Team:KIT-Kyoto/Notebook/Protocol
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Revision as of 06:01, 8 October 2014
Protocol
Miniprep
Materials
Buffer 1 | 250μL |
Buffer 2 | 250μL |
Buffer 3 | 350μL |
Buffer 4 | 500μL |
Buffer 5 | 700μL |
Distilled water | 100μL |
Sample |
Procedure
- Suspend the sample in buffer 1 (1.5 ml sample tube)
- Add buffer 2 to the sample and mix it
- Add buffer 3 to the sample and mix it
- Centrifuge for 5 minutes at 13,000 rpm and apply the supernatants to the column
- Add buffer 4 and centrifuge for 1 minute at 13,000rpm then throw away the filter paper
- Add buffer 5 and centrifuge for 1 minute at 13,000rpm then throw away the filter paper
- Centrifuge again for 1 minute at 13,000 rpm
- Place the column on a new sample tube and add 100 microL distilled water
- Centrifuge for 1 minute at 6,000 rpm
Recipes for Buffer
Buffer 1 (Suspension Buffer) | 50 mM Tris-HCl and 10 mM EDTA, pH 8.0 (25°C) 50 μg/ml RNase A |
Buffer 2 (Lysis Buffer) | 0.2 M NaOH and 1% SDS |
Buffer 3 (Neutralization and Binding Buffer) | 4 M guanidine hydrochloride and 0.5 M potassium acetate, pH 4.2 |
Buffer 4 (Wash Buffer) | 5 M guanidine hydrochioride and 0.5 M potassium acetate, pH 4.2 |
Buffer 5 (Wash Buffer) | 20 mM NaCl, 2 mM Tris-HCl, pH 7.5 (25°C) [final conentrations after addition of ethanol] with 80% ethanol |
PCR-1
Materials
Buffer for KOD-FX-NEO | 50μL |
dNTP | 20μL |
Primer mix | 1.0μL |
Template DNA | 0.5μL |
KOD-FX-NEO (TOYOBO) | 2.0μL |
H2O | 26.5μL |
Total | 100μL |
---|
Procedure
- Add buffer, dNTP, primer mix, Template DNA, KOD-FX-NEO and distilled water to an Eppendorf tube and mix
- Place the PCR tubes into the PCR machine and set the program
PCR Profile for KOD-FX-NEO
Predenature | Denature | Annealing | Extension | Final Extension |
98.0°C KOD-FX-NEO | 98.0°C | 51.0°C | 68.0°C | 68.0°C |
2 minutes | 10 seconds | 30 seconds | 1 minutes | 2 minutes |
1 cycle | 30 cycles | 1 cycle |
PCR-2
Materials
Buffer for KOD-FX-NEO | 50μL |
dNTP | 20μL |
Primer mix | 1.0μL |
Template DNA | 0.5μL |
KOD-FX-NEO (TOYOBO) | 2.0μL |
H2O | 26.5μL |
Total | 100μL |
---|
Procedure
- Add buffer, dNTP, primer mix, Template DNA, KOD-FX-NEO and distilled water to an Eppendorf tube and mix
- Place the PCR tubes into the PCR machine and set the program
PCR Profile for KOD-FX-NEO
Predenature | Denature | Annealing | Extension | Final Extension |
98.0°C KOD-FX-NEO | 98.0°C | 51.0°C | 68.0°C | 68.0°C |
2 minutes | 10 seconds | 30 seconds | 1 minutes | 2 minutes |
1 cycle | 30 cycles | 1 cycle |
AGE
Materials
Sample | 5μL |
Agarose gel | |
2X Loading Buffer Triple Dye (NIPPON GENE) | 5μL |
1X TAE Buffer |
Procedure
- Set an agarose gel on an electrophoresis chamber
- Add 1X TAE buffer to the electrophoresis chamber
Note: Do not generate bubbles under the gel - Add 2X loading buffer to electrophoresis samples
- Apply samples on agarose gel wells
- Set an appropriate voltage (100v) and run the electrophoresis
- Stop the electrophoresis when the BPB reaches 2/3 of the gel
- Soak the gel in EtBr (ethidium bromide) and dye it for 20 minutes
- Place plastic cooking wrap on the trans-illuminator and irradiate UV to the gel on the wrap
- Take photographs of the gel by using a trans-illuminator
Agarose Concentration Versus Optical Range of DNA Size
Agarose Concentration (%) | DNA (kbp) |
0.3 | 5-60 |
0.6 | 1-20 |
1.0 | 0.3-7 |
1.5 | 0.2-4 |
2.0 | 0.1-2 |
Ligation
Materials
