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Team:Hannover/Protocols/Cloning/EMP
From 2014.igem.org
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<h1><a href="https://2014.igem.org/Team:Hannover/Protocols" target="_blank">Protocols</a> / Exponential Megaprimer PCR (EMP)</h1> | <h1><a href="https://2014.igem.org/Team:Hannover/Protocols" target="_blank">Protocols</a> / Exponential Megaprimer PCR (EMP)</h1> | ||
| - | <p class="text">The exponential megaprimer PCR (EMP) was used to replace the metal-binding-related sequences of our pORE-E3_2x35S_T4MBP by GFP. In theory, the EMP is based on two PCR reaction: | + | <p class="text">The exponential megaprimer PCR (EMP) was used to replace the metal-binding-related sequences of our pORE-E3_2x35S_T4MBP by GFP. In theory, the EMP is based on two PCR reaction: while the insert is amplified by a standard PCR in the first (EMP1), the second places the insert in the final vector backbone already (EMP2). To try different weight ratios of vector backbone and megaprimer turned out be helpful in prior experiments (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053360">Jung et. al., 2012)</a>). Since a correct nucleotide sequence was important here, the F-530 Phusion® High-Fidelity DNA Polymerase (Thermo Scientific) was used. </p> |
<h2>Workflow</h2><p class="text"><ol><li>Isolate both the source and final vector.<li>Use a <a href="https://2014.igem.org/Team:Hannover/Protocols/Cloning/PCR">standard PCR</a> to add single-stranded 3´end overhangs to the megaprimer and dilute the purified product 1:10 before using it for the final EMP reaction.<li>Test different weight ratios of Vector:Megaprimer for the best EMP (Table 1).<ul><li>Test different ratios of insert and vector DNA amounts. We recommend to <u>test five mixes</u> including: 10 ng of megaprimer, 20 ng of megaprimer, two mixes lacking the F1 oligonucleotide but containing 80 and 160 ng of megaprimer respectively and a last one containing F1 as well as 160 ng of megaprimer.</li></ul><li>Modify the EMP2 product.<ul><li>Phosphorylate its 5´ends (Table 2)</li><li>Circularize the EMP2 product by adding 1 µl ATP and 1 µl T4 DNA Ligase. Incubate the mix at 16 °C overnight and inactivate the enzyme for 10 min at 80 °C.</li><li>Degrade the source vector by adding 1 µl of DpnI. Incubate the mix for 15 min at 37 °C and inactivate the enzyme for 15 min at 80 °C.</li></ul><li>Transferthe EMP product into <a href="https://2014.igem.org/Team:Hannover/Protocols/Transformation/E.coli_Heatshock">competent bacteria</a>.</ol></p> | <h2>Workflow</h2><p class="text"><ol><li>Isolate both the source and final vector.<li>Use a <a href="https://2014.igem.org/Team:Hannover/Protocols/Cloning/PCR">standard PCR</a> to add single-stranded 3´end overhangs to the megaprimer and dilute the purified product 1:10 before using it for the final EMP reaction.<li>Test different weight ratios of Vector:Megaprimer for the best EMP (Table 1).<ul><li>Test different ratios of insert and vector DNA amounts. We recommend to <u>test five mixes</u> including: 10 ng of megaprimer, 20 ng of megaprimer, two mixes lacking the F1 oligonucleotide but containing 80 and 160 ng of megaprimer respectively and a last one containing F1 as well as 160 ng of megaprimer.</li></ul><li>Modify the EMP2 product.<ul><li>Phosphorylate its 5´ends (Table 2)</li><li>Circularize the EMP2 product by adding 1 µl ATP and 1 µl T4 DNA Ligase. Incubate the mix at 16 °C overnight and inactivate the enzyme for 10 min at 80 °C.</li><li>Degrade the source vector by adding 1 µl of DpnI. Incubate the mix for 15 min at 37 °C and inactivate the enzyme for 15 min at 80 °C.</li></ul><li>Transferthe EMP product into <a href="https://2014.igem.org/Team:Hannover/Protocols/Transformation/E.coli_Heatshock">competent bacteria</a>.</ol></p> | ||
