Team:Wageningen UR/Project/ProtocolsProj1

From 2011.igem.org

(Difference between revisions)
(→Main Project)
(→Main Project)
Line 109: Line 109:
====Procedures====
====Procedures====
 +
'''Preparation of chemically competent cells'''
 +
 +
''Preparing glassware and media''
 +
 +
 +
Detergent is a major inhibitor of competent cell growth and transformation. Glass and plastic must be detergent free for these protocols. The easiest way to do this is to avoid washing glassware, and simply rinse it out. Autoclaving glassware filled 3/4 with DI water is an effective way to remove most detergent residue. Media and buffers should be prepared in detergent free glassware and cultures grown up in detergent free glassware.
 +
 +
''Prechill plasticware and glassware''
 +
 +
Prechill 250mL centrifuge tubes and screw cap tubes before use.
 +
 +
''Preparing seed stocks''
 +
 +
Streak TOP10 cells on an SOB plate and grow for single colonies at 23°C works well. Pick single colonies into 2 ml of SOB medium and shake overnight at 23°C.
 +
Add glycerol to 15% and aliquot 1 ml samples into cryotubes.
 +
Place tubes into a zip lock bag, immerse bag into a dry ice/ethanol bath for 5 minutes
 +
 +
This step may not be necessary
 +
 +
Place in -80°C freezer indefinitely.
 +
 +
Preparing competent cells
 +
 +
Inoculate 250 ml of SOB medium with 1 ml vial of seed stock and grow at 20°C to an
 +
 +
OD600nm 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 5x108 and 5x109
 +
 +
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 --Meaganl 15:50,
 +
 +
25 January 2007 (EST)
 +
 +
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
   }}
   }}

Revision as of 18:49, 8 September 2011

Building a Synchronized Oscillatory System

Main Project

Protocols

Media

LB

Ingredients:

10 g Bacto-tryptone

5 g yeast extract

10 g NaCl


SOB

Ingredients

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


SOC

Ingredients

SOB

20 mM glucose


CCMB80 buffer for preparation of chemically competent cells


Materials

Detergent-free, sterile glassware and plasticware

Table-top OD600nm spectrophotometer

SOB


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

Filter sterilize and store at 4°C

Slight dark precipitate appears not to affect its function

Procedures

Preparation of chemically competent cells

Preparing glassware and media


Detergent is a major inhibitor of competent cell growth and transformation. Glass and plastic must be detergent free for these protocols. The easiest way to do this is to avoid washing glassware, and simply rinse it out. Autoclaving glassware filled 3/4 with DI water is an effective way to remove most detergent residue. Media and buffers should be prepared in detergent free glassware and cultures grown up in detergent free glassware.

Prechill plasticware and glassware

Prechill 250mL centrifuge tubes and screw cap tubes before use.

Preparing seed stocks

Streak TOP10 cells on an SOB plate and grow for single colonies at 23°C works well. Pick single colonies into 2 ml of SOB medium and shake overnight at 23°C. Add glycerol to 15% and aliquot 1 ml samples into cryotubes. Place tubes into a zip lock bag, immerse bag into a dry ice/ethanol bath for 5 minutes

This step may not be necessary

Place in -80°C freezer indefinitely.

Preparing competent cells

Inoculate 250 ml of SOB medium with 1 ml vial of seed stock and grow at 20°C to an

OD600nm 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 5x108 and 5x109

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 --Meaganl 15:50,

25 January 2007 (EST)

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

Retrieved from "http://2011.igem.org/Team:Wageningen_UR/Project/ProtocolsProj1"