DNA sample (cut out from the gel) | |
Distilled water | 5μL |
DNA ligase | 5μL |
Procedure
- Add DNA sample, distilled water and DNA ligase into a micro test tube and vortex
- Ligation for 5minutes at room temperature
Transformation (E.coli)
Materials
DNA Sample | 10μL |
Competent cell | 50μL |
Procedure
- Thaw the competent cells on ice
- Add 10 μL of sample into thawed competent cells
- Cool the sample tube, which contains competent cells and DNA samples, with ice for 1 hour, then Heat shock the cells by immersion in pre-hearted water bath at 42°C for 30 seconds
- Place the tube on ice for 2 minutes to cool it down
- At a clean bench, add 1.0 ml of LB medium into the tube and suspend it
- Incubate the tube at 37°C for 35 minutes
- Harvest the cells by centrifuge
- Spread the transformed competent cells onto the agar plate and incubate it at 37°C overnight
Pre-culture
Materials
Sample | |
Medium | 20ml |
Procedure
- Scrape samples from the agar plate and inoculate them on medium
- Cultivate at 37°C in a shaken culture overnight
Main Culture
Materials
LB medium with appropriate antibiotics (20 ml) | 100ml |
Sample (E.coli cells) |
Procedure
- Scrape samples from the agar plate and inoculate them in liquid media
- Cultivate overnight (37˚C, 120 rpm)
Protein Extraction (E.coli)
Materials
Sample | |
Fast Break Cell Lysis Reagent, 10X (Promega) | |
50mM potassium phosphate buffer (=pH6.8) | |
SDS sample buffer |
Procedure
- Separate samples into two and harvest by centrifuge
- Add potassium phosphate buffer, then mix and remove medium completely
- Add Fast Break Cell Lysis Reagent, 10X at the ratio of Fast Break Buffer Cell Lysis Readent,10X: Samples=1:9 and extract protein for 15 minutes at room temperature
Colony Sweep
Materials
Sample | |
Phenol/Chloroform water-saturated solution (Phe/Chl) | |
Cracking solution 3% w/v SDS, 50 mM Tris-base, pH12.6 |
Procedure
- Dispense cracking solution (50 μL) each into sample tubes
- Collect the sample and suspend it into cracking solution
- Incubate at 65°C for 10 minutes
- Add Phe/Chl and BPB pigment and vortex
- Centrifuge at 14,000 rpm for 5 minutes
- Apply the samples (upper layer) to agarose gel with loading dye
- Check the bands by agar gel electrophoresis
SDS-PAGE
Materials
Sample | |
Separating Gel | |
Stacking Gel |
Procedure
- Place stacking gel on separating gel
- Rinse the wells of gel with distilled water
- Load prepared samples into wells
- Run the electrophoresis (25 mA for 75 min)
- Check the bands with CBB stain
Separating Gel
Acylamide (%) | 7.5 | 10 | 12.5 | 15 | 17.5 |
MiliQ H2O (ml) | 3.89 | 3.22 | 2.55 | 1.87 | 1.2 |
Acrylamide/Bis-acrylamide (30%/0.8% w/v) | 1.99 | 2.7 | 3.38 | 4.04 | 4.7 |
1.5M Tris-HCl(pH8.8) (ml) | 2 | 2 | 2 | 2 | 2 |
10% (w/v)SDS (μl) | 80 | 80 | 80 | 80 | 80 |
10% (w/v) ammonium persulfate (AP) (μl) | 27 | 27 | 27 | 27 | 27 |
TEMED (μl) | 4 | 4 | 4 | 4 | 4 |
Stacking Gel
MiliQ H2O (ml) | 2.89 |
30% (w/v) acrylamide (ml) | 0.79 |
0.5M Tris-HCl(pH6.8) (ml) | 1.25 |
10% SDS (μl) (ml) | 50 |
10% APS (μl) (ml) | 17 |
TEMED (μl) (ml) | 5 |
Western Blotting
Materials
BufferⅠ | |
BufferⅡ | |
BufferⅢ | |
Distilled water | 2ml |
PBS | |
PBS-S | |
PBS-T | |
PBS-TS | |
PonceauS | |
PVDF membrane | 1 sheet |
Whatman paper | 6 sheets |
Hybridization bag | 1 |
Peroxidase Stain Kit | one drop for each |
antiglutathione S - transferase (和光純薬工業株式会社製) | 1μL |
Procedure
- Cut the gel in appropriate size
- Add BