Difference between revisions of "Part:BBa K3038000:Experience"

(→‎Applications of BBa_K3038000: Characterization of BBa K3038000)
 
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how you used this part and how it worked out.
 
how you used this part and how it worked out.
  
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===Applications of BBa_K3038000===
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===Applications of BBa_K3038001===
  
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==Manipulations==
  
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PCR amplification of the PCR products
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===PCR amplification===
  
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Following the design of the synthetic gene, it is amplified by PCR thanks to the design of primers upstream and downstream of the sequence.
  
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<center>https://2019.igem.org/wiki/images/4/40/T--Poitiers--PCR_amplification_ADR-tab3.jpg<br>
  
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<strong>Electrophoresis photography following loads on agarose gel 0.8% of PCR products.</strong><br> The migration was performed at 100 volts for 30 minutes in TAE 1X. The marker used during the migration is the NEB 1 kb Plus DNA Ladder. Lane 1 corresponds to the marker, lane 2 to the control without DNA, lane 3 to the amplified N-term ADR and lane 4 to the amplified C-term ADR.</center><br>
  
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The expected size of the fragment is about 1600 pb. The band obtained correspond to this size.
  
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===Enzymatic digestion===
  
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Plasmid construction
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After amplification of the synthetic gene, sample is purified, the amplicons are digested with restriction enzymes EcoRI and PstI. Similarly for the cloning vector pSB1A3. The insert (N-term ADR or C-term) is then ligated into the plasmid.
  
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<Center>https://2019.igem.org/wiki/images/2/27/T--Poitiers--electrophor%C3%A8se_gel4_tab4.png<br>
  
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<strong>Electrophoresis photography following loads on agarose gel 0.8% of enzymatic digestion products.</strong><br> The migration was performed at 100 volts for 30 minutes in TAE 1X. The marker used during the migration is the NEB 1 kb Plus Ladder (left in the figure). Lane 1 corresponds to the marker, lane 2 to the digested N-term ADR, lane 3 to the digested C-term ADR and lane 4 to the digested pSB1A3 plasmid.</center>
  
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===Ligation in pSB1A3===
  
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<Center>https://2019.igem.org/wiki/images/5/5b/T--Poitiers--plasmid_construction_ADR-tab3.jpg<br>
  
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Expression of the recombinant protein  
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<strong>Design of ADR N-ter/pSB1A3 and ADR C-ter/pSB1A3 with Geneious software.</strong><br> This map shows the pBAD promoter and its terminator flanking the coding sequence of the ADR protein. Also present in N-ter or C-ter are 6-His and c-myc tag. Finally, in the plasmid is present and ampicillin resistance cassette.</center>
  
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===Cloning into <i> E. coli</i> Thermocompetent cells JM109===
  
