subcloning techniques created by: sara cormier hill park secondary school, the co-op & science...
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Subcloning TechniquesSubcloning Techniques
Created By: Sara Cormier
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Hill Park Secondary School, The Co-Op & Science Departments and Mr. Watts
wish to thank
Dr. D. Tang
for allowing Sara Cormier to do a Co-Op placement in his lab (McMaster University/St. Joseph’s Hospital)
and
Dr. Jing Zhang,
a research fellow in Dr. Tang’s lab who both graciously gave of their time to supervise Sara’s work on a daily basis.
AcknowledgementAcknowledgement
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What Does Subcloning Mean?What Does Subcloning Mean?
Subcloning is the transfer of a cloned DNA fragment from one vector to another.
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What Is the Purpose?What Is the Purpose?
Protein expression is generally the purpose of subcloning.
The insert most likely will contain the gene that codes for the desired protein.
The effects of this protein on a cell can then be studied.
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Steps Required To Steps Required To Successfully SubcloneSuccessfully Subclone
1. Obtain plasmid maps.
2. Select enzymes.
3. Perform 1st enzyme cut.
4. Precipitate.
5. Perform 2nd enzyme cut.
6. Gel purification.
7. Check plasmid concentration.
8. Ligation.
9. Transformation.
10. Screen.
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Step 1: Obtain Plasmid MapsStep 1: Obtain Plasmid Maps
• Use plasmid map to select enzymes for ligation.
• Each enzyme provided on multiple-cloning site makes a single cut in the plasmid resulting in linear DNA.
• Plasmid maps also provide other important information such as which antibiotic resistance is present.
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Best Case Scenario: Enzymes Best Case Scenario: Enzymes MatchMatch
If possible select the same 2 enzymes to cleave the vector and insert.
Enzymes that produce sticky ends are preferred as they make ligation easier.
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Step 2: Perform 1Step 2: Perform 1stst Enzyme Enzyme CutCut
Purpose: to make the circular plasmid linear.
Cut vector and insert seperately.Select the appropriate buffer based on the
enzyme selected.If the enzymes are compatible (use the same
buffer) make both cuts at the same time.
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Steps RequiredSteps Required
1. Determine how much plasmid should be used (2µg).
2. 10% of the total volume should be the buffer.
3. The enzyme should not be more than 10% of the total volume.
4. Add DNA H2O to make the final volume.5. Incubate at 37ºC overnight.
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Step 3: Precipitate Vector and Step 3: Precipitate Vector and Insert Insert
Add 10% of the total volume sodium acetate (ph 5.2).
Add 2x the total volume 100% ethanol.Incubate on ice 20 min.Centrifuge 4ºC for 10 min on maximum
speed.
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Step 4: Perform 2Step 4: Perform 2ndnd Enzyme Enzyme CutCut
Follow same basic procedure as the first cut.
1. Dissolve the pellet in water.
2. Add buffer and enzyme.
3. Incubate at 37ºC overnight.
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Step 5: Gel PurificationStep 5: Gel Purification
Make DNA gel. Cut out the band
needed . Use a gel
purification kit to purify the DNA.
Use the molecular weight markers to determine which band is correct.
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Step 6: Check Plasmid Step 6: Check Plasmid ConcentrationConcentration
Purpose: to know how much to use in ligation.
1. Make DNA gel.2. Run about 3 wells of both vector and
insert (different concentrations, all diluted).
3. Chose the band that is visible but not too dark.
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Step 7: LigationStep 7: Ligation
Ligation – insert the insert into the plasmid to make a new plasmid (recombinant DNA).
1. Add the appropriate amount of vector and insert to a new tube (more insert than vector).
2. Add H2O (not always necessry).3. Use ligation kit and add:
- 2 µL buffer 2 (warm and vortexed).- 10 µL buffer 1 (warm and vortexed).- 1 µL buffer 3.
4. Incubate at room temperature for 15 min.
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Step 8: Transformation:Step 8: Transformation: Transformation - introduction of foreign DNA, in
this case a plasmid into a bacterial cell.
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Steps RequiredSteps Required
1. Add total volume of ligated plasmid to a competent cell.
2. Incubate on ice for 30 min.3. Heat shock (42ºC for 90 sec.).4. Incubate on ice for 2 min.5. Add to 0.8mL LB medium and shake at 37ºC for
1 hour.6. Centrifuge and spread on ampicillin plate (if this
is the antibiotic being used).7. Incubate overnight at 37ºC.
