Part:BBa_K3380602

TXO ArsR regulated construct under T7 promoter (BBa_K3380103) expressing DIR2s-Apt The Edinburgh iGEM team 2020 designed a construct comprising a fluorescent RNA aptamer (DIR2s-Apt BBa_K3380151) flanked by a tRNA scaffold (F30 BBa_K3380101 and BBa_K3380102) under an ArsR transcription factor regulated promoter (BBa_K3380103). It was designed to test the ArsR regulated promoter. The construct is capable of exhibiting red fluorescence when binding to the DIR (dimethylindole red) or blue fluorescence when binding to OTB (oxazole thiazole blue) fluorophore being a transcription only construct . Simultaneously we tested the efficiency of transcription in the absence of a terminator in a cell-free extract. The T7 RNA polymerase is capable of synthesizing transcripts via run-off transcription in the absence of a terminator (because the DNA template is linear). Figure 1 illustrates a schematic design of the construct.

Figure 1 illustrates a schematic design of the construct.

Figure 1: Construct BBa_K3380602 design. The DIR2s-Apt fluorescent RNA aptamer (shown in red) was flanked by the F30 upstream and downstream scaffolds (shown in blue) to protect it from the RNAse degradation (from the cell free extract), it was expressed under the BBa_K3380103 promoter (shown in black). The promoter has an ArsR binding site (shown in yellow) that represses the transcription in the absence of Arsenic.

Usage and Biology

The construct could be used in a As biosensor in cell-free extracts or buffers containing T7 RNA polymerase, chemical energy (ATP), NTPs, fluorophore and adequate cofactors and pH. The construct functioning solely on transcription and having a small length of only 197 nucleotides has multiple advantages over the conventional fluorescent proteins. The time required for the fluorescence formation is much shorter than compared to the time needed for the synthesis of the fluorescent proteins. Moreover, there is less burden exhibited on the cell (if expressed in cells) or it requires less resources (NTPs, energy if expressed in cell free extract) when expressing the transcription only construct. Also, individual parts can be "de novo" synthesized and ligated rather than expressing them in cells using plasmids, which is more expensive and requires more time

The efficiency of the ArsR transcription factor repression can be tested using a cell-free extract under a class III T7 strong promoter. The ArsR proteins from the cell extracts can be used to induce the repression of the DNA template transcription (containing the fluorescent RNA aptamer). In the presence of arsenic, the ArsR homodimer would unbind the ArsR binding site allowing the T7 RNA polymerase to bind and initiate the transcription of the DIR2s-Apt, resulting in the fluorescence. In the absence of arsenic, the fluorescence would not be observed. A more detailed explanation of the ArsR transcription factor can be found in BBa_K190015.

Sequence and Features

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 25