Team:EPF-Lausanne/Protocols/TetR

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{{:Team:EPF-Lausanne/Templates/Header|title=Linear template- TetR}}
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{{:Team:EPF-Lausanne/Templates/ProtocolHeader|title=Linear template- TetR}}
Two step extension PCR
Two step extension PCR
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*0.5 µl Polymerase
*0.5 µl Polymerase
*36.5 µl H2O
*36.5 µl H2O
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Primers:
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TetR Forward: CTC GAG AAT TCG CCA CCA TGT CCA GAT TAG ATA AAA GTA AAG ; <b>Tm=62.6ºC</b>
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TetR-His6 Reverse: GTA GCA GCC TGA GTC GTT ATT AAT GAT GAT GAT GAT GAT GAG AAC CCC CAG ACC CAC TTT CAC ATT TAA G ; <b>Tm=68.5 ºC </b>
== PCR Cycle (30 cycles) ==
== PCR Cycle (30 cycles) ==
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<b>1.</b> 98°C for 30s
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:<b>1.</b> 98°C for 30s
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<b>2.</b> 98°C for 7.5 seconds
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:<b>2.</b> 98°C for 7.5 seconds
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<b>3.</b> 58°C for 20 sec (this depends on the primers,  
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:<b>3.</b> 58°C for 20 sec (this depends on the primers,  
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therefore look up the annealing temperature of the primers used)
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therefore look up the annealing temperature of the primers used
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<b>4.</b> 72°C for 15 sec; you have to calculate the time required.
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:<b>4.</b> 72°C for 15 sec; you have to calculate the time required.
This polymerase has an effciency of 15-30s/kb.(calculate for the longest fragment)  
This polymerase has an effciency of 15-30s/kb.(calculate for the longest fragment)  
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<b>5.</b> 72°C for 5 min
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:<b>5.</b> 72°C for 5 min
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<b>6.</b> 4°C "forever"
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:<b>6.</b> 4°C "forever"
*Save the file in the MAIN folder→ OK→ SAVE→RUN→Select the block you use→ RUN→ Change sample volume to 50µl, LidT should be 105°C and the box just below ("hotlid") should ALWAYS be checked
*Save the file in the MAIN folder→ OK→ SAVE→RUN→Select the block you use→ RUN→ Change sample volume to 50µl, LidT should be 105°C and the box just below ("hotlid") should ALWAYS be checked
*Press STATUS to check the progress
*Press STATUS to check the progress
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== <b>Extension PCR</b> ==
== <b>Extension PCR</b> ==
== Materials ==
== Materials ==
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* 10µl 5x iProof HF buffer
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* 0.5 µl of each extension primer@500nM
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* 1 µl dNTP mix of 10mM
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* 0.5 µl High Fidelity Polymerase
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* 1 µl of gene specific PCR product from previous step
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* 0.5 µl Polymerase
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* 36.5 µl H2O
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* Gene PCR product
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Extension Primers:
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* Extension primers 500nM
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== PCR Cycle (30 cycles) ==
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Forward: GAT CTT AAG GCT AGA GTA CTA ATA CGA CTC ACT ATA GGG AAT ACA AGC TAC TTG TTC TTT TTG CAC TCG AGA ATT CGC CAC C <b>Tm=68.4 ºC</b>
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<b>1.</b> 98°C for 30s
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Reverse: CAA AAA ACC CCT CAA GAC CCG TTT AGA GGC CCC AAG GGG TTA TGC TAG TTT TTT TTT TTT TTT TTT TTT TTT TTT TTT GTA GCA GCC TGA GTC G; <b>Tm=70.4ºC</b>
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<b>2.</b> 98°C for 7.5 seconds
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<b>3.</b> 58°C for 20 sec
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<b>4.</b> 72°C for 15 sec;  
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(calculate for the longest fragment)
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<b>5.</b> 72°C for 5 min
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<b>6.</b> 4°C "forever"
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== PCR Cycle (10 cycles) ==
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:<b>1.</b> 98°C for 30s
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:<b>2.</b> 98°C for 7.5 seconds
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:<b>3.</b> 58°C for 20 sec
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:<b>4.</b> 72°C for 15 sec;
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:<b>5.</b> 72°C for 5 min
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:<b>6.</b> 4°C "forever"
== Materials ==
== Materials ==
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* 1µl Final primers
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* 10µl 5x iProof HF buffer
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* 0.5 µl of each final primer @50µM/1µl of primer mix@1µM
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* 1 µl dNTP mix of 10mM
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* 0.5 µl High Fidelity Polymerase
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* 1 µl of previous PCR product(extension PCR)
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* 0.5 µl Polymerase
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* 36.5 µl H2O
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== PCR Cycle (10 cycles) ==
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Final primers
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Forward: GAT CTT AAG GCT AGA GTA C; <b>Tm=46.0ºC </b>
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Reverse: CAA AAA ACC CCT CAA GAC; <b>Tm=48.6ºC </b>
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== PCR Cycle (30 cycles) ==
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<b>1.</b> 98°C for 30s
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:<b>1.</b> 98°C for 30s
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<b>2.</b> 98°C for 7.5 seconds
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:<b>2.</b> 98°C for 7.5 seconds
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<b>3.</b> 58°C for 20 sec
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:<b>3.</b> 53°C for 20 sec
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<b>4.</b> 72°C for 15 sec; <b>5.</b> 72°C for 5 min
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:<b>4.</b> 72°C for 15 sec;  
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<b>6.</b> 4°C "forever"
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:<b>5.</b> 72°C for 5 min
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:<b>6.</b> 4°C "forever"
{{:Team:EPF-Lausanne/Templates/Footer}}
{{:Team:EPF-Lausanne/Templates/Footer}}

Latest revision as of 08:48, 15 July 2011