Team:ETH Zurich/lab/protocols

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(Materials)
(Multi site directed mutagenesis)
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===Multi site directed mutagenesis===
===Multi site directed mutagenesis===
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Single Primer Method
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This protocol only uses one oligo per mutation site (cuts the oligo cost in half) and can mutate more than one site at a time. While this protocol is less reliable than the previous protocol (only ~25% of colonies will contain the desired mutation(s)), if you're doing multiple mutations on the same piece of DNA than this can save you many days of work by just sequencing a few more colonies. In this protocol there is an initial Kinase (phosphorylation) reaction to allow your primers to be available for ligation. The polymerase will extend from one primer to another and then the Taq ligase will seal the nick. This allows multiple mutations to be done at the same time.
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Method
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1. Design mutagenesis primer(s).
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The targeted mutation should be in the middle of the primer
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Design your primers (including the mutations) to have a Tm >=78°C.
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2. Purify template plasmid from a dam+ E. coli strain via miniprep.
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3. Set up mutagenesis PCR mix:
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16 μL Water
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1.5 μL DMSO(100%)
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0.5 μL MgSO4(50 µM)
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10 μL Phusion HF Buffer
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5 μL T4 Ligase Buffer
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5 μL 10x Taq Ligase Buffer
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0.5 μL Each Mutagenesis Primer (at 40 µM)
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2 μL Reverse Biobrick Primer
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2 μL dNTPs
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2 μL Template
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2 μL PNK
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2 μL Taq Ligase
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1 μL Phusion Polymerase (hotstart)
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4. Run PCR
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37°C for 30 minutes (this is the kinase step)
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95°C for 3 minutes
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Run the following for 20 cycles:
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95°C for 1 minute
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55°C for 1 minute
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65°C for 30 sec/kb of plasmid length minimum
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4°C infinite
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5. Add 1μL DpnI restriction enzyme to the PCR tube directly. (Purification is not necessary)
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6. Incubate 4-6 hours at 37°C.
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7. Purify PCR product and elute into 30μL.
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8. Transform 3μL purified DNA into highly competent cells.
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9. Screen the transformants for the desired mutation using restriction digest or sequencing.
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Notes
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Because the inital kinase step could lead to non-specific binding, it would be best to use a hot-start polymerase for this procedure.
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Any combination of DMSO and MgSO4 has shown significant improvments in product.
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http://openwetware.org/wiki/Richard_Lab:Site_Directed_Mutagenesis
===Preparation of alginate beads===
===Preparation of alginate beads===

Revision as of 15:57, 10 October 2014

iGEM ETH Zurich 2014