Part:BBa_K4195078
This sequence is the first part of guide designed for detection of toxin gene pirB.
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.
Usage and Design
The conserved region of pirB 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 215.36 kcal/mol and 205.86 kcal/mol (Fig. 2). 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. 2 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 = -16.10 kcal/mol, ΔGGuide2 = -13.5 kcal/mol, ΔGRNAinpu = -31.00 kcal/mol, ΔGSC = -266.46 kcal/mol, ΔGGuide 1 + ΔGGuide 2 + ΔGRNA input − ΔGSC = 205.86 kcal/mol.
Two parts of the split ribozyme are separately transcribed with different transcription start sites. We separately designed two split ribozymes as different parts BBa_K4195059 and BBa_K4195078, then the combined one (BBa_K4195188) was assembled into the vector pSB3K3 by standard BioBrick assembly. The constructed plasmids were transformed into E. coli BL21(DE3), then the positive transformants were selected by kanamycin and confirmed by colony PCR and sequencing. Plasmid BBa_K4195188_pSB3K3 and plasmid BBa_K4195180_pSB1C3 were transformed into E. coli BL21(DE3). The positive transformants were selected by kanamycin and chloramphenicol.
Characterization
In vivo Verification
1) Agarose Gel Electrophoresis
BBa_K4195180 and BBa_K4195171 were 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.
Fig. 3 The result of colony PCR. Plasmid pSB1C3.
2) Double transformation
Plasmid BBa_K4195171_pSB3K3 and plasmid BBa_K4195180_pSB1C3 were transformed into E. coli BL21(DE3). The positive transformants were selected by kanamycin and chloramphenicol.
3) Fluorescence measurement
Colonies harboring the correct plasmid were cultivated and induced. The expression behavior of GFP is observed by measuring the Fluorescence/OD600 as time progressed using microplate reader.
Fig. 4 In vivo behavior of detection systems. a pirA detection systems and ori detection system were assembled into the vector pSB1C3. b pirA/ ori detection system and the target input were assembled separately into the vector pSB1C3 and pSB3K3. c pirB detection systems and ori detection system were assembled into the vector pSB1C3. d pirB/ ori detection system and the target input were assembled separately into the vector pSB1C3 and pSB3K3.
Reference
1. L. Gambill et al., https://www.biorxiv.org/content/10.1101/2022.01.12.476080v1 (2022).
2. 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]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE WITH RFC[1000]
| None |