Part:BBa_K4195046
pirA_g2βR_Nu
This sequence is the second part of guide designed for detection of toxin gene pirA.
Biology
Ribozyme ENabled Detection of RNA (RENDR)
RENDR is a high-performing, plug-and-play RNA-sensing platform(1). RENDR utilizes a split variant of the Tetrahymena thermophila ribozyme by synthetically splitting it into two non-functional fragments (Fig. 1). Two fragments are each appended with designed RNA guide sequences, which can interact with the RNA input of interest. The split ribozyme is then inserted within a desired gene output. When bound with the RNA input, two transcribed split ribozyme fragments are triggered to self-splice and thus the intact transcript of the protein output will form.
Fig. 1 Schematic illustration of RENDR.
NanoLuc
NanoLuc is a novel engineered luciferase enzyme that relies on the substrate furimazine to produce high intensity, glow-type luminescence. With high stability, small size and bright luminescence, it is an attractive luminescent reporter (2).
Fig. 2 The bioluminescent reaction catalyzed by NanoLuc® luciferase (2).
Usage and Design
The conserved region of pirA gene is set as the RNA input. The guide sequences were designed based on NUPACK prediction(2). Based on the model provided (Equation. 1), we calculate the free energy difference of candidate sequences at 37 °C, and select guide pair g1 and g2 with 244.16 kcal/mol and 232.86 kcal/mol. The optimized ribozyme split sites are selected from the literature, and named α (split site 15) and β (split site 402)(1).
Equation. 1 ln(FL/OD) ~ΔGGuide 1 + ΔGGuide 2 + ΔGRNA input − ΔGSC.
Fig. 3 The MFE structure of g2 guide-input complex at 37℃. ΔGGuide1 and ΔGGuide2 = The minimum free energy (MFE) of the two RNA guide sequences attached to each fragment of the RENDR ribozyme. ΔGRNAinput = The MFE of the RNA input. ΔGSC = The duplex binding energy of the complex.ΔGGuide1= -10.1 kcal/mol, ΔGGuide2= -28.4 kcal/mol, ΔGRNAinput= -38.0 kcal/mol, ΔGSC= -309.36 kcal/mol, ΔGGuide 1 + ΔGGuide 2 + ΔGRNA input − ΔGSC= 232.86 kcal/mol.
NanoLuc was chosen as the reporter, and the split ribozyme was inserted between the Ribosome-binding site and the coding sequence of reporter gene. Two parts of the split ribozyme are separately transcribed with different transcription start sites. We separately designed two split ribozymes as different parts BBa_K4195046 and BBa_K4195081 and obtained the combined one (BBa_K4195146). We add BBa_K4195179 to construct the expression system and obtained the composite BBa_K4195151, which are assembled on the expression vector pSB1C3 by standard assembly. The constructed plasmids were transformed into E. coli BL21(DE3), then the positive transformants were selected by chloramphenicol and confirmed by colony PCR and sequencing.
Characterization
1. In Vivo Verification
1) Agarose Gel Electrophoresis
BBa_K4195151 was assembled into the vector pSB1C3 by standard BioBrick assembly. The constructed plasmids were transformed into E. coli BL21(DE3), then the positive transformants were selected by chloramphenicol and confirmed by colony PCR and sequencing.
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Fig. 4 The result of colony PCR. Plasmid pSB1C3.
2) Bioluminescence measurement
Colonies harboring the correct plasmid were cultivated and induced. The expression behavior of NanoLuc is observed by measuring the bioluminescence as time progressed using microplate reader.
Fig. 5 In vivo behavior of pirA_g2β_Nu as time progressed.
Reference
1. L. Gambill et al., https://www.biorxiv.org/content/10.1101/2022.01.12.476080v1 (2022).
2. C. G. England, E. B. Ehlerding, W. Cai, NanoLuc: A Small Luciferase Is Brightening Up the Field of Bioluminescence. Bioconjug Chem 27, 1175-1187 (2016).
3. J. N. Zadeh et al., NUPACK: Analysis and design of nucleic acid systems. J Comput Chem 32, 170-173 (2011).
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25INCOMPATIBLE WITH RFC[25]Illegal NgoMIV site found at 177
- 1000COMPATIBLE WITH RFC[1000]
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