Team:UIUC-Illinois/Notebook/Protocols/PCR

From 2012.igem.org

(Difference between revisions)
Line 72: Line 72:
<div id="protocoloverview">
<div id="protocoloverview">
-
<center><h1>PCR Protocols</h1></center>
+
<center><h1>PCR Protocols</h1></center><br/>
-
<h2>PCR</h2>
+
<h2>PCR</h2><br/>
-
What you need:
+
What you need:<br/>
-
A container of ice
+
- A container of ice<br/>
-
Small PCR tubes
+
- Small PCR tubes<br/>
-
Template DNA containing the gene of interest
+
- Template DNA containing the gene of interest<br/>
-
DNA primers designed to amplify the gene of interest
+
- DNA primers designed to amplify the gene of interest<br/>
-
Phusion DNA polymerase
+
- Phusion DNA polymerase<br/>
-
dNTP solution
+
- dNTP solution<br/>
-
DMSO (optional)
+
- DMSO (optional)<br/>
-
5X HF or GC buffer
+
- 5X HF or GC buffer<br/>
-
Autoclaved MilliQ water
+
- Autoclaved MilliQ water<br/><br/>
-
Procedure:
+
Procedure:<br/>
-
1. Keep all components on ice as you work
+
1. Keep all components on ice as you work<br/>
-
2. Label clearly one small PCR tube for each sample you wish to run.  
+
2. Label clearly one small PCR tube for each sample you wish to run. <br/>
-
3. For each sample, mix: 0.75 uL template DNA, 1uL each of the two primers, 0.5uL DNA polymerase, 1uL dNTPs, 1.5 uL DMSO (optional), 10uL 5X HF/CG buffer, 33.5 uL autoclaved water
+
3. For each sample, mix the following:<br/>
-
4. Use your pipet to mix thoroughly
+
- 0.75 uL template DNA<br/>
-
5. Load samples in the PCR machine and select the phusion protocol, using an extension time of roughly one minute per kb of DNA to be amplified. However – consult the bootcamp optimized PCR protocol if necessary.  
+
- 1uL each of the two primers<br/>
-
Note: When running PCR with the supermix use 25 uL of supermix, 1.5 uL of DMSO (optional), 0.5uL DNA polymerase, 1uL each of the two primers, 0.75 uL of template, and autoclaved water to 50uL volume.  
+
- 0.5uL DNA polymerase<br/>
 +
- 1uL dNTPs<br/>
 +
- 1.5 uL DMSO (optional)<br/>
 +
- 10uL 5X HF/CG buffer<br/>
 +
- 33.5 uL autoclaved water<br/><br/>
 +
4. Use your pipet to mix thoroughly<br/>
 +
5. Load samples in the PCR machine and select the phusion protocol, using an extension time of roughly one minute per kb of DNA to be amplified. However – consult the bootcamp optimized PCR protocol if necessary. <br/><br/>
 +
Note: When running PCR with the supermix use 25 uL of supermix, 1.5 uL of DMSO (optional), 0.5uL DNA polymerase, 1uL each of the two primers, 0.75 uL of template, and autoclaved water to 50uL volume. <br/><br/>
-
<h2>PCR Cleanup</h2>
+
<h2>PCR Cleanup</h2><br/>
-
What you need:
+
What you need:<br/>
-
Large Zymo-spin columns in collection tubes
+
- Large Zymo-spin columns in collection tubes<br/>
-
The completed PCR of interest
+
- The completed PCR of interest<br/>
-
DNA binding buffer
+
- DNA binding buffer<br/>
-
DNA wash buffer
+
- DNA wash buffer<br/>
-
DNA wash buffer
+
- DNA wash buffer<br/>
-
Autoclaved 1.5 mL centrifuge tubes
+
- Autoclaved 1.5 mL centrifuge tubes<br/>
-
Autoclaved MilliQ water
+
- Autoclaved MilliQ water<br/><br/>
-
Procedure:
+
Procedure:<br/><br/>
-
1. To the PCR liquid, add 2 volumes of DNA binding buffer
+
