Difference between revisions of "Part:BBa K4195183"

(Characterization)
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==='''Characterization'''===
 
==='''Characterization'''===
 
====''In vivo'' Verification====
 
====''In vivo'' Verification====
'''1)Agarose Gel Electrophoresis'''
+
'''1) Agarose Gel Electrophoresis'''
  
 
<partinfo>BBa_K4195179</partinfo> and <partinfo>BBa_K4195168</partinfo> 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.<br/>
 
<partinfo>BBa_K4195179</partinfo> and <partinfo>BBa_K4195168</partinfo> 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.<br/>
 
[[File:T--XMU-China--pirA g1α.png|400px]]<br/>
 
[[File:T--XMU-China--pirA g1α.png|400px]]<br/>
 
'''Fig. 3 The result of colony PCR. Plasmid pSB1C3.'''<br/><br/>
 
'''Fig. 3 The result of colony PCR. Plasmid pSB1C3.'''<br/><br/>
'''2)Double transformation'''
+
'''2) Double transformation'''
  
 
Plasmid <partinfo>BBa_K4195168</partinfo>_pSB3K3 and plasmid <partinfo>BBa_K4195179</partinfo>_pSB1C3 were transformed into ''E. coli'' BL21(DE3). The positive transformants were selected by kanamycin and chloramphenicol.<br/>
 
Plasmid <partinfo>BBa_K4195168</partinfo>_pSB3K3 and plasmid <partinfo>BBa_K4195179</partinfo>_pSB1C3 were transformed into ''E. coli'' BL21(DE3). The positive transformants were selected by kanamycin and chloramphenicol.<br/>
'''3)Fluorescence measurement'''
+
'''3) Fluorescence measurement'''
  
 
Colonies harboring the correct plasmid were cultivated and induced. The expression behavior of GFP is observed by measuring the Fluorescence/OD<sub>600</sub> as time progressed using microplate reader.<br/>
 
Colonies harboring the correct plasmid were cultivated and induced. The expression behavior of GFP is observed by measuring the Fluorescence/OD<sub>600</sub> as time progressed using microplate reader.<br/>
 
[[File:T--XMU-China--GFP detection.png|400px]]<br/>
 
[[File:T--XMU-China--GFP detection.png|400px]]<br/>
''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.<br/><br/>
+
'''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.<br/><br/>
  
 
===Reference===
 
===Reference===
 
1. L. Gambill ''et al''. https://www.biorxiv.org/content/10.1101/2022.01.12.476080v1 (2022).
 
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)
+
 
 +
2. J. N. Zadeh ''et al''. NUPACK: Analysis and design of nucleic acid systems. ''J Comput Chem''. '''32''', 170-173 (2011).

Revision as of 05:32, 13 October 2022


Biology

This composite is the detection system of pirA.
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.
T--XMU-China--RENDR.png
Fig. 1 Schematic illustration of RENDR.

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.
output will form.
T--XMU-China--A g1 Nupack.png
Fig. 2 The MFE structure of g1 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= -11.5 kcal/mol, ΔGGuide2= -17.0 kcal/mol, ΔGRNAinput= -38.0 kcal/mol, ΔGSC= -310.66 kcal/mol, ΔGGuide 1 + ΔGGuide 2 + ΔGRNA input − ΔGSC= 244.16 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_K4195057 and BBa_K4195076, then the combined one (BBa_K4195183) 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_K4195168_pSB3K3 and plasmid BBa_K4195179_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_K4195179 and BBa_K4195168 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.
T--XMU-China--pirA g1α.png
Fig. 3 The result of colony PCR. Plasmid pSB1C3.

2) Double transformation

Plasmid BBa_K4195168_pSB3K3 and plasmid BBa_K4195179_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.
T--XMU-China--GFP detection.png
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).