Team:Groningen/Protocols
From 2009.igem.org
m (→Restriction) |
m (→TBS74 buffer=) |
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===4 M NaOH=== | ===4 M NaOH=== | ||
===1 M HCl=== | ===1 M HCl=== | ||
- | === | + | ===TB74S Buffer=== |
+ | *0.605 g Tris (5mM) | ||
+ | *8.76 g NaCl (150mM) | ||
+ | *Dissolve in 1 L Demi water | ||
+ | *Set pH with HCl to pH 7.4 | ||
+ | |||
+ | ===Sodium Arsenite (III)=== | ||
+ | *100mM Na-As solution | ||
+ | *filter sterilize | ||
Revision as of 13:01, 17 October 2009
Protocols
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Protocols
Cloning
PCR
21 μL mastermix*
1 μL forward primer
1 μL reverse primer
1 μL template
1 μL Taq polymerase
*master mix contains:
100 μL Taq NH4
8 μL dNTP's
80 μL MgCl
652 μL MilliQ water
PCR Reaction
- Hotstart
- 95 °C, 2 min.
- 25 cycles
- 95 °C, 30 sec.
- 61 °C, 20 sec.
- 72 °C, 1.5 min.
- End
- 72 °C, 10 min.
- 4 °C, ∞
Plasmid isolation
(NucleoSpin® Plasmid, Machery nagel])
(GeneElute™ Plasmid Miniprep Kit, Sigma-Aldrich)
Restriction
- Cut plasmids containing promotor with SpeI and PstI
- 1 μL 10x fast digest buffer
- 0.5 μL SpeI
- 0.5 μL PstI
- 8 μL Vector
- Incubate 1 h @ 37 °C
- Purify cut plasmid using PCR clean up kit
Restriction vectors
- 10 μL 10x Fast digest buffer (Fermentas)
- 2 μL SpeI (Fast digest, Fermentas)
- 2 μL EcoRI (Fast digest, Fermentas)
- 50 μL DNA (pSB3K3 or pSB1AC3)
- 36 μL MilliQ
Incubate 0.5 h @ 37 °C
Bring vectors to 1% agarose gel and cut out with scalpel, purify using gel purification kit (NucleoSpin® Extract II, Machery nagel) to an end volume of 50 μL.
(alternatively, Phosphatase treatment of linearized vector)
Gel isolation
- Put restriction on 1% Agarose (TBE) gel
- Cut band of desired bp out
- Purify using gel purification kit
- End volume 30 μL*
*End volume determines concentration, variations are possible
Annealing synthetic oligo’s
Protocol #2
Phosphorylation
- Mix
- 1 μL PNK
- 1 μL T4 DNA Ligase buffer
- 8 μL Oligo’s (FW and REV seperate reactions)
100x diluted oligo’s (1 μM)
- Procedure
- 30 min 37 °C
- 20 min 65 °C
Annealing
- Mix
- 8 μL FW Phosphorylation mix
- 8 μL REV Phosphorylation mix
- 4 μL 10 mM NaCl low?
- 20 μL MilliQ
- Procedure
- Put reactions in (close to) boiling water
- Let it cool down naturally to ~35 °C
Restriction vector
- Mix
- 1 μL EcoRI
- 1 μL XbaI
- 2 μL Fast digest buffer (10x)
- 8 μL Vector DNA
- 8 μL MilliQ
- Procedure
- 37 °C, 30 min. incubation
- Heat inactivation EcoRI and XbaI
5 min. 80 °C 15 min. 65 °C
Ligation of Metal sensitive promoters in vector
- Mix
- 2 μL T4 Ligase Buffer
- 0.5 μL T4 Ligase
- 1 μL Restriction product (unpurified)
- 1 μL Annealed oligo’s
- 18 μL MilliQ
- Procedure
- Incubation 16 °C, 1 hour
- Heat inactivation Ligase
65 °C, 10 min.
Protocol #3
Restriction vectors
- Mix
- Incubate 1.5 h @ 37 °C
- Put to 1% agarose (1xTBE)
- Isolate ~3000 bp vector
- Check for presence of cut out ccdB death gene (~600 bp)
- Purify vector using gel purification kit
- End volume 30 μL H2O (MilliQ)
- Determine concentration using nanodrop
- Store to 4 °C until ligation
Phosphorylation of 5' ends & hybridization [1]
- (SENSE) Mix:
- 3 μL 100 µM sense oligo
- 1 μL 10 x PNK (polynucleotide kinase) buffer (Fermentas Buffer A)
- 2 μL 10mM ATP
- 1 μL T4 polynucleotide kinase (PNK)
- 3 μL MilliQ
- (for selfcloser control, do not add oligo's. Instead 6 μL MilliQ in total)
- (ANTI-SENSE) Mix:
- 3 μL 100 µM anti-sense oligo
- 1 μL 10 x PNK (polynucleotide kinase) buffer (Fermentas Buffer A)
- 2 μL 10mM ATP
- 1 μL T4 polynucleotide kinase (PNK)
- 3 μL MilliQ
- (for selfcloser control, do not add oligo's. Instead 6 μL MilliQ in total)
- Incubate @ 37 °C for 1.5 hours.
