Part:BBa_K3328011

trigger of toehold

binding to toehold switch (Bba_K3328008) to express the downstream gene

The stability of RNA is a key factor affecting the mechanism of its interaction. Therefore, we hope to optimize the ON/OFF ratio of the toehold switch by improving the stability of trigger RNA. After consulting many pieces of literature, we learned that adding hairpin structure at the 5 'end of RNA could prevent the degradation mediated by RNase, thus improving the stability of RNA. Therefore, we tried to add the hairpin structure at the 5' end of triggers. We used NUPACK and RNAfold to analyze the structure of the trigger with the 5’ end hairpin, and then used NUPACK to analyze the combination of triggers with the 5’ end hairpin and switches.

(A) The secondary structure of 5’ hairpins analyzed using NUPACK. (B) The secondary structure of 5’ hairpins combining with trigger analyzed using NUPACK.

Sequence and Features

Assembly Compatibility:

• 10
  INCOMPATIBLE WITH RFC[10]

  Illegal PstI site found at 20
  
• 12
  INCOMPATIBLE WITH RFC[12]

  Illegal PstI site found at 20
  
• 21
  INCOMPATIBLE WITH RFC[21]

  Illegal XhoI site found at 13
  
• 23
  INCOMPATIBLE WITH RFC[23]

  Illegal PstI site found at 20
  
• 25
  INCOMPATIBLE WITH RFC[25]

  Illegal PstI site found at 20
  
• 1000
  COMPATIBLE WITH RFC[1000]