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Revision as of 20:22, 5 August 2015

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Restriction digestion protocol

1. Prepare restriction digestion mixture:
   IDT gBlocks
   - 10 ul of DNA (10 ng/ul)
   - 2 ul of 10 x 2.1 buffer
   - 0.3 ul of EcoR1
   - 0.3 ul of Pst1
   - 7.4 ul of milliQ H2O
   
   
   PSB1C3, PSB1A3, PSB1K3 backbones
   - Required amount of vector DNA (50 ng per ligation)
   - 1 ul of 10 x 2.1 buffer
   - 0.3 ul of EcoR1
   - 0.3 ul of Pst1
   - add milliQ H2O up to 10 ul
   (if using total volume greater than 10ul, increase the amount of buffer accordingly)
   
   
   Other digestions
   - Required amount of vector DNA
   - 1 ul of 10 x 2.1 buffer
   - 0.3 ul of EcoR1
   - 0.3 ul of Pst1
   - add milliQ H2O up to 10 ul
   (if using total volume greater than 10ul, increase the amount of buffer accordingly)
   
   
2. Incubate at 37C for an hour
3. Heat inactivate by incubating at 80C for 20 minutes
4. Run a sample of digested DNA on a gel in order to confirm digestion:
   - 2 ul of DNA
   - 1 ul of 6 x Gel Loading Dye
   - 3 ul of milliQ H2O
5. If digestion is confirmed, proceed to ligation

Ligation protocol

1. Calculate the amount of insert DNA required to maintain 1:3 backbone:insert molar ratio using formula below. For standard ligations use 50 ng of vector DNA, increase the amounts of DNA if unsuccessful.
   .
2. Prepare the ligation mixture:
   - required amount of insert DNA
   - required amount of vector DNA
   - 1 ul of T4 ligase
   - 2 ul of 10 x ligase buffer
   - add milliQ H2O up to 20 ul
3. Incubate at 16C for 30 minutes
4. Heat inactivate by incubating at 80C for 20 minutes
5. Keep on ice until ready to proceed with transformation protocol

Transformation protocol

1. (If using part from the distribution: resuspend the DNA in 10 ul of MiliQ water, making sure that it turns red. Wait 10 minutes before adding the DNA to cells)
2. Put a tube of NEB DH 5 alpha E. coli cells on ice and wait until they thaw completely. Divide the cells into 50 ul aliquotes.
3. Add 1 ul of plasmid DNA to 50 ul of cells.
4. Mix by carefully flicking the tube. Do not vortex or pipette in and out!
5. Place the mixture on ice for 30 minutes.
6. Heat shock the cells at 42 °C for 30 seconds and immediately put on back on ice.
7. Keep cells on ice for next 5 minutes. Do not mix.
8. Pipette 950 ul of SOC media kept at room temperature into the mixture. If SOC is not available, use LB.
   
9. Incubate the mixture at 37 °C for 60 minutes
10. Prepare plates with appropriate antibiotics. Bring plates to room temperature before plating. Use 2 plates per transformation reaction.
11. Plate 200 ul of cells on one plate.
12. Pellet the remaining cells and resuspend in 200ul of LB.
13. Plate the remaining cells on second plate.
14. Incubate plates overnight at 37 °C.

Agarose gel electrophoresis

1. Measure 0.50 g of agarose
2. Measure 50 ml of 1x TAE buffer using measuring cylinder
3. Add agarose and TAE buffer to conical flask and gently mix
4. Microwave the flask for 1 min
5. Wait for the mixture to cool down slightly before proceeding
6. Add 10 ul of 10mg/ml ethidium bromide solution and mix
7. Assemble the casting tray and pour the gel into it
8. Wait around 30 minutes until gel gets solidified
9. Put the gel into the gel chamber and pour 1x TAE buffer until it is fully covered
10. Load 6 ul of DNA ladder to the first well.
11. Prepare the samples by adding appropriate volume of 6x gel loading dye and load them
12. Assemble the gel chamber and run the gel for 40 minutes at 120V
13. Visualise the gel using the gel visualizer

Assembly of 2 parts using gel extraction

1. Digest at least 500 ng of each part according to the restriction digestion
2. Run the digested DNA on the gel according to gel electrophoresis protocol
3. Identify the parts that you want to ligate on a gel and cut the bands out using razor blade
4. Purify the excised bands using the commercial kit according to the manufacturer's instructions
5. Quantify the DNA yield using DNA nanodrop
6. Proceed to ligation

Polymerase Chain Reaction

1. Prepare the PCR mix:
   - 12.5 ul of 2 x Q5 PCR master mix
   - 1.25 ul of 10 uM forward primer
   - 1.25 ul of 10 uM reverse primer
   - 2 ng of DNA to be PCRed
   - add milliQ H2O up to 25
2. Set up the PCR cycles according to the following rules:
   Initial denaturation
   - 98C for 30 seconds
   35 cycles
   - 98C for 10 seconds
   - 30 seconds at primer melting temperature
   - 72C for 30sec/kb of PCRed fragment
   Final extension
   - 72C for 2 minutes
   - Hold at 4C
3. - Confirm the PCR by running 2 ul of the product on the gel according to the gel electrophoresis protocol