- Mix
- 10 μL Sense mixture
- 10 μL Anti-sense mixture
- 3 μL 0.5 M NaCl
- Place in boiling water for 3 min., and allow the reaction to cool to room temperature.
Ligation
- Mix
- 1 μL T4 ligase buffer
- 7.5 μL restricted vector (purified from gel)
- 1 μL annealing mix
- 0.5 μL T4 ligase
- Incubate
- 1h RT
- or
- ON @ 4 °C
Transformation
- Add 5 μL of ligation mixture to 50 μL of TOP10 chemically competent cells
- Heatshock, 45 sec. 42 °C
- Incubate 1 h @ 37 °C, 200 RPM
- Plate out on LB-agar + Kanamycin (30 μg/ml for pSB3K3) or Ampicillin (100 μg/mL for pSB1AC3)
- Plate out 50 μL & 200 μL of cell suspension
- Grow ON @ 37 °C
Checking transformations
- See if - control is empty for functioning antibiotics and death gene
- See how many colonies on + control for functioning competent cells
- See how many selfclosers and compare to samples (>10x on sample vs. selfcloser)
- If enough transformants, inoculate 3 - 5 colonies in an ON culture
- Alternatively perform colony PCR
Ligation
- Ligation
- μL ligation buffer
- 1 μL ligase
- μL vector
- μL insert
- Incubate
Making competent cells
Competent cells: TOP10 & DB3.1
- 10 mL ON culture is used to inoculate LB, 100 μL ON culture per 20 mL*
- Cultures are grown @ 37 °C until an OD600 of 0.2 ~ 0.3 is reached.
- Cultures are spinned down 5 min. @ 4000 rpm, 4 °C
- Supernatant is removed and pellet (per 20 mL culture) is resuspended in 5 mL chilled 0.1 M CaCl2
- Suspension is incubated on ice for 10 min.
- Suspensions are spinned down 5' @ 4000 rpm, 4 °C
- Supernatant is removed and pellet is resuspended in 1770 μL chilled 0.1 M CaCl2 and supplemented with 230 μL 87% glycerol prior to making aliquots.
- Cells are divided in 50 μL aliquotes
- Cells are snapfrozen in liquid nitrogen and stored @ -80 °C
* Cultures should be grown in the ratio 1:5 (medium:air), so 10 mL culture in a 50 mL greiner tube.
Transformation
Quality control
Colony PCR
Restriction analysis
List of solutions
Media
LB(Agar)
- 10 g (Bacto)Trypton
- 10 g NaCl
- 5 g Yeast extract
- Dissolve in 1 L demi water
- (1.5% Agar)
- Autoclave
- Store @ 60 °C
TB
Antibiotics
Ampicillin
100 mg/ml Ampicillin (1000x) Stock
- 1 g of Ampicillin sodium salt in 10 mL of demiwater (or 50% EtOH)
- Add NaOH or KOH to allow the Ampicillin to dissolve
- Filter sterilize 0.2 μm filter and aliquot
- Store -20 °C
Chloramphenicol
35 mg/ml Chloramphenicol (1000x) Stock
- 0.35 g in 10 mL 100% EtOH
- Filter sterilize 0.2 μm filter and aliquot
- Store -20 °C
Kanamycin
50 mg/ml Kanamycin(1000x) Stock
- g in 10 mL
- Filter sterilize 0.2 μm filter and aliquot
- Store -20 °C
Chemicals
0.1 M CaCl2
- 0.3319 g CaCl2
- Dissolve in 30 mL demi water
0.15 M NaCL (Saline solution, 0.9% NaCl)
- 9 g NaCl
- Dissolve in 1 L demi water
TBE buffer
4 M NaOH
1 M HCl
TB74S Buffer
- 0.605 g Tris (5mM)
- 8.76 g NaCl (150mM)
- Dissolve in 1 L Demi water
- Set pH with HCl to pH 7.4
Sodium Arsenite (III)
- 100mM Na-As solution
- filter sterilize