Regulatory

Part:BBa_K3905006:Design

Designed by: Peter Heywood, Harry Weiniger   Group: iGEM21_City_of_London_UK   (2021-09-09)
Revision as of 09:56, 4 October 2021 by PHeywood (Talk | contribs) (→‎Design Notes)

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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