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Protocols


E.coli Protocols

Two-day Efficient Cloning Cycle

We used an efficient two day cloning cycle split into a "Light" day and a "Heavy" day.

Light Day

The light day consists of Colony PCR and liquid culture of colonies transformed from a previous day.

  1. The 3-in-1

    First, count the number of colonies you want to check. Then, do the following 3 things sequentially:

    • Liquid culture
    • 2nd time plate
    • Colony PCR

    (Use the same tip to add the template to these three things)

  2. Make The Gel For Electrophoresis
  3. Run Gel Electrophoresis To Check The Colony PCR Product

Heavy Day

The heavy day consists of:

  1. Previously grown plasmid extraction
  2. Plasmid PCR
  3. Gel extraction
  4. Digestion
  5. Ligation
  6. Transformation
Colony PCR (Thermo DreamTaq®)
  1. Make the Colony PCR mix (we use Thermo' DreamTaq) with the mix amount slightly modified:
    Item uL
    Primer(Forward and reverse) 1
    dNTP (10mM) 1
    10x DreamTaq buffer 5
    Taq Polymerase 0.2
    ddH20 42.8
    Total 50
  2. Select a colony using a tip or toothpick.
  3. Dip it in a PCR tube and swirl it around.

    PCR run protocol

    Temperature Time  
    94℃ 60s  
    94℃ 15s  
    55℃ 20s 30-35 cycles
    72℃ 1kb/min + 5-10s  
    72℃ 300s  
Liquid culture
  1. Aliquot 4 mL of LB medium in a centrifugal tube for each colony.
  2. Use a tip and dip it in the LB culture and swirl it around.
Draw on 2nd time plate

Take out new plates from the fridge and divide them into smaller sections. This is the second-time plate. Make sure to write the date on it. Cross out in red pen any sections you know is wrong after the Colony PCR check.

Making Gel for gel electrophoresis
  1. Make either 100mL or 150mL of gel at at time and select a relevant percentage (e.g. 1%, 1.5%, or 2%)
  2. Measure out the relevant percentage in agarose (e.g. 1g of agarose for 100mL of 1% gel).
  3. Fill it up with 1xTAE buffer.
  4. Microwave on low, constantly taking it out every so often to swirl and mix it. Keep microwaving until clear. Make sure it is completely clear
  5. Cool to a temperature that is still hot but still can be held in your hand. If the gel gets too cold and starts to harden, start microwaving again until clear.
  6. Add 5uL of Safe-seeing dye for every 100mL of gel after cooled to the correct tempearature. Mix it well by swirling
  7. Pour it onto the molds quickly. Put a cover on it to block out the light.
  8. Wait at least 15-20 min until using it.
  9. Store in 4°C and away from light.
Gel electrophoresis
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Plasmid Extraction
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Plasmid Extraction
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Plasmid Extraction
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