Difference between revisions of "Team:Pasteur Paris/Experiments"
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<img src="https://static.igem.org/mediawiki/2015/c/c5/Experiments_%26_Protocols_pasteur2015.jpg" style="width: 100%;"/> | <img src="https://static.igem.org/mediawiki/2015/c/c5/Experiments_%26_Protocols_pasteur2015.jpg" style="width: 100%;"/> | ||
− | <p> | + | |
+ | <h3> Polymerase Chain Reaction </h3> | ||
+ | |||
+ | <h4> 1) PCR Amplification using Takara <i>Ex Taq</i> DNA polymerase</h4> | ||
+ | <p> | ||
+ | <ul> | ||
+ | <li>In a 0.2ml tube, set up the following reaction: tableau | ||
+ | </li> | ||
+ | <li> Set up the following cycles in a PCR machine | ||
+ | <ul> | ||
+ | <li>Initial denaturation : 94°C for 30 sec</li> | ||
+ | <li>30 cycles : </li> | ||
+ | <ul><li> 94°C for 30s</li> | ||
+ | <li>55°C - 65°C for 1 min depending on your annealing temperature</li> | ||
+ | <li>72°C 0.5-1 min per kb</li></ul> | ||
+ | <li> Final extension: 72°C for 5min.</li> | ||
+ | </ul> | ||
+ | </ul> | ||
+ | </p> | ||
+ | |||
+ | <p> | ||
+ | <h4> 2) PCR Amplification using Phusion DNA polymerase</h4> | ||
+ | <p> | ||
+ | <ul> | ||
+ | <li>In a 0.2ml tube, set up the following reaction: tableau | ||
+ | </li> | ||
+ | <li> Set up the following cycles in a PCR machine | ||
+ | <ul> | ||
+ | <li>Initial denaturation : 98°C for 30 sec</li> | ||
+ | <li>30 cycles : </li> | ||
+ | <ul><li> 94°C for 5-10s</li> | ||
+ | <li>45°C - 72°C for 10 to 30s depending on your annealing temperature</li> | ||
+ | <li>72°C for 15-30s per kb</li></ul> | ||
+ | <li> Final extension: 72°C for 5min.</li> | ||
+ | </ul> | ||
+ | </ul> | ||
+ | </p> | ||
+ | |||
+ | <p> | ||
+ | <h4>3) PCR Amplification using Q5 High Fidelity Master Mix DNA polymerase</h4> | ||
+ | <p> | ||
+ | <ul> | ||
+ | <li>In a 0.2ml tube, set up the following reaction: tableau | ||
+ | </li> | ||
+ | <li> Set up the following cycles in a PCR machine | ||
+ | <ul> | ||
+ | <li>Initial denaturation : 98°C for 30 sec</li> | ||
+ | <li>30 cycles : </li> | ||
+ | <ul><li> 94°C for 5-10s</li> | ||
+ | <li> 45°C - 72°C for 10 to 30s depending on your annealing temperature</li> | ||
+ | <li>72°C for 20-30s per kb</li></ul> | ||
+ | <li> Final extension: 72°C for 2min.</li> | ||
+ | </ul> | ||
+ | </ul> | ||
+ | </p> | ||
+ | |||
+ | <h3> Enzymatic Digestion </h3> | ||
+ | <h4> 1) Single restriction enzyme digestion</h4> | ||
+ | <p> | ||
+ | <ul> | ||
+ | <li>In a MicroCentrifuge tube, set up the following reaction on ice: tableau | ||
+ | </li> | ||
+ | <li>Pipette up and down to homogenize the solution.</li> | ||
+ | <li>Quick spin in a MicroCentrifuge (5s).</li> | ||
+ | <li>Incubation at 37°C for 1h.</li> | ||
+ | <li>Heat inactivation for 20min at 80°C.</li> | ||
+ | <b>Optional</b> | ||
+ | <li>Add the phosphatase: Add 1 unit of Shrimp Alkaline Phosphatase for each pmol of phosphate end.</li> | ||
+ | <li>Incubate for 30min at 37°C. </li> | ||
+ | <li>Inactivate the phosphatase at 65°C for 15 min. </li> | ||
+ | </ul> | ||
+ | </p> | ||
+ | |||
+ | <h4> 2) Double digestion</h4> | ||
+ | <p> | ||
+ | <ul> | ||
+ | <li>In a MicroCentrifuge tube, set up the following reaction on ice: tableau | ||
+ | </li> | ||
+ | <li>Pipette up and down to homogenize the solution.</li> | ||
