Difference between revisions of "Part:BBa K3905010:Design"

 
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===Design Notes===
 
===Design Notes===
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Had to ensure that only half the bases were bound with the complementary miRNA 517-5p and the other half would remain unbound to serve as a trigger. Needed to have a base trigger different to that of the anti-MiRNA 210-3p to ensure that these miRNAs wouldn't bind to each other.
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For the AND gate, we were unable to use the NUPACK API as the minimum free energy structure would show each strand binding, independent of the position of the other strands. Therefore, we designed the anti-miRNA and the toehold switch  base by base. To ensure that the switch would unfold, we had to ensure that the difference in Gibbs free energy between the ‘off’ and ‘on’ state was such that unfolding was energetically favourable when the anti-miRNA-miRNA complex had formed. In order to help us achieve this energetically favourable state we replaced an adequate amount of C-G bonds with U-G bonds.
  
  

Latest revision as of 21:13, 30 September 2021


T7 / gen3 210-3p-517-5p AND-Gate / Luciferase / Double Terminator


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal XbaI site found at 44
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal XbaI site found at 44
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal XbaI site found at 44
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI.rc site found at 108
    Illegal SapI.rc site found at 932


Design Notes

For the AND gate, we were unable to use the NUPACK API as the minimum free energy structure would show each strand binding, independent of the position of the other strands. Therefore, we designed the anti-miRNA and the toehold switch base by base. To ensure that the switch would unfold, we had to ensure that the difference in Gibbs free energy between the ‘off’ and ‘on’ state was such that unfolding was energetically favourable when the anti-miRNA-miRNA complex had formed. In order to help us achieve this energetically favourable state we replaced an adequate amount of C-G bonds with U-G bonds.


Source

This is synthetic, designed in silico, using NUPACK.

References