Difference between revisions of "PhiX:Mutagenesis"
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| + | '''This protocol is now superseded - UPDATE SOON'''<br> | ||
| + | ''With credit to Bentley Fane and Maniartis.'' | ||
| + | |||
==Step 1: Primer phosphorylation== | ==Step 1: Primer phosphorylation== | ||
We phosphorylate 200pmol primer (Fane carries this out in 2ul reaction mixture): | We phosphorylate 200pmol primer (Fane carries this out in 2ul reaction mixture): | ||
* 2ul 100uM primer | * 2ul 100uM primer | ||
| − | * | + | * 2ul 10mM ATP |
| − | * | + | * 2ul T4 ligase buffer |
| − | * | + | * 1ul 10U/ul T4 polynucleotide kinase |
| − | -> 37<sup>o</sup>C for 30 minutes | + | * 13ul water |
| + | -> 37<sup>o</sup>C for 30 minutes. | ||
==Step 2: Relax secondary structure and anneal== | ==Step 2: Relax secondary structure and anneal== | ||
| − | We add 10pmol of phosphorylated primer to 0.5pmol ssDNA in ligase buffer (Fane uses [[PhiX:Recipes|PE1 buffer]] | + | We add 10pmol of phosphorylated primer to 0.5pmol ssDNA in ligase buffer (Fane uses [[PhiX:Recipes|PE1 buffer]]). Start boiling water in a bowl using tripod arrangement. Meanwhile to each tube add: |
| − | * 2ul ssDNA diluted 1/100, 1/10, or 1 times | + | * 2ul ssDNA diluted 1/100, 1/10, or 1 times (SHOULD PURIFY BAND) |
| − | * 1ul | + | * 1ul phosphorylated primer mix (above) |
| − | * | + | * 6ul water |
| − | * 1ul ligase buffer | + | * 1ul T4 ligase buffer |
| − | When water is boiled, remove | + | When water is boiled, remove bowl from heat and immerse tubes in it. Store bowl (with tubes) in cold room or fridge (+4<sup>o</sup>C) for 40 minutes to 1 hour. |
==Step 3: Non-gapped extension reaction== | ==Step 3: Non-gapped extension reaction== | ||
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Reaction kept on ice for 5 minutes, room temperature for 5 minutes, then two hours at 37<sup>o</sup>C. After which the reaction may be frozen. | Reaction kept on ice for 5 minutes, room temperature for 5 minutes, then two hours at 37<sup>o</sup>C. After which the reaction may be frozen. | ||
| + | ==Step 4: Prepare for transformation== | ||
Fane uses 2ul of 1/10 dilution of this for transformation into 100ul competent cells. Transformation efficiency improved by O/N storage. | Fane uses 2ul of 1/10 dilution of this for transformation into 100ul competent cells. Transformation efficiency improved by O/N storage. | ||
Latest revision as of 19:19, 6 August 2013
This protocol is now superseded - UPDATE SOON
With credit to Bentley Fane and Maniartis.
Contents
Step 1: Primer phosphorylation
We phosphorylate 200pmol primer (Fane carries this out in 2ul reaction mixture):
- 2ul 100uM primer
- 2ul 10mM ATP
- 2ul T4 ligase buffer
- 1ul 10U/ul T4 polynucleotide kinase
- 13ul water
-> 37oC for 30 minutes.
Step 2: Relax secondary structure and anneal
We add 10pmol of phosphorylated primer to 0.5pmol ssDNA in ligase buffer (Fane uses PE1 buffer). Start boiling water in a bowl using tripod arrangement. Meanwhile to each tube add:
- 2ul ssDNA diluted 1/100, 1/10, or 1 times (SHOULD PURIFY BAND)
- 1ul phosphorylated primer mix (above)
- 6ul water
- 1ul T4 ligase buffer
When water is boiled, remove bowl from heat and immerse tubes in it. Store bowl (with tubes) in cold room or fridge (+4oC) for 40 minutes to 1 hour.
Step 3: Non-gapped extension reaction
We add ATP to 1mM, dNTPs to 0.5mM, 4 Weiss Units ligase, 2U polymerase in ligase buffer to 20ul (Fane uses PE1 buffer). The following is added to each tube (error here unless 10ul in previous):
- 1ul ligase buffer
- 2ul 10mM ATP
- 1ul 2mM (each) dNTPs
- 3.3ul water
- 0.7ul 3U/ul T4 DNA polymerase
- 2ul 2U/ul (400 c.e.u.s) T4 DNA ligase
Reaction kept on ice for 5 minutes, room temperature for 5 minutes, then two hours at 37oC. After which the reaction may be frozen.
Step 4: Prepare for transformation
Fane uses 2ul of 1/10 dilution of this for transformation into 100ul competent cells. Transformation efficiency improved by O/N storage.
From Fane: We incubate the transformation mixtures for 30 minutes on ice, heat shock for 1 minute at 42oC, then ice again for 5 minutes, and then we plate. This typically gives us 200 plaques per plate.
The repair can go either way in the cells, so you will need a way to either directly select for your mutant, or an efficient way to screen the plaques by toothpicking into indicator lawns.
