Difference between revisions of "Part:BBa K4604029:Design"
 
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After assembling the two plasmid parts, this new plasmid, the sensor backbone, was again used as PCR template to clone the correct overhangs for the insertion of the AdoCbl SY riboswitch between lacI promoter and <i>lacI</i> gene. The synthesised DNA of the SY riboswitch from IDT was used it as a template for PCR. For this we used the general protocol for the Q5 polymerase with varying parameters (elongation time and annealing temperature):
 
After assembling the two plasmid parts, this new plasmid, the sensor backbone, was again used as PCR template to clone the correct overhangs for the insertion of the AdoCbl SY riboswitch between lacI promoter and <i>lacI</i> gene. The synthesised DNA of the SY riboswitch from IDT was used it as a template for PCR. For this we used the general protocol for the Q5 polymerase with varying parameters (elongation time and annealing temperature):
 
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     <caption><b>Fig. 1:</b> table showing parameters varying from PCR protocol for piG_SYBS</caption>
 
     <caption><b>Fig. 1:</b> table showing parameters varying from PCR protocol for piG_SYBS</caption>
 
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  The DNA of the plasmid fragments, pIG23_04 and pIG23_03, was loaded onto an agarose gel. The correct bands were cut out and extracted. Plasmid fragments of pIG23_03 and pIG23_04 were first assembled to form the sensor backbone with Gibson Assembly and AQUA cloning, according to the protocols. A transformation was done and the resulting colonies after an approximate 12-14h incubation time were screened by colony PCR. DNA of potential colonies containing the insert was isolated from overnight cultures (5mL LB-medium, 50 mg/mL spectinomycin) and sent for sequencing to check for correct insertion and no mutation.  
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The DNA of the plasmid fragments, pIG23_04 and pIG23_03, was loaded onto an agarose gel. The correct bands were cut out and extracted. Plasmid fragments of pIG23_03 and pIG23_04 were first assembled to form the sensor backbone with Gibson Assembly and AQUA cloning, according to the protocols. A transformation was done and the resulting colonies after an approximate 12-14h incubation time were screened by colony PCR. DNA of potential colonies containing the insert was isolated from overnight cultures (5mL LB-medium, 50 mg/mL spectinomycin) and sent for sequencing to check for correct insertion and no mutation.  
 
Then with the sensor backbone as a template, a PCR was performed to create overhangs to insert the riboswitch between lacI promoter and <i>lacI</i>. A Dpn1 digest was done at 37°C for an hour, afterwards the DNA was loaded onto an agarose gel. The correct bands were cut out and extracted.  
 
Then with the sensor backbone as a template, a PCR was performed to create overhangs to insert the riboswitch between lacI promoter and <i>lacI</i>. A Dpn1 digest was done at 37°C for an hour, afterwards the DNA was loaded onto an agarose gel. The correct bands were cut out and extracted.  
 
The PCR for the PF riboswitch was also performed and the DNA was loaded onto an agarose gel. The correct bands were cut out and extracted.  
 
The PCR for the PF riboswitch was also performed and the DNA was loaded onto an agarose gel. The correct bands were cut out and extracted.  
 
Riboswitch and sensor backbone were assembled via Gibson Assembly and AQUA cloning according to the protocols. A transformation was done and the resulting colonies after an approximate 12-14h incubation time were screened by colony PCR. DNA of potential colonies containing the insert was isolated from overnight cultures (5mL LB-medium, 50 mg/mL spectinomycin ) and sent for sequencing to check for correct insertion and no mutation.
 
Riboswitch and sensor backbone were assembled via Gibson Assembly and AQUA cloning according to the protocols. A transformation was done and the resulting colonies after an approximate 12-14h incubation time were screened by colony PCR. DNA of potential colonies containing the insert was isolated from overnight cultures (5mL LB-medium, 50 mg/mL spectinomycin ) and sent for sequencing to check for correct insertion and no mutation.

Latest revision as of 01:01, 12 October 2023


piG_SYBS


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal NgoMIV site found at 220
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

If we had placed the sfGFP/marker protein directly after the riboswitch, its negative regulation in the presence of AdoCbl would have resulted in a decrease in fluorescence. In this BioBrick the riboswitch is placed in front of a repressor gene (lacI) which inturn suppresses sfGFP expression. If the riboswitch is triggered by binding of AdoCbl, the repressor expression is stopped leading to a detectable fluorescent signal.


Cloning of piG_SYBS

The lacI promoter, lacI gene, trc promoter, sfGFP and rrnB terminator were given to us by iGEM Freiburg 2022 on a plasmid called pIG23_04. We took plasmid pIG23_03 (also given to us by iGEM Freiburg 2022) as our backbone, including an antibiotic resistance (spectinomycin) gene and Ori. SfGFP, trc promoter, lacI and lacI promoter were taken from pIG23_04 and cloned into pIG23_03 using Gibson Assembly and AQUA cloning. Both plasmids were templates for PCR, to amplify the parts and add correct overhangs via gibson primers. After assembling the two plasmid parts, this new plasmid, the sensor backbone, was again used as PCR template to clone the correct overhangs for the insertion of the AdoCbl SY riboswitch between lacI promoter and lacI gene. The synthesised DNA of the SY riboswitch from IDT was used it as a template for PCR. For this we used the general protocol for the Q5 polymerase with varying parameters (elongation time and annealing temperature):

Fig. 1: table showing parameters varying from PCR protocol for piG_SYBS
fragment Annealing temp. Elongation time Fragment size (in bp)
trc promoter, sfGFP, lacI promoter, lacI gene 72°C 1.5 min 2670
backbone (Ori and resistance) 72°C 1.5 min 2080
SY riboswitch 65°C 20 s 210
create overhangs to add riboswitch between lacI prom. and lacI 68°C 3 min 4700


The DNA of the plasmid fragments, pIG23_04 and pIG23_03, was loaded onto an agarose gel. The correct bands were cut out and extracted. Plasmid fragments of pIG23_03 and pIG23_04 were first assembled to form the sensor backbone with Gibson Assembly and AQUA cloning, according to the protocols. A transformation was done and the resulting colonies after an approximate 12-14h incubation time were screened by colony PCR. DNA of potential colonies containing the insert was isolated from overnight cultures (5mL LB-medium, 50 mg/mL spectinomycin) and sent for sequencing to check for correct insertion and no mutation. Then with the sensor backbone as a template, a PCR was performed to create overhangs to insert the riboswitch between lacI promoter and lacI. A Dpn1 digest was done at 37°C for an hour, afterwards the DNA was loaded onto an agarose gel. The correct bands were cut out and extracted. The PCR for the PF riboswitch was also performed and the DNA was loaded onto an agarose gel. The correct bands were cut out and extracted. Riboswitch and sensor backbone were assembled via Gibson Assembly and AQUA cloning according to the protocols. A transformation was done and the resulting colonies after an approximate 12-14h incubation time were screened by colony PCR. DNA of potential colonies containing the insert was isolated from overnight cultures (5mL LB-medium, 50 mg/mL spectinomycin ) and sent for sequencing to check for correct insertion and no mutation.