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The thermocompetent <i>E. coli</i> JM109 bacteria are then transformed and clones are obtained.
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<center>https://2019.igem.org/wiki/images/3/39/T--Poitiers--culture_gauche2_tab4.png<br>
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<strong>Clones on a selective LB medium (+ ampicillin 100 µg/mL) following the transformation of <i> E. coli</i> thermocompetent cells with the pSB1A3-ADR ligations.</strong><br/>
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A: Clones obtained from pSB1A3 N-ter ADR ligations.<br/>
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B: Clones obtained from the pSB1A3 C-ter ADR ligations.</center>
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===PCR colony screening===
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After bacterial transformation, colony PCR is performed with the forward primer of the ADR gene and a reverse primer of the plasmid. 12 clones of each condition (ADR N-ter/pSB1A3 and ADR C-ter/pSB1A3) are tested. The PCR products are loaded on 0.8% agarose gel.
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 +
<center>https://2019.igem.org/wiki/images/5/55/T--Poitiers--electrophor%C3%A8se_gel5_tab4.png<br>
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<strong>Electrophoresis photography following loads on agarose gel 0.8% of colony PCR products.</strong><br> The migration was performed at 100 volts for 30 minutes in TAE 1X. The marker used during the migration is the NEB 1 kb Plus Ladder (in the center on the figure). Lane 1 to 12 corresponds to colony PCR performed on ADR N-ter/pSB1A3 ligation, lane 13 to 24 corresponds to colony PCR performed on ADR C-ter/pSB1A3.</center>
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Clones 4, 5, 10, 11 and 12 have the right profile, an insert-vector fragment of 1800 pb. Wells 13 to 24 show PCR products on clones transformed with ADR C-ter/pSB1A3. Clones 13, 21 and 22 have the right profile, an insert-vector fragment of 1800 pb.
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===Control enzymatic digestion===
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Clones with the right profile are returned to liquid culture and minipreparations are performed. Enzymatic digestion is carried out with BamHI and PstI restriction enzymes. The expected band sizes are 2300 and 1400 pb.
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 +
<center>https://2019.igem.org/wiki/images/4/4d/T--Poitiers--electrophor%C3%A8se_gel6_tab4.png<br>
 +
 +
<strong>Electrophoresis photography following loads on agarose gel 0.8% of enzymatic digestion  products by BamHI and PstI.</strong><br> The migration was performed at 100 volts for 30 minutes in TAE 1X. The marker used during the migration is the NEB 1 kb Plus Ladder (left in the figure). Lane 1 to 5 corresponds to enzymatic digestion product of ADR N-ter/pSB1A3, lane 7 to 9 corresponds to enzymatic digestion product of ADR C-ter/pSB1A3.</center>
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Wells 1 to 5 comprise clones 4, 5, 10, 11 and 12 transformed with ADR N-ter/pSB1A3. Wells 7 to 9 contain clones 13, 21 and 23 transformed with ADR C-ter/pSB1A3. All present the right profile of digestion. This experiment therefore confirms the plasmid constructs.
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In order to avoid any risk of point mutation, sequencing is performed with the plasmid primer.
 +
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===Expression of the CMYC-6HIS-ADR and ADR-CMYC-6HIS recombinant proteins===
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After sequencing, induction is performed on the <i> E. coli</i> thermocompetent bacteria JM109. The objective is to verify if the cloned gene leads to the production of a protein. The expected size of the ADR protein is 40 kDa. A very strong expression of the ADR protein is observed at this size when the pBAD promoter is induced with arabinose. The gene has therefore been correctly cloned into the strain and the protein is produced.
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 +
<center>https://2019.igem.org/wiki/images/6/67/T--Poitiers--recombinantexpression_ADR-tab3.png<br>
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<strong>SDS Page 8% photography following the induction of JM109 with arabinose after 4 hours of culture.</strong><br> Coloring with coomassie blue. The lane 1 to 4 correspond to induce or non induce cultures transformed with ADR N-ter/pSB1A3. Lane 6 to 8 correspond to induce or non induce cultures transformed with ADR C-ter/pSB1A3.<br>
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NI : Not induced; I: Induced; M: Marker</center>
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The last step consist in evaluating the enzymatic activity of the protein in vitro.
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===Activity===
  
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Activity
 
  
 
===User Reviews===
 
===User Reviews===
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</div>

Latest revision as of 08:31, 21 October 2019


This experience page is provided so that any user may enter their experience using this part.
Please enter how you used this part and how it worked out.

Applications of BBa_K3038001

Manipulations

PCR amplification

Following the design of the synthetic gene, it is amplified by PCR thanks to the design of primers upstream and downstream of the sequence.

T--Poitiers--PCR_amplification_ADR-tab3.jpg
Electrophoresis photography following loads on agarose gel 0.8% of PCR products.
The migration was performed at 100 volts for 30 minutes in TAE 1X. The marker used during the migration is the NEB 1 kb Plus DNA Ladder. Lane 1 corresponds to the marker, lane 2 to the control without DNA, lane 3 to the amplified N-term ADR and lane 4 to the amplified C-term ADR.

The expected size of the fragment is about 1600 pb. The band obtained correspond to this size.

Enzymatic digestion

After amplification of the synthetic gene, sample is purified, the amplicons are digested with restriction enzymes EcoRI and PstI. Similarly for the cloning vector pSB1A3. The insert (N-term ADR or C-term) is then ligated into the plasmid.

T--Poitiers--electrophor%C3%A8se_gel4_tab4.png
Electrophoresis photography following loads on agarose gel 0.8% of enzymatic digestion products.
The migration was performed at 100 volts for 30 minutes in TAE 1X. The marker used during the migration is the NEB 1 kb Plus Ladder (left in the figure). Lane 1 corresponds to the marker, lane 2 to the digested N-term ADR, lane 3 to the digested C-term ADR and lane 4 to the digested pSB1A3 plasmid.