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<tr><td> ~</td><td>megaprimer</td></tr> | <tr><td> ~</td><td>megaprimer</td></tr> | ||
<tr><td>0.20</td><td>Phusion® High-Fidelity DNA Polymerase</td></tr> | <tr><td>0.20</td><td>Phusion® High-Fidelity DNA Polymerase</td></tr> | ||
| - | <tr><td> ~</td><td>template</td></tr><tr><td colspan="2">ad 20 µl H2O</td></tr></table></td><td> | + | <tr><td> ~</td><td>20-50 ng template</td></tr><tr><td colspan="2">ad 20 µl H2O</td></tr></table></td><td> |
<table colspan="2" ><tr><td><b>Cylcer Program</b></td></tr><tr><td>Step</td><td>Temperature [°C]</td><td>Time [min]</td><td>Cycle no.</td></tr><tr><td>1.</td><td>98</td><td>2.0</td><td>1</td></tr><tr><td>2.</td><td>98</td><td>0.5</td><td>35</td></tr><tr><td>3.</td><td>TA</td><td>0.5</td><td>35</td></tr> | <table colspan="2" ><tr><td><b>Cylcer Program</b></td></tr><tr><td>Step</td><td>Temperature [°C]</td><td>Time [min]</td><td>Cycle no.</td></tr><tr><td>1.</td><td>98</td><td>2.0</td><td>1</td></tr><tr><td>2.</td><td>98</td><td>0.5</td><td>35</td></tr><tr><td>3.</td><td>TA</td><td>0.5</td><td>35</td></tr> | ||
<tr><td>4.</td><td>72</td><td>-</td><td>35</td></tr></table></td></tr></table></td></tr></table> | <tr><td>4.</td><td>72</td><td>-</td><td>35</td></tr></table></td></tr></table></td></tr></table> | ||
Revision as of 21:10, 15 October 2014
Protocols / Exponential Megaprimer PCR (EMP)
The exponential megaprimer PCR (EMP) was used to replace the metal-binding-related sequences of our pORE-E3_2x35S_T4MBP by GFP. In theory, the EMP is based on two PCR reaction: while the insert is amplified by a standard PCR in the first (EMP1), the second places the insert in the final vector backbone already (EMP2). To try different weight ratios of vector backbone and megaprimer turned out be helpful in prior experiments (Jung et. al., 2012)). Since a correct nucleotide sequence was important here, the F-530 Phusion® High-Fidelity DNA Polymerase (Thermo Scientific) was used.
Workflow
- Isolate both the source and final vector.
- Use a standard PCR to add single-stranded 3´end overhangs to the megaprimer and dilute the purified product 1:10 before using it for the final EMP reaction.
- Test different weight ratios of Vector:Megaprimer for the best EMP (Table 1).
- Test different ratios of insert and vector DNA amounts. We recommend to test five mixes including: 10 ng of megaprimer, 20 ng of megaprimer, two mixes lacking the F1 oligonucleotide but containing 80 and 160 ng of megaprimer respectively and a last one containing F1 as well as 160 ng of megaprimer.
- Modify the EMP2 product.
- Phosphorylate its 5´ends (Table 2)
- Circularize the EMP2 product by adding 1 µl ATP and 1 µl T4 DNA Ligase. Incubate the mix at 16 °C overnight and inactivate the enzyme for 10 min at 80 °C.
- Degrade the source vector by adding 1 µl of DpnI. Incubate the mix for 15 min at 37 °C and inactivate the enzyme for 15 min at 80 °C.
- Transferthe EMP product into competent bacteria.
Table 1: EMP Mixes and Temperature Program
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Table 2: Phosphorylation Mix and Temperature Program
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