Difference between revisions of "Part:BBa K3905006: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 would not 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.
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===Source===
 
===Source===

Latest revision as of 09:56, 4 October 2021


gen3 210-3p-517-5p AND-Gate Toehold Switch


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
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI.rc site found at 82


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

Synthetic. Nupack

References