Team:Edinburgh/Parts/BasicParts


Team Edinburgh Finding NEMO

Basic parts for the modular, cell-free transcription only biosensor.

    The biosensor proposed by our team is transcription only. Therefore we added to the iGEM registry several fluorescent RNA aptamers (such as iSpinach, Broccoli and DIR2s-Apt) that can exhibit fluorescence on addition of fluorophores and replace the canonical fluorescent proteins. The RNA aptamers would reduce the time needed to visualise the results of the tests. Also we added a tRNA scaffold that is meant to increase the stability of the RNA aptamers by protecting them from degradation by RNAses. Furthermore, there was a need to add multiple promoters that had transcription factor binding sites, to help with the heavy metals identification. Some of the transcripts are repressed by the binding of transcription factors (present in the cell extracts) to the promoters. In the presence of metals, the transcription factors would unbind and allow the transcription of fluorescent RNA aptamers, that could further be visually identified. Due to the pandemic, we managed to test constructs using the BBa_K3380150 (iSpinach aptamer), BBa_K3380101 and BBa_K3380102 F30 tRNA scaffolds and BBa_K3380103 T7 promoter. All the Basic Parts are presented in the table below.


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NameTypeDescriptionDesignerLength
  WBBa_K3380101RNA F30 Upstream RNA aptamer scaffoldYing Yang, Alexandru Popov18
  WBBa_K3380102RNAF30 Downstream RNA aptamer scaffoldAlexandru Popov40
  WBBa_K3380103RegulatoryT7 strong promoter with ArsR binding siteAlexandru Popov70
  WBBa_K3380150ReporteriSpinach fluorescent RNA aptamerAlexandru Popov78
U  BBa_K3380104RegulatoryFluoride RiboswitchAlexandru Popov99
   BBa_K3380105RegulatoryE.coli promoter with Zinc transcription factor binding site Alexandru Popov73
  BBa_K3380106RegulatoryPromoter with Pb transcription factor binding siteAlexandru Popov58
  BBa_K3380107RegulatoryPromoter with Hg transcription factor binding siteAlexandru Popov60
  BBa_K3380108RegulatoryPromoter with Cu transcription factor binding siteAlexandru Popov45
  BBa_K3380109RegulatoryC. Metallidurans promoter with Zn transcription factor binding site Alexandru Popov78
  BBa_K3380110RegulatoryPromoter with Co and Ni transcription factor binding siteAlexandru Popov55
  BBa_K3380151ReporterDIR2s-Apt fluorescent RNA aptamerAlexandru Popov57
  BBa_K3380153ReporterBroccoli fluorescent RNA aptamerAlexandru Popov49