3WJ repressor====
 +
https://2020.igem.org/wiki/images/thumb/a/af/T--OUC-China--design_fig4.png/800px-T--OUC-China--design_fig4.png.jpeg
  
 +
3WJ repressor switch RNA employs an unstable hairpin secondary structure. This unstable hairpin was previously demonstrated to be translationally active. When a complementary trigger RNA is expressed, the trigger will bind to the switch RNA, making the originally unstable 3WJ structure stable, and represses translation.
  
 +
==== NOT gate====
 +
NOT gate is made up of 3WJ repressor. Its unstable hairpin was previously demonstrated to be translationally active.
 +
https://2020.igem.org/wiki/images/thumb/1/1f/T--OUC-China--design_lunbo_not.jpg/799px-T--OUC-China--design_lunbo_not.jpg
  
 +
When a complementary trigger RNA is expressed, the trigger will bind to the switch RNA, making the originally unstable 3WJ structure stable, and represses translation.
  
−
As an integral part of IMPLY boolean calculation
+
==== IMPLY gate====
 +
We combined the 3WJ switch and toehold switch to realize the IMPLY Boolean calculation.
  
−
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.
+
https://2020.igem.org/wiki/images/thumb/8/88/T--OUC-China--design_fig6.jpg/799px-T--OUC-China--design_fig6.jpg
 +
 
 +
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.
  
 
===Source===
 
===Source===

Revision as of 02:35, 23 October 2020


trigger of OFF-switch1 and NOT gate;triggerB of IMPLY gate


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

3WJ repressor

800px-T--OUC-China--design_fig4.png.jpeg

3WJ repressor switch RNA employs an unstable hairpin secondary structure. This unstable hairpin was previously demonstrated to be translationally active. When a complementary trigger RNA is expressed, the trigger will bind to the switch RNA, making the originally unstable 3WJ structure stable, and represses translation.

NOT gate

NOT gate is made up of 3WJ repressor. Its unstable hairpin was previously demonstrated to be translationally active. 799px-T--OUC-China--design_lunbo_not.jpg

When a complementary trigger RNA is expressed, the trigger will bind to the switch RNA, making the originally unstable 3WJ structure stable, and represses translation.

IMPLY gate

We combined the 3WJ switch and toehold switch to realize the IMPLY Boolean calculation.

799px-T--OUC-China--design_fig6.jpg

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.

Source

synthesize from company

References

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