Biomod/2013/Waterloo: Difference between revisions
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#Add 2.5 uL of 100 mM EDTA to the PCR tube | #Add 2.5 uL of 100 mM EDTA to the PCR tube | ||
#Vortex the PCR tube for 30 seconds | #Vortex the PCR tube for 30 seconds | ||
Determine A260 of each strand using the spectrophotometer using Oligocalc (http://www.basic.northwestern.edu/biotools/OligoCalc.html) and the sequence of the strand, determine the concentration of the strand. The concentration of each strand in the PCR tube must be 50nM. Add a volume of the DNA working stock to the PCR tube equal to the | #Determine A260 of each strand using the spectrophotometer using Oligocalc (http://www.basic.northwestern.edu/biotools/OligoCalc.html) and the sequence of the strand, determine the concentration of the strand. The concentration of each strand in the PCR tube must be 50nM. Add a volume of the DNA working stock to the PCR tube equal to the table below. | ||
#Close the PCR tube, tap down any droplets that may be on the sides of the container and vortex for one minute | |||
#Open the PCR machine and place the PCR tube inside any of the compartments | |||
#Close the PCR machine, go to the computer and run qCycle.exe | |||
#Press the Load/Edit button and open the appropriate walker synthesis script, depending on the cooling duration requirements for that trial | |||
#Press Start Program | |||
#Enter 100 uL into the text box when prompted for the solution volume | |||
#Allow the PCR machine to run. This process will take a variable amount of time, depending on the length of the cooling process. | |||
{| class="wikitable" | {| class="wikitable" |
Revision as of 08:21, 26 October 2013
Video
Movie:http://www.youtube.com/watch?v=a7fymvFQ0CQ Kristopher hurry up.
Required Materials
- 1M Tris-HCl, pH 7.5
- 0.5M Acetic Acid
- 100mM EDTA
- 100mM Magnesium Acetate
- DNA Working Stocks (~1uM): Walker-{1-7}
- 1x 200uL PCR tube
Procedure
- Remove DNA working stocks from the freezer and allow them to thaw
- Prepare the buffer:
- Add 49.5 uL of milli-Q water to the PCR tube
- Add 12.5 uL (6+6.5uL) of 100mM Magnesium Acetate to the PCR tube
- Add 4 uL of 1M Tris-HCl to the PCR tube
- Add 4 uL of 500 mM Acetic Acid to the PCR tube
- Add 2.5 uL of 100 mM EDTA to the PCR tube
- Vortex the PCR tube for 30 seconds
- Determine A260 of each strand using the spectrophotometer using Oligocalc (http://www.basic.northwestern.edu/biotools/OligoCalc.html) and the sequence of the strand, determine the concentration of the strand. The concentration of each strand in the PCR tube must be 50nM. Add a volume of the DNA working stock to the PCR tube equal to the table below.
- Close the PCR tube, tap down any droplets that may be on the sides of the container and vortex for one minute
- Open the PCR machine and place the PCR tube inside any of the compartments
- Close the PCR machine, go to the computer and run qCycle.exe
- Press the Load/Edit button and open the appropriate walker synthesis script, depending on the cooling duration requirements for that trial
- Press Start Program
- Enter 100 uL into the text box when prompted for the solution volume
- Allow the PCR machine to run. This process will take a variable amount of time, depending on the length of the cooling process.
Strand-ID | Volume (μL) |
---|---|
Walker 1 | 3.9 |
Walker 2 | 5.3 |
Walker 3 | 4.3 |
Walker 4 | 3.3 |
Walker 5 | 3.9 |
Walker 6 | 3.9 |
Walker 6 | 2.9 |