+ | <li>Quick spin in a MicroCentrifuge (5s).</li> | ||
+ | <li>Incubation at 37°C for 1h.</li> | ||
+ | <li>Heat inactivation for 20min at 80°C.</li> | ||
+ | <b>Optional</b> | ||
+ | <li>Add the phosphatase: Add 1 unit of Shrimp Alkaline Phosphatase for each pmol of phosphate end.</li> | ||
+ | <li>Incubate for 30min at 37°C. </li> | ||
+ | <li>Inactivate the phosphatase at 65°C for 15 min. </li> | ||
+ | </ul> | ||
+ | </p> | ||
+ | |||
+ | <h5> Ligation</h5> | ||
+ | <p> | ||
+ | <ul> | ||
+ | <li>Thaw the T4 DNA Ligase Buffer and DNA at room temperature.</li> | ||
+ | <li> Set up the following reaction in a microcentrifuge tube on ice : tableau </li> | ||
+ | <li> Gently mix the reaction by pipetting up and down</li> | ||
+ | <li>Quick spin in a MicroCentrifuge (5s).</li> | ||
+ | <li>For cohesive ends, incubation at 16°C for 1h.</li> | ||
+ | <li>Heat inactivation for 10min at 65°C.</li> | ||
+ | </ul> | ||
+ | </p> | ||
+ | |||
+ | <h3> MiniPrep </h3> | ||
+ | <h4> 1) Bacterial Culture Growth</h4> | ||
+ | <p> | ||
+ | <ul> | ||
+ | <li> Pick a single colony from a freshly streaked selective plate and inoculate a culture of 1–5 ml LB medium containing the appropriate selective antibiotic.</li> | ||
+ | <li> Incubate for 12–16 h at 37°C with vigorous shaking. </li> | ||
+ | <li>Centrifugation at > 8000 rpm (6800 x g) in MicroCentrifuge for 3 min at room temperature (15–25°C).</li> | ||
+ | <li> Remove all traces of supernatant by inverting the open centrifuge tube until all medium has been drained. </li> | ||
+ | </ul> | ||
+ | </p> | ||
+ | |||
+ | <h4> 2) Plasmid purification</h4> | ||
+ | <p> | ||
+ | <ul> | ||
+ | <li>Resuspend pelleted bacterial cells in 250 μl Buffer P1 and transfer to a micro- centrifuge tube.</li> | ||
+ | <li>Add 250 μl Buffer P2 and mix thoroughly by inverting the tube 4–6 times. </li> | ||
+ | <li>Add 350 μl Buffer N3 and mix immediately and thoroughly by inverting the tube 4–6 times. </li> | ||
+ | <li>Centrifuge for 10 min at 13,000 rpm in a MicroCentrifuge. </li> | ||
+ | <li>Apply the supernatants to the QIAprep spin column by decanting or pipetting.</li> | ||
+ | <li>Centrifuge for 30–60 s. Discard the flow-through. </li> | ||
+ | <li>Recommended: Wash the QIAprep spin column by adding 0.5 ml Buffer PB and centrifuging for 30–60 s. Discard the flow-through. </li> | ||
+ | <li>Add 0.75 ml Buffer PE and centrifuge for 30–60 s. </li> | ||
+ | <li>Discard the flow-through, and centrifuge at full speed for an additional 1 min. </li> | ||
+ | <li>Place the QIAprep column in a clean 1.5 ml microcentrifuge tube. </li> | ||
+ | <li>Add 50 μl Buffer EB (10 mM Tris·Cl, pH 8.5) or water to the center of each QIAprep spin column. </li> | ||
+ | <li>Let stand for 1 min. </li> | ||
+ | <li>Centrifuge for 1 min. </li> | ||
+ | </ul> | ||
+ | </p> | ||
+ | |||
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Revision as of 12:57, 18 September 2015
Polymerase Chain Reaction
1) PCR Amplification using Takara Ex Taq DNA polymerase
- In a 0.2ml tube, set up the following reaction: tableau
- Set up the following cycles in a PCR machine
- Initial denaturation : 94°C for 30 sec
- 30 cycles :
- 94°C for 30s
- 55°C - 65°C for 1 min depending on your annealing temperature
- 72°C 0.5-1 min per kb
- Final extension: 72°C for 5min.