1. To the PCR liquid, add 2 volumes of DNA binding buffer<br/>
-
2. Mix briefly by pipetting and add all of the mixture to a large Zymo-spin column
+
2. Mix briefly by pipetting and add all of the mixture to a large Zymo-spin column<br/>
-
3. Centrifuge at full speed for 30 seconds
+
3. Centrifuge at full speed for 30 seconds<br/>
-
4. Discard the waste liquid in the collection tube
+
4. Discard the waste liquid in the collection tube<br/>
-
5. To the column, add 200 uL wash buffer
+
5. To the column, add 200 uL wash buffer<br/>
-
6. Centrifuge for 30 seconds and discard the waste liquid
+
6. Centrifuge for 30 seconds and discard the waste liquid<br/>
-
7. Repeat steps 5-6
+
7. Repeat steps 5-6<br/>
-
8. Centrifuge the empty column for 1 minute
+
8. Centrifuge the empty column for 1 minute<br/>
-
9. Replace the collection tube with 1.5 mL centrifuge tube
+
9. Replace the collection tube with 1.5 mL centrifuge tube<br/>
-
10. Gently add 30uL of autoclaved water to the column
+
10. Gently add 30uL of autoclaved water to the column<br/>
-
11. Let the column incubate at room temperature for 2 minutes
+
11. Let the column incubate at room temperature for 2 minutes<br/>
-
12. Centrifuge 1 minute
+
12. Centrifuge 1 minute<br/>
-
13. Discard the column  
+
13. Discard the column <br/>
-
14. Label the collected liquid and store it in the -20˚C freezer until use
+
14. Label the collected liquid and store it in the -20˚C freezer until use<br/><br/>
-
<h2>PCR Troubleshooting</h2>
+
<h2>PCR Troubleshooting</h2><br/>
-
Ran a diagnostic test to optimize buffer and temperature for the PCR. After doing the PCR (it’s nice to do this in linked PCR tubes) we run on a gel to test which worked
+
-
Buffers tested: GC + DMSO, HF + DMSO, GC, buffer G supermix + DMSO (3 tubes of each)
+
-
Made a master mix of primers, phusion, template DNA, and dNTPs. This was then used this for all the tubes of GC+DMSO, HF+DMSO, and GC.
+
-
Master Mix: 10 uL dNTP’s, 2 uL forward primers, 2 uL reverse primers, 2 uL template DNA, 1 uL phusion
+
-
GC + DMSO: 18 uL H2O, 6 uL GC buffer, 5.1 uL of master mix, 0.9 uL DMSO, now divide into 3 tubes (10 uL into each PCR tube)
+
-
HF + DMSO: 18 uL H2O, 6 uL HF buffer, 5.1 uL of master mix, 0.9 uL DMSO, now divide into 3 tubes (10 uL into each PCR tube)
+
-
GC: 18.9 uL H2O, 6 uL GC buffer, 5.1 uL master mix, now divide into 3 tubes (10 uL into each PCR tube)
+
-
Supermix: 15 uL buffer G, 12 uL H2O, 0.9 uL DMSO, 0.6 uL forward primer, 0.6 uL reverse primer, 0.6 uL template DNA, 0.3 uL phusion
+
-
PCR program:
+
-
1. 98 degrees Celsius for 3 minutes
+
-
2. 98 degrees C for 15 seconds
+
-
3. Temperature gradient 48-55-63 degrees for 30 seconds
+
-
4. 72 degrees C for 1 minute
+
-
5. Go to step 2, repeat 30 times
+
-
6. 72 degrees C for 5 minutes
+
-
Gel results: Only buffer G +DMSO works and it works at all temperatures.
+
 +
Ran a diagnostic test to optimize buffer and temperature for the PCR. After doing the PCR (it’s nice to do this in linked PCR tubes) we run on a gel to test which worked best.<br/><br/>
-
<h2>Optomized PCR</h2>
+
Buffers tested: GC + DMSO, HF + DMSO, GC, buffer G supermix + DMSO (3 tubes of each)<br/><br/>
-
Worked using buffer G +DMSO supermix at 63o C.  
+
 
