SOB

    * 0.5% (w/v) yeast extract
    * 2% (w/v) tryptone
    * 10 mM NaCl
    * 2.5 mM KCl
    * 20 mM MgSO4
Per liter:

    * 5 g yeast extract
    * 20 g tryptone
    * 0.584 g NaCl
    * 0.186 g KCl
    * 2.4 g MgSO4
Note: Some formulations of SOB use 10 mM MgCl2 and 10 mM MgSO4 instead of 20 mM MgSO4.
SOB medium is also available dry premixed from Difco, 0443-17.
Adjust to pH 7.5 prior to use. This requires approximately 25 ml of 1M NaOH per liter

SOC   

  * SOB with 20 mM glucose

CCMB80 buffer

• 10 mM KOAc pH 7.0 (10 ml of a 1M stock/L)

• 80 mM CaCl₂.2H₂O (11.8 g/L)
• 20 mM MnCl₂.4H₂O (4.0 g/L)
• 10 mM MgCl₂.6H₂O (2.0 g/L)
• 10% glycerol (100 ml/L)
• adjust pH DOWN to 6.4 with 0.1N HCl if necessary
  
  • adjusting pH up will precipitate manganese dioxide from Mn containing solutions.
• sterile filter and store at 4°C
• slight dark precipitate appears not to affect its function

Procedure

Preparing glassware and media

Eliminating detergent

Do not wash glassware with soap, rinse it with H2O and autoclave.

Prechill plasticware and glassware

Prechill centrifuge tubes and screw cap tubes before use.

Preparing seed stocks

• Streak TOP10 cells on an SOB plate and grow for single colonies at room temperatur
• Pick single colonies into 2 ml of SOB medium and shake overnight at room temperature 25 oC
• Add glycerol to 15%
• Aliquot 1 ml samples to Nunc cryotubes
• Store in a -80°C freezer.

Preparing competent cells

• Inoculate 250 ml of SOB medium with 1 ml vial of seed stock and grow at 20°C to an OD600 of 0.3
  
  • This takes approximately 16 hours.
  • Controlling the temperature makes this a more reproducible process, but is not essential.
  • Room temperature will work. You can adjust this temperature somewhat to fit your schedule
  • Aim for lower, not higher OD if you can’t hit this mark
• Centrifuge at 3000g at 4°C for 10 minutes in a flat bottom centrifuge bottle.
  
  • Flat bottom centrifuge tubes make the fragile cells much easier to resuspend
  • It is often easier to resuspend pellets by mixing before adding large amounts of buffer
• Gently resuspend in 80 ml of ice cold CCMB80 buffer
  
  • sometimes this is less than completely gentle. It still works.
• Incubate on ice 20 minutes
• Centrifuge again at 4°C and resuspend in 10 ml of ice cold CCMB80 buffer.
• Test OD of a mixture of 200 μl SOC and 50 μl of the resuspended cells.
• Add chilled CCMB80 to yield a final OD of 1.0-1.5 in this test.
• Incubate on ice for 20 minutes
• Aliquot to chilled screw top 2 ml vials or 50 μl into chilled microtiter plates
• Store at -80°C indefinitely.
  
  • Flash freezing does not appear to be necessary
• Test competence (see below)
• Thawing and refreezing partially used cell aliquots dramatically reduces transformation efficiency by about 3x the first time, and about 6x total after several freeze/thaw cycles.

Measurement of competence

• Transform 50 μl of cells with 1 μl of standard pUC19 plasmid (Invitrogen)
  
  • This is at 10 pg/μl or 10^-5 μg/μl
  • This can be made by diluting 1 μl of NEB pUC19 plasmid (1 μg/μl, NEB part number N3401S) into 100 ml of TE
• Hold on ice 0.5 hours
• Heat shock 60 sec at 42C
• Add 250 μl SOC
• Incubate at 37 C for 1 hour in 2 ml centrifuge tubes rotated
  
  • using 2ml centrifuge tubes for transformation and regrowth works well because the small volumes flow well when rotated, increasing aeration.
  • For our plasmids (pSB1AC3, pSB1AT3) which are chloramphenicol and tetracycline resistant, we find growing for 2 hours yields many more colonies
  • Ampicillin and kanamycin appear to do fine with 1 hour growth
• Plate 20 μl on AMP plates using sterile 3.5 mm glass beads
  
  • Good cells should yield around 100 – 400 colonies
  • Transformation efficiency is (dilution factor=15) x colony count x 10⁵/µgDNA
  • We expect that the transformation efficiency should be between 5×10⁸ and 5×10⁹
    cfu/µgDNA

5x Ligation Adjustment Buffer

• Intended to be mixed with ligation reactions to adjust buffer composition to be near the CCMB80 buffer
• KOAc 40 mM (40 ml/liter of 1 M KOAc solution, pH 7.0)
• CaCl₂ 400 mM (200 ml/l of a 2 M solution)
• MnCl₂ 100 mM (100 ml/l of a 1 M solution)
• Glycerol 46.8% (468 ml/liter)
• pH adjustment with 2.3% of a 10% acetic acid solution (12.8ml/liter)
  
  • Previous protocol indicated amount of acetic acid added should be 23 ml/liter but that amount was found to be 2X too much per tests on 1.23.07
• water to 1 liter
• autoclave or sterile filter
• Test pH adjustment by mixing 4 parts ligation buffer + 1 part 5x ligation adjustment buffer and checking pH to be 6.3 – 6.5
• Use of the ligation adjustment buffer is optional.

References

US Patent 6,709,852; 6,855,494; 6,960,464