Ligation in pSB1A3

T--Poitiers--plasmid_construction_ADR-tab3.jpg
Design of ADR N-ter/pSB1A3 and ADR C-ter/pSB1A3 with Geneious software.
This map shows the pBAD promoter and its terminator flanking the coding sequence of the ADR protein. Also present in N-ter or C-ter are 6-His and c-myc tag. Finally, in the plasmid is present and ampicillin resistance cassette.

Cloning into E. coli Thermocompetent cells JM109

The thermocompetent E. coli JM109 bacteria are then transformed and clones are obtained.

T--Poitiers--culture_gauche2_tab4.png

Clones on a selective LB medium (+ ampicillin 100 µg/mL) following the transformation of E. coli thermocompetent cells with the pSB1A3-ADR ligations.
A: Clones obtained from pSB1A3 N-ter ADR ligations.

B: Clones obtained from the pSB1A3 C-ter ADR ligations.

PCR colony screening

After bacterial transformation, colony PCR is performed with the forward primer of the ADR gene and a reverse primer of the plasmid. 12 clones of each condition (ADR N-ter/pSB1A3 and ADR C-ter/pSB1A3) are tested. The PCR products are loaded on 0.8% agarose gel.

T--Poitiers--electrophor%C3%A8se_gel5_tab4.png
Electrophoresis photography following loads on agarose gel 0.8% of colony PCR products.
The migration was performed at 100 volts for 30 minutes in TAE 1X. The marker used during the migration is the NEB 1 kb Plus Ladder (in the center on the figure). Lane 1 to 12 corresponds to colony PCR performed on ADR N-ter/pSB1A3 ligation, lane 13 to 24 corresponds to colony PCR performed on ADR C-ter/pSB1A3.

Clones 4, 5, 10, 11 and 12 have the right profile, an insert-vector fragment of 1800 pb. Wells 13 to 24 show PCR products on clones transformed with ADR C-ter/pSB1A3. Clones 13, 21 and 22 have the right profile, an insert-vector fragment of 1800 pb.

Control enzymatic digestion

Clones with the right profile are returned to liquid culture and minipreparations are performed. Enzymatic digestion is carried out with BamHI and PstI restriction enzymes. The expected band sizes are 2300 and 1400 pb.

T--Poitiers--electrophor%C3%A8se_gel6_tab4.png
Electrophoresis photography following loads on agarose gel 0.8% of enzymatic digestion products by BamHI and PstI.
The migration was performed at 100 volts for 30 minutes in TAE 1X. The marker used during the migration is the NEB 1 kb Plus Ladder (left in the figure). Lane 1 to 5 corresponds to enzymatic digestion product of ADR N-ter/pSB1A3, lane 7 to 9 corresponds to enzymatic digestion product of ADR C-ter/pSB1A3.

Wells 1 to 5 comprise clones 4, 5, 10, 11 and 12 transformed with ADR N-ter/pSB1A3. Wells 7 to 9 contain clones 13, 21 and 23 transformed with ADR C-ter/pSB1A3. All present the right profile of digestion. This experiment therefore confirms the plasmid constructs. In order to avoid any risk of point mutation, sequencing is performed with the plasmid primer.

Expression of the CMYC-6HIS-ADR and ADR-CMYC-6HIS recombinant proteins

After sequencing, induction is performed on the E. coli thermocompetent bacteria JM109. The objective is to verify if the cloned gene leads to the production of a protein. The expected size of the ADR protein is 40 kDa. A very strong expression of the ADR protein is observed at this size when the pBAD promoter is induced with arabinose. The gene has therefore been correctly cloned into the strain and the protein is produced.

T--Poitiers--recombinantexpression_ADR-tab3.png

SDS Page 8% photography following the induction of JM109 with arabinose after 4 hours of culture.
Coloring with coomassie blue. The lane 1 to 4 correspond to induce or non induce cultures transformed with ADR N-ter/pSB1A3. Lane 6 to 8 correspond to induce or non induce cultures transformed with ADR C-ter/pSB1A3.

NI : Not induced; I: Induced; M: Marker

The last step consist in evaluating the enzymatic activity of the protein in vitro.

Activity

User Reviews

UNIQcf923a5cffaba028-partinfo-00000000-QINU UNIQcf923a5cffaba028-partinfo-00000001-QINU