Difference between revisions of "Part:BBa K4207002:Design"

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<partinfo>BBa_K4207000 short</partinfo>
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<partinfo>BBa_K4207002 short</partinfo>
  
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<partinfo>BBa_K4207000 SequenceAndFeatures</partinfo>
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<partinfo>BBa_K4207002 SequenceAndFeatures</partinfo>
  
  
 
===Design Notes===
 
===Design Notes===
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This toehold switch was designed according to the A-series toehold structure (Pardeee et. al. 2016). The A-series structure was designed to reduce translational leakage compared to older toehold switches. The binding site of the toehold switch was designed to bind to a conserved sequence in the BYDV genome, allowing it to sense the presence of this trigger sequence. This toehold switch consists of a 30-nt linker sequence from sensor 27B (Pardee et. al. (2016)) upstream of the Type IIS junction site as opposed to the more conventional 21-nt linker sequence of toehold switches. The last nucleotide of this linker sequence is part of the junction site (AATG), so it is not registered here.
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This toehold switch was designed according to the A-series toehold structure (Pardeee et. al., 2016). The A-series structure was designed to reduce translational leakage compared to older toehold switches (Green et. al., 2014). The binding site of the toehold switch was designed to bind to a conserved sequence in the BYDV genome, allowing it to sense the presence of this trigger sequence. This toehold switch consists of a 30-nt linker sequence from sensor 27B (Pardee et. al. (2016)) upstream of the Type IIS junction site as opposed to the more conventional 21-nt linker sequence of toehold switches. The last nucleotide of this linker sequence is part of the junction site (AATG), so it is not registered here.
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===Source===
 
===Source===
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===References===
 
===References===
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Pardee, K., Green, A. A., Takahashi, M. K., Braff, D., Lambert, G., Lee, J. W., et al. (2016). "Rapid, Low-Cost Detection of Zika Virus Using Programmable Biomolecular Components." Cell  165, 1255–1266. doi:10.1016/j.cell.2016.04.059
 
Pardee, K., Green, A. A., Takahashi, M. K., Braff, D., Lambert, G., Lee, J. W., et al. (2016). "Rapid, Low-Cost Detection of Zika Virus Using Programmable Biomolecular Components." Cell  165, 1255–1266. doi:10.1016/j.cell.2016.04.059
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Green, A. A., Silver, P. A., Collins, J. J., and Yin, P. (2014). Toehold Switches: De-novo-designed Regulators of Gene Expression. Cell 159, 925–939. doi:10.1016/j.cell.2014.10.002
 
Green, A. A., Silver, P. A., Collins, J. J., and Yin, P. (2014). Toehold Switches: De-novo-designed Regulators of Gene Expression. Cell 159, 925–939. doi:10.1016/j.cell.2014.10.002

Latest revision as of 10:59, 26 September 2022


BYDV toehold switch A70


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

This toehold switch was designed according to the A-series toehold structure (Pardeee et. al., 2016). The A-series structure was designed to reduce translational leakage compared to older toehold switches (Green et. al., 2014). The binding site of the toehold switch was designed to bind to a conserved sequence in the BYDV genome, allowing it to sense the presence of this trigger sequence. This toehold switch consists of a 30-nt linker sequence from sensor 27B (Pardee et. al. (2016)) upstream of the Type IIS junction site as opposed to the more conventional 21-nt linker sequence of toehold switches. The last nucleotide of this linker sequence is part of the junction site (AATG), so it is not registered here.

Source

This part was created by us, using 10 different barley yellow dwarf virus (BYDV) whole genomes to screen for conserved sequences to be detected by the toehold switches.

References

Pardee, K., Green, A. A., Takahashi, M. K., Braff, D., Lambert, G., Lee, J. W., et al. (2016). "Rapid, Low-Cost Detection of Zika Virus Using Programmable Biomolecular Components." Cell 165, 1255–1266. doi:10.1016/j.cell.2016.04.059

Green, A. A., Silver, P. A., Collins, J. J., and Yin, P. (2014). Toehold Switches: De-novo-designed Regulators of Gene Expression. Cell 159, 925–939. doi:10.1016/j.cell.2014.10.002