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Step 9: ScreenStep 9: Screen Purpose: to determine if the
ligation was successful. Select 2 enzymes (one from
vector and one from insert). Based on the bands
appearing in the gel you can determine if ligation was successful.
The insert orientation must be checked if the same enzyme was used or blunt ligation was used.
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Example:Example:
In the above example 6 samples were run. The 3rd and 4th samples were successful.
1 2 3 4 5 6Sample
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Steps RequiredSteps Required
1. Pick up colonies (number varies) from plate and place each in 5mL LB medium and (3 µL antibiotic).
2. Shake overnight at 37°C.3. Centrifuge 1mL from each tube for 5 min.
speed 2000rpm at room temperature.4. Make enzyme cuts together.5. Run gel to check if ligation successful.
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What Happens When the What Happens When the Enzymes Don’t Match?Enzymes Don’t Match?
Subcloning becomes more difficult and less successful when it is not possible to cleave the insert and vector with the same 2 enzymes.
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Steps To Successfully Steps To Successfully Subclone When Only ONE Subclone When Only ONE
Enzyme MatchesEnzyme Matches1. Obtain plasmid maps.2. Select enzymes.3. Perform 1st enzyme
cut (enzyme that does NOT match).
4. Blunt vector & insert.6. Perform 2nd enzyme
cut (enzyme that matches).
7. Gel purification.
8. Check plasmid concentration.
9. Ligation.
10. Transformation.
11. Screen.
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General ExampleGeneral Example
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Blunting: Get Rid of the Blunting: Get Rid of the OverhangsOverhangs
In order to allow for ligation the overhangs must be removed by a process known as blunting.
This step may be eliminated if possible to cut with an enzyme that produces blunt ends.
Any blunt ends can ligate together.
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Steps RequiredSteps Required
1. In small PCR tubes add:
- 34 µL H2O
- 5 µL Pfu buffer (10x buffer) (warm)
- 10 µL 1mm DNTP (warm)
- 1 µL Pfu enzyme
Total volume: 50 L• Centrifuge to get rid of any bubbles.• In PCR machine heat at 72ºC for 30 min.
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Steps To Successfully Steps To Successfully Subclone When NO Enzymes Subclone When NO Enzymes
MatchMatch1. Obtain plasmid maps.2. Select enzyme.3. Perform 1st enzyme
cuts.4. Perform 2nd cut on
insert.5. Blunt vector & insert.6. Dephosphorylate
(vector only).
7. Gel purification.
8. Check plasmid concentration.
9. Ligation.
10. Transformation.
11. Screen.
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General Example:General Example:
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DephosphorylationDephosphorylation
Dephosphorylation – to remove the phospate group from the 5’ ends on the vector.
Purpose: insures that the vector does not self-ligate.
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Steps RequiredSteps Required
1. Precipitate vector2. In separate tube mix: - 9 µL H2O - 1 µL AP bufferThrow out 1 µL from tube and
replace with 1 µL phosphatase.
3. To precipitated vector add:
- 44 µL H20 - 5 µL AP buffer - 1 µL mix (from above)
4. In PCR machine set: - 15 min. 37°C - 45 min. 55°C - 15 min. 74°C5. After the first 15 min. add
another 1 µL of the mix.6. After 1 hour add 1 µL 0.5M
EDTA7. After completed put on ice.
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My ProjectsMy Projects
pcDNA 3.0/BCL-2 (sticky end ligation)PBind/P58 (blunt end ligation)pcDNA 3.1/hygro/BCL-2 (sticky end
ligation)
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pcDNA 3.0/BCL-2pcDNA 3.0/BCL-2
Checking Concentration (to know how much to ligate):
BCL-2 pcDNA 3.0
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pcDNA 3.0/BCL-2pcDNA 3.0/BCL-2Screening:
All 8 samples were successful.
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pcDNA 3.1/hyrgo/BCL-2pcDNA 3.1/hyrgo/BCL-2
The pupose of inserting BCL-2 into this vector is that it contains hygromycin. This selection marker was required during transfection.
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THANK-YOUTHANK-YOU