Difference between revisions of "Team:UCL/Experiments"

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<div id="gelextraction"><h2>Assembly of 2 parts using gel extraction</h2>
 
<div id="gelextraction"><h2>Assembly of 2 parts using gel extraction</h2>
 
<ol>
 
<ol>
−
<li>- Digest at least 500 ng of each part according to the <a href="#digestion">restriction digestion</a></li>
+
<li>Digest at least 500 ng of each part according to the <a href="#digestion">restriction digestion</a></li>
−
<li>- Run the digested DNA on the gel according to <a href="#gel">gel electrophoresis protocol</a></li>
+
<li>Run the digested DNA on the gel according to <a href="#gel">gel electrophoresis protocol</a></li>
−
<li>- Identify the parts that you want to ligate on a gel and cut the bands out using razor blade</li>
+
<li>Identify the parts that you want to ligate on a gel and cut the bands out using razor blade</li>
−
<li>- Purify the excised bands using the commercial kit according to the manufacturer's instructions</li>
+
<li>Purify the excised bands using the commercial kit according to the manufacturer's instructions</li>
−
<li>- Quantify the DNA yield using DNA nanodrop</li>
+
<li>Quantify the DNA yield using DNA nanodrop</li>
−
<li>- Proceed to <a href="#ligation">ligation</a></li>
+
<li>Proceed to <a href="#ligation">ligation</a></li>
  
 
</ol>
 
</ol>

Revision as of 16:33, 5 August 2015

Experiments & Protocols

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

    ..

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