Team:UANL Mty-Mexico/Results/Protocols


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  • Preparation of E. coli Calcium Chloride competent cells
      1. Inoculate a single colony into 3 mL of LB media without any antibiotics and grow overnight at 37 °C with vigorous shaking.
      2. Inoculate 1 mL of the desired strain into 100 mL of fresh LB, use a 500 mL flask.
      3. Incubate at 37 °C with vigorous shaking until 0.3 - 0.4 sideOD600
      4. Put the flask on ice. Pre-chill 50 mL centrifuge tubes and the centrifuge itself at 4°C.
      5. Centrifuge 50 mL of the culture at 8,000 rpm for 5 minutes at 4 °C.
      6. Remove the supernatant and add 10 mL of cold CaCl2 0.1 M. Vortex until the pellet is resuspended.
      7. Incubate on ice for 30 minutes, shake the tube once in a while.
      8. Centrifuge at 8,000 rpm for 5 minutes at 4°C. Remove the supernatant and add 2 mL of CaCl2 0.1 M. Resuspend carefully using a micropipette. Keep always on ice.
      9. Mix the two preparations in a tube and store on ice, or use for transformation.

      Note: The competent cells can be stored on ice up to two weeks.

  • Preparation of E. coli Rubidium Chloride competent cells
      1. Inoculate 3 mL of LB broth with DH5α and incubate the culture overnight at 37°C with vigorous shacking.
      2. Use small culture to inoculate 100 mL of LB broth. Incubate at 37°C with shacking until the culture reaches an optical density (OD595) 0.4-0.6.
      3. Transfer to two 50 mL centrifuge tubes.
      4. Spin at maximum speed for 5 minutes at 4°C.
      5. Remove supernatant.
      6. Add 20 mL of TBF1 and resuspend the pellet.
      7. Incubate on ice for 20 minutes.
      8. Pour off supernatant.
      9. Centrifuge 5 minutes at 8000 rpm/4°C.
      10. Resuspend cellular pellet with 4 mL of TBF2.
      11. Place aliquots of 100 µL at -70°C.
  • Transformation of E. coli competent cells
      1. Add 50 µL of Ca+2 competent cells to a pre-chilled centrifuge tube. Keep always on ice until step 4.
      2. Add plasmid DNA (100 ng) or ligation (up to 5 µL) depending on DNA concentration.
      3. Use 1 µL of a 1 ng/µL DNA sample as positive test in a separate tube. It is recommended to use a DNA-free negative test tube as well.
      4. Chill the tube on ice for 20 - 30 minutes.
      5. Expose the reaction mixture to a 42ºC for 1 minute heat-shock.
      6. Put the tube on ice for 2 minutes.
      7. Add 200 µL of antibiotic-free LB media.
      8. Incubate at 37ºC for 20 - 30 minutes.
      9. Spread the appropriate quantity of cells (50-200 µL) on selective LB agar plates.
      10. Incubate overnight at 37ºC.
      11. The positive plate must have around 1,000 colonies as an optimal (1X106 transformants per µg supercoiled DNA).

      Notes: Until heat-shock, handle the tubes from the upper part to avoid warming the cells. Low temperature is critical for successful transformation. Avoid transforming with more than 5 µL of ligation mixture, as ligation buffer may reduce transformation efficiency.

  • Mini preparation of plasmid DNA
      1. Pour 1.5 mL of the culture in a 1.5 mL microcentrifuge tube and centrifuge at 14,000 rpm for 30 seconds. Remove the supernatant.
      2. Add 200 µL of Solution I. Resuspend the pellet by using vortex briefly or by pipetting up and down. Incubate at room temperature for 5 minutes.
      3. Add 200 µL of Solution II and mix gently by inverting and rotating the tube several times. Do not vortex. Incubate at room temperature for 5 minutes.
      4. Add 200 µL of Solution III and mix gently by inverting and rotating the tube several times. Incubate the tube on ice for 5 minutes.
      5. Centrifuge at 14,000 rpm for 5 minutes.
      6. Transfer the supernatant to a fresh tube containing 1 mL of 100% ethanol.
      7. Incubate at -20 ºC for 10 minutes. (Max. 2 h)
      8. Centrifuge at 14,000 rpm for 10 minutes. Remove the supernatant.
      9. Add 200 µL of 70% ethanol and vortex gently for 10 seconds.
      10. Centrifuge at 14,000 rpm for 5 minutes. Remove the supernatant by pipetting. Aspirate off any residual supernatant.
      11. Dry at 37ºC for 5 minutes.
      12. Add 20 µL of H2O + 20 µg/mL of RNase. Resuspend by using vortex briefly.
      13. Verify the Plasmidic DNA with agarose gel (0.8%) or store at 4ºC.
  • Solutions for Mini preparation of Plasmid DNA

      Solution I (200 mL)

      milliliters or grams

      - Tris HCl 1 M (pH 8.0)

      5 mL

      - EDTA 0.5 M (pH 8.0)

      4 mL

      - Distilled H2O

      Bring the final volume up to 200 mL

      Solution II (200 mL)

      - NaOH 10N

      4 mL

      - SDS (powder)

      2.0 gr

      - Bidistilled H20

      Bring the final volume up to 200 mL

      Soll III (200 mL)

      - Potassium acetate (CH3CO2K)

      58.8 gr

      - Acetic acid (CH3-COOH)

      23.0 mL

      - Distilled H20

      Bring the final volume up to 200 mL

      Notes: When preparing Solution II, first add a little bidistilled water, then add NaOH and dissolve carefully SDS. Finally, bring the final volume up to 200 mL with bidistilled water.