-
Supermix (for three reactions. 10uL/rxn): 15 uL buffer G, 12 uL H2O, 0.9 uL DMSO, 0.6 uL forward primer, 0.6 uL reverse primer, 0.6 uL template DNA, 0.3 uL phusion  
+
Made a master mix of primers, phusion, template DNA, and dNTPs. This was then used this for all the tubes of GC+DMSO, HF+DMSO, and GC.<br/><br/>
-
PCR program (running time of just under 2 hours):  
+
-
1. 98 degrees Celsius for 3 minutes  
+
Master Mix: <br/>
-
2. 98 degrees C for 15 seconds  
+
- 10 uL dNTP’s<br/>
-
3. 63 degrees C for 30 seconds  
+
- 2 uL forward primers<br/>
-
4. 72 degrees C for 1 minute  
+
- 2 uL reverse primers<br/>
-
5. Go to step 2, repeat 30 times  
+
- 2 uL template DNA<br/>
-
6. 72 degrees C for 5 minutes  
+
- 1 uL phusion <br/><br/>
 +
 
 +
GC + DMSO: <br/>
 +
- 18 uL H2O<br/>
 +
- 6 uL GC buffer<br/>
 +
- 5.1 uL of master mix<br/>
 +
- 0.9 uL DMSO<br/>
 +
- now divide into 3 tubes (10 uL into each PCR tube) <br/><br/>
 +
 
 +
HF + DMSO:<br/>
 +
- 18 uL H2O<br/>
 +
- 6 uL HF buffer<br/>
 +
- 5.1 uL of master mix<br/>
 +
- 0.9 uL DMSO<br/><br/>
 +
Now divide into 3 tubes (10 uL into each PCR tube)<br/><br/>
 +
 
 +
GC:<br/>
 +
- 18.9 uL H2O<br/>
 +
- 6 uL GC buffer<br/>
 +
- 5.1 uL master mix<br/><br/>
 +
Now divide into 3 tubes (10 uL into each PCR tube) <br/><br/>
 +
 
 +
Supermix:<br/>
 +
- 15 uL buffer G<br/>
 +
- 12 uL H2O<br/>
 +
- 0.9 uL DMSO<br/>
 +
- 0.6 uL forward primer<br/>
 +
- 0.6 uL reverse primer<br/>
 +
- 0.6 uL template DNA<br/>
 +
- 0.3 uL phusion <br/><br/>
 +
 
 +
PCR program: <br/><br/>
 +
 
 +
1. 98 degrees Celsius for 3 minutes <br/>
 +
2. 98 degrees C for 15 seconds <br/>
 +
3. Temperature gradient 48-55-63 degrees for 30 seconds <br/>
 +
4. 72 degrees C for 1 minute <br/>
 +
5. Go to step 2, repeat 30 times <br/>
 +
6. 72 degrees C for 5 minutes <br/><br/>
 +
Gel results: Only buffer G +DMSO works and it works at all temperatures.<br/><br/>
 +
 
 +
 
 +
<h2>Optomized PCR</h2><br/>
 +
Worked using buffer G +DMSO supermix at 63o C. <br/><br/>
 +
Supermix (for three reactions. 10uL/rxn):
 +
- 15 uL buffer G<br/>
 +
- 12 uL H2O<br/>
 +
- 0.9 uL DMSO<br/>
 +
- 0.6 uL forward primer<br/>
 +
- 0.6 uL reverse primer<br/>
 +
- 0.6 uL template DNA<br/>
 +
- 0.3 uL phusion <br/><br/>
 +
 
 +
PCR program (running time of just under 2 hours): <br/><br/>
 +
1. 98 degrees Celsius for 3 minutes <br/>
 +
2. 98 degrees C for 15 seconds <br/>
 +
3. 63 degrees C for 30 seconds <br/>
 +
4. 72 degrees C for 1 minute <br/>
 +
5. Go to step 2, repeat 30 times <br/>
 +
6. 72 degrees C for 5 minutes <br/><br/>

Revision as of 15:16, 4 June 2012

Header

Protocols

Select Protocol

PCR Protocols


PCR


What you need:
- A container of ice
- Small PCR tubes
- Template DNA containing the gene of interest
- DNA primers designed to amplify the gene of interest
- Phusion DNA polymerase
- dNTP solution
- DMSO (optional)
- 5X HF or GC buffer
- Autoclaved MilliQ water

Procedure:
1. Keep all components on ice as you work
2. Label clearly one small PCR tube for each sample you wish to run.
3. For each sample, mix the following:
- 0.75 uL template DNA
- 1uL each of the two primers
- 0.5uL DNA polymerase
- 1uL dNTPs
- 1.5 uL DMSO (optional)
- 10uL 5X HF/CG buffer
- 33.5 uL autoclaved water

4. Use your pipet to mix thoroughly
5. Load samples in the PCR machine and select the phusion protocol, using an extension time of roughly one minute per kb of DNA to be amplified. However – consult the bootcamp optimized PCR protocol if necessary.