2) PCR Amplification using Phusion DNA polymerase
- In a 0.2ml tube, set up the following reaction: tableau
- Set up the following cycles in a PCR machine
- Initial denaturation : 98°C for 30 sec
- 30 cycles :
- 94°C for 5-10s
- 45°C - 72°C for 10 to 30s depending on your annealing temperature
- 72°C for 15-30s per kb
- Final extension: 72°C for 5min.
3) PCR Amplification using Q5 High Fidelity Master Mix DNA polymerase
- In a 0.2ml tube, set up the following reaction: tableau
- Set up the following cycles in a PCR machine
- Initial denaturation : 98°C for 30 sec
- 30 cycles :
- 94°C for 5-10s
- 45°C - 72°C for 10 to 30s depending on your annealing temperature
- 72°C for 20-30s per kb
- Final extension: 72°C for 2min.
Enzymatic Digestion
1) Single restriction enzyme digestion
- In a MicroCentrifuge tube, set up the following reaction on ice: tableau
- Pipette up and down to homogenize the solution.
- Quick spin in a MicroCentrifuge (5s).
- Incubation at 37°C for 1h.
- Heat inactivation for 20min at 80°C. Optional
- Add the phosphatase: Add 1 unit of Shrimp Alkaline Phosphatase for each pmol of phosphate end.
- Incubate for 30min at 37°C.
- Inactivate the phosphatase at 65°C for 15 min.
2) Double digestion
- In a MicroCentrifuge tube, set up the following reaction on ice: tableau
- Pipette up and down to homogenize the solution.
- Quick spin in a MicroCentrifuge (5s).
- Incubation at 37°C for 1h.
- Heat inactivation for 20min at 80°C. Optional
- Add the phosphatase: Add 1 unit of Shrimp Alkaline Phosphatase for each pmol of phosphate end.
- Incubate for 30min at 37°C.
- Inactivate the phosphatase at 65°C for 15 min.
Ligation
- Thaw the T4 DNA Ligase Buffer and DNA at room temperature.
- Set up the following reaction in a microcentrifuge tube on ice : tableau
- Gently mix the reaction by pipetting up and down
- Quick spin in a MicroCentrifuge (5s).
- For cohesive ends, incubation at 16°C for 1h.
- Heat inactivation for 10min at 65°C.
MiniPrep
1) Bacterial Culture Growth
- Pick a single colony from a freshly streaked selective plate and inoculate a culture of 1–5 ml LB medium containing the appropriate selective antibiotic.
- Incubate for 12–16 h at 37°C with vigorous shaking.
- Centrifugation at > 8000 rpm (6800 x g) in MicroCentrifuge for 3 min at room temperature (15–25°C).
- Remove all traces of supernatant by inverting the open centrifuge tube until all medium has been drained.
2) Plasmid purification
- Resuspend pelleted bacterial cells in 250 μl Buffer P1 and transfer to a micro- centrifuge tube.
- Add 250 μl Buffer P2 and mix thoroughly by inverting the tube 4–6 times.
- Add 350 μl Buffer N3 and mix immediately and thoroughly by inverting the tube 4–6 times.
- Centrifuge for 10 min at 13,000 rpm in a MicroCentrifuge.
- Apply the supernatants to the QIAprep spin column by decanting or pipetting.
- Centrifuge for 30–60 s. Discard the flow-through.
- Recommended: Wash the QIAprep spin column by adding 0.5 ml Buffer PB and centrifuging for 30–60 s. Discard the flow-through.
- Add 0.75 ml Buffer PE and centrifuge for 30–60 s.
- Discard the flow-through, and centrifuge at full speed for an additional 1 min.
- Place the QIAprep column in a clean 1.5 ml microcentrifuge tube.
- Add 50 μl Buffer EB (10 mM Tris·Cl, pH 8.5) or water to the center of each QIAprep spin column.
- Let stand for 1 min.
- Centrifuge for 1 min.
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