Difference between revisions of "Part:BBa K4195050"

 
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[[File:T--XMU-China--AmpC.png|300px]]
 
[[File:T--XMU-China--AmpC.png|300px]]
  
'''Fig. 2 The color transformation catalyzed by AmpC (''2'')'''
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'''Fig. 2 The color transformation catalyzed by AmpC (''2'').'''
  
  
 
===Usage and design===
 
===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'').<br/>
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The conserved region of ''pirB'' gene is set as the RNA input. The guide sequences were designed based on NUPACK prediction(''3''). 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. 3). The optimized ribozyme split sites are selected from the literature, and named α (split site 15) and β (split site 402)(''1'').<br/>
 
'''Equation. 1 ln(FL/OD) ~ΔG<sub>Guide 1</sub> + ΔG<sub>Guide 2</sub> + ΔG<sub>RNA input</sub> − ΔG<sub>SC</sub>.'''<br/>
 
'''Equation. 1 ln(FL/OD) ~ΔG<sub>Guide 1</sub> + ΔG<sub>Guide 2</sub> + ΔG<sub>RNA input</sub> − ΔG<sub>SC</sub>.'''<br/>
 
[[File:T--XMU-China--pirB g1α Nupack.png|400px]]<br/>
 
[[File:T--XMU-China--pirB g1α Nupack.png|400px]]<br/>
'''Fig. 2 The MFE structure of g1 guide-input complex at 37℃.''' ΔG<sub>Guide1</sub> and ΔG<sub>Guide2</sub> = The minimum free energy (MFE) of the two RNA guide sequences attached to each fragment of the RENDR ribozyme. ΔG<sub>RNAinput</sub> = The MFE of the RNA input. ΔG<sub>SC</sub> = The duplex binding energy of the complex. ΔG<sub>Guide1</sub> = -13.2 kcal/mol, ΔG<sub>Guide2</sub> = -10.6 kcal/mol, ΔG<sub>RNAinpu</sub> = -27.9 kcal/mol, ΔG<sub>SC</sub> = -267.06 kcal/mol, ΔG<sub>SC</sub> - ΔG<sub>Guide1</sub> + ΔG<sub>Guide2</sub> + ΔG<sub>RNAinput</sub> = 215.36 kcal/mol.
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'''Fig. 3 The MFE structure of g1 guide-input complex at 37℃.''' ΔG<sub>Guide1</sub> and ΔG<sub>Guide2</sub> = The minimum free energy (MFE) of the two RNA guide sequences attached to each fragment of the RENDR ribozyme. ΔG<sub>RNAinput</sub> = The MFE of the RNA input. ΔG<sub>SC</sub> = The duplex binding energy of the complex. ΔG<sub>Guide1</sub> = -13.2 kcal/mol, ΔG<sub>Guide2</sub> = -10.6 kcal/mol, ΔG<sub>RNAinput</sub> = -27.9 kcal/mol, ΔG<sub>SC</sub> = -267.06 kcal/mol, ΔG<sub>Guide 1</sub> + ΔG<sub>Guide 2</sub> + ΔG<sub>RNA input</sub> ΔG<sub>SC</sub> = 215.36 kcal/mol.
  
  
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[[File:T--XMU-China--K4195158 (K4195158 pSB3K3, colony PCR).png|300px]]
 
[[File:T--XMU-China--K4195158 (K4195158 pSB3K3, colony PCR).png|300px]]
  
'''Fig. 4 The result of colony PCR. Plasmid pSB3K3'''
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'''Fig. 4 The result of colony PCR. Plasmid pSB3K3.'''
  
  
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'''3) Absorbance measurement'''
 
'''3) Absorbance measurement'''
  
Colonies harboring the correct plasmid were cultivated and induced. The expression behavior of AmpC is observed by measuring the absorbance in 482 nm as time progressed using microplate reader.
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Colonies harboring the correct plasmid were cultivated and induced. The expression behavior of AmpC is observed by measuring the absorbance in 490 nm as time progressed using microplate reader.
  
 
[[File:T--XMU-China--B1α-B pSB3K3.png|300px]]
 
[[File:T--XMU-China--B1α-B pSB3K3.png|300px]]
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'''Fig. 5 ''In vivo'' behavior of pirB_g1α_B as time progressed.'''
 
'''Fig. 5 ''In vivo'' behavior of pirB_g1α_B as time progressed.'''
  
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====2. ''In Vitro'' Verification====
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Plasmid was put into the cell-free system for expression. The expression behavior of AmpC is observed by measuring the absorbance in 490 nm as time progressed using microplate reader.
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[[File:T--XMU-China--B1a.png|300px]]
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'''Fig. 6 ''In vitro'' behavior of pirB_g1α_B .'''
  
 
===Reference===
 
===Reference===

Latest revision as of 09:26, 13 October 2022


pirB_g1αR_B


This sequence is the second 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.
T--XMU-China--RENDR.png
Fig. 1 Schematic illustration of RENDR.


AmpC

β-lactamase (AmpC) is a bacterial enzyme that facilitates resistance against β-lactam antibiotics by hydrolyzing the β-lactam ring, deactivating the antibiotic. It can also catalyze the hydrolysis reaction of nitrocefin, resulting in a distinct color change from yellow to red (2).

T--XMU-China--AmpC.png

Fig. 2 The color transformation catalyzed by AmpC (2).


Usage and design

The conserved region of pirB gene is set as the RNA input. The guide sequences were designed based on NUPACK prediction(3). 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. 3). 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.
T--XMU-China--pirB g1α Nupack.png
Fig. 3 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 = -13.2 kcal/mol, ΔGGuide2 = -10.6 kcal/mol, ΔGRNAinput = -27.9 kcal/mol, ΔGSC = -267.06 kcal/mol, ΔGGuide 1 + ΔGGuide 2 + ΔGRNA input − ΔGSC = 215.36 kcal/mol.


β-lactamase (AmpC) 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_K4195050 and BBa_K4195077, then the combined one (BBa_K4195158) 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.


Characterization

1. In Vivo Verification

1) Agarose Gel Electrophoresis

BBa_K4195158 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.

T--XMU-China--K4195158 (K4195158 pSB3K3, colony PCR).png

Fig. 4 The result of colony PCR. Plasmid pSB3K3.


2) Double transformation

Plasmid BBa_K4195158_pSB3K3 and plasmid BBa_K4195180_pSB1C3 were transformed into E. coli BL21(DE3). The positive transformants were selected by kanamycin and chloramphenicol.

3) Absorbance measurement

Colonies harboring the correct plasmid were cultivated and induced. The expression behavior of AmpC is observed by measuring the absorbance in 490 nm as time progressed using microplate reader.

T--XMU-China--B1α-B pSB3K3.png

Fig. 5 In vivo behavior of pirB_g1α_B as time progressed.

2. In Vitro Verification

Plasmid was put into the cell-free system for expression. The expression behavior of AmpC is observed by measuring the absorbance in 490 nm as time progressed using microplate reader.

T--XMU-China--B1a.png

Fig. 6 In vitro behavior of pirB_g1α_B .

Reference

1. L. Gambill et al., https://www.biorxiv.org/content/10.1101/2022.01.12.476080v1 (2022).

2. K. E. Boehle, C. S. Carrell, J. Caraway, C. S. Henry, Paper-Based Enzyme Competition Assay for Detecting Falsified β-Lactam Antibiotics. ACS Sens 3, 1299-1307 (2018).

3. J. N. Zadeh et al., NUPACK: Analysis and design of nucleic acid systems. J Comput Chem 32, 170-173 (2011).



Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 409
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 311
    Illegal XhoI site found at 776
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]