Note: When running PCR with the supermix use 25 uL of supermix, 1.5 uL of DMSO (optional), 0.5uL DNA polymerase, 1uL each of the two primers, 0.75 uL of template, and autoclaved water to 50uL volume.

PCR Cleanup


What you need:
- Large Zymo-spin columns in collection tubes
- The completed PCR of interest
- DNA binding buffer
- DNA wash buffer
- DNA wash buffer
- Autoclaved 1.5 mL centrifuge tubes
- Autoclaved MilliQ water

Procedure:

1. To the PCR liquid, add 2 volumes of DNA binding buffer
2. Mix briefly by pipetting and add all of the mixture to a large Zymo-spin column
3. Centrifuge at full speed for 30 seconds
4. Discard the waste liquid in the collection tube
5. To the column, add 200 uL wash buffer
6. Centrifuge for 30 seconds and discard the waste liquid
7. Repeat steps 5-6
8. Centrifuge the empty column for 1 minute
9. Replace the collection tube with 1.5 mL centrifuge tube
10. Gently add 30uL of autoclaved water to the column
11. Let the column incubate at room temperature for 2 minutes
12. Centrifuge 1 minute
13. Discard the column
14. Label the collected liquid and store it in the -20˚C freezer until use

PCR Troubleshooting


Ran a diagnostic test to optimize buffer and temperature for the PCR. After doing the PCR (it’s nice to do this in linked PCR tubes) we run on a gel to test which worked best.

Buffers tested: GC + DMSO, HF + DMSO, GC, buffer G supermix + DMSO (3 tubes of each)

Made a master mix of primers, phusion, template DNA, and dNTPs. This was then used this for all the tubes of GC+DMSO, HF+DMSO, and GC.

Master Mix:
- 10 uL dNTP’s
- 2 uL forward primers
- 2 uL reverse primers
- 2 uL template DNA
- 1 uL phusion

GC + DMSO:
- 18 uL H2O
- 6 uL GC buffer
- 5.1 uL of master mix
- 0.9 uL DMSO
- now divide into 3 tubes (10 uL into each PCR tube)

HF + DMSO:
- 18 uL H2O
- 6 uL HF buffer
- 5.1 uL of master mix
- 0.9 uL DMSO

Now divide into 3 tubes (10 uL into each PCR tube)

GC:
- 18.9 uL H2O
- 6 uL GC buffer
- 5.1 uL master mix

Now divide into 3 tubes (10 uL into each PCR tube)

Supermix:
- 15 uL buffer G
- 12 uL H2O
- 0.9 uL DMSO
- 0.6 uL forward primer
- 0.6 uL reverse primer
- 0.6 uL template DNA
- 0.3 uL phusion

PCR program:

1. 98 degrees Celsius for 3 minutes
2. 98 degrees C for 15 seconds
3. Temperature gradient 48-55-63 degrees for 30 seconds
4. 72 degrees C for 1 minute
5. Go to step 2, repeat 30 times
6. 72 degrees C for 5 minutes

Gel results: Only buffer G +DMSO works and it works at all temperatures.

Optomized PCR


Worked using buffer G +DMSO supermix at 63o C.

Supermix (for three reactions. 10uL/rxn): - 15 uL buffer G
- 12 uL H2O
- 0.9 uL DMSO
- 0.6 uL forward primer
- 0.6 uL reverse primer
- 0.6 uL template DNA
- 0.3 uL phusion

PCR program (running time of just under 2 hours):

1. 98 degrees Celsius for 3 minutes
2. 98 degrees C for 15 seconds
3. 63 degrees C for 30 seconds
4. 72 degrees C for 1 minute
5. Go to step 2, repeat 30 times
6. 72 degrees C for 5 minutes

Retrieved from "http://2012.igem.org/Team:UIUC-Illinois/Notebook/Protocols/PCR"