      When preparing Solution III, first add 100 mL of H2O and then the potassium acetate. Once it has been add the acetic acid and finally bring the final volume up to 200 ml with bidistilled water.

  • Agarose Gel Electrophoresis Protocol

      To be Loaded:

      • DNA molecular size marker (λ PstI): 2 - 3 μL

      • Plasmid DNA: 2 - 3 μL

      • Enzyme restrictions: 10 μL

      • PCR products: 5 μL


      1. Prepare an agarose gel of the desired concentration (see Agarose gels section).
      2. Add the necessary SB 1X buffer into the electrophoresis tank to cover the gel.
      3. Load the first well with marker, and then load the DNA samples mixed with loading buffer into the wells.
      4. Plug in the anode and cathode cables so that the DNA samples can move through the gel toward the anode.
      5. Run the electrophoresis at 200 volts.
      6. Wait approximately 20 - 30 minutes or until the bromophenol blue reaches the end of the gel and stop the electrophoresis.

      Note: DNA moves toward the positive electric field (anode, usually red cable) due to the negative charges.

  • Agarose gel

      Concentration for supercoiled and plasmid DNA: 0.8%

      For digestion reaction fragments over 1,000 bp: 0.8%

      For digestion reaction fragments below 500 bp: 1.5%

      DNA size marker (λ + PstI): Use 2 or 3 μL per gel.

      Note: Not needed when running supercoiled DNA samples, like plasmid DNA.

  • SB buffer 20X

      SB (Sodium Borate) electrophoresis buffer, 20X Stock:

      1. In 700 mL of distilled H2O, dissolve 8 gr of NaOH.
      2. Weight 51 of Boric Acid and dissolve ¾ parts in the NaOH solution
      3. Dissolve the remaining Boric Acid until the buffer reach pH 8.0.
      4. Complete to 1 L with distilled H2O and store in a sterile flask.

      Note: Use SB 1X as buffer to run agarose gels up to 200 volts

  • Ethidium Bromide Gel Staining

      1. Dilute the stock to 20 μg/mL in a special container with the gel buffer.
      2. Put the gel into the container.
      3. Let it stain for 3 - 5 minutes.
      4. Take the gel out of the container and soak the stained gel in water for 5 minutes or more to clear background ethidium bromide from the gel.
      5. View the gel under a UV light source or on a UV transilluminator.

      Note: If you want to use ethidium bromide, confine its use to a small area of your laboratory. Wear gloves when staining, handle stained gels, and dispose of any waste.

  • Lambda/PstI Molecular Size Marker
      Lambda molecular size marker.


      • phage λ DNA (500 ng/μL) 50.0 μL
      • PstI 2.5 μL
      • Buffer 10X 6.0 μL
      • H20 1.5 μL


      1. Mix the ingredients listed above
      2. Incubate at 37ºC / 45 minutes
      3. Again add 2.5 μL PstI
      4. Incubate 37ºC / 45 minutes
      5. Add 6.0 μL Loading buffer 6X

      Check on agarose gel.

      Notes: Final concentration: 0.30 μgr/μL. Final Volume: 66.0 μL.

  • Restriction enzyme digestion of DNA

      Mix for 1 reaction, final volume of 20 µL

      Add the following to a microcentrifuge tube:


      2-3 µg

      Buffer 10x

      2.0 µL

      Enzyme (10 U/µL)

      0.3 µL (1 enzyme unit per µg DNA)


      Until 20.0 µL

      Incubate the mixture at 37°C (it may change, check enzyme specifications) for 1 - 1.5 hours.

      Note: Prepare a mix when possible to minimize enzyme handling.

  • PCR

      PCR reaction mix:

      DNA template

      Total 100 ng (In 25 μl)

      Buffer 10x

      2.5 μL

      Mg++ 50 mM

      0.75 μL

      dNTPs 20 mM

      0.25 μL

      Primer Fwd 100 ng/μL

      0.50 μL

      Primer Rv 100 ng/μL

      0.50 μL

      Taq Pol 5 U/μL

      0.25 μL


      To bring the volume up to 25 μL


      1. Add the corresponding H2O to a sterile PCR tube.
      2. Add the rest of the components but the enzyme and DNA.
      3. Add the enzyme, mix gently.
      4. Add the respective DNA sample and mix gently.
      5. Spin the tube briefly.
      6. Place the sample in the thermocycler and start your PCR program.


      Put on gloves before taking the PCR mix components out of the freezer.

      DNA must be added at last because it may form complexes with Mg++ and inhibit the reaction.

      When possible, make a mix with all the common components to minimize enzyme waste.

  • Antibiotics


      Final concentration

      Stock concentration

      µL per mL

      Spectinomycin (Sp)

      100 µg/mL

      20 µg/µL


      Ampicillin (Amp)

      50 µg/mL

      10 µg/µL


      Kanamycin (Kan)

      50 µg/mL

      50 µg/µL


      Chloramphenicol (Cm)

      34 µg/mL

      34 µg/µL


      Tetracycline (Tet)

      10 µg/mL

      5 µg/ µL



      Always verify stock concentration, in case of unknown assume the one indicated above.

      When using more than one antibiotic simultaneously use half the concentration for each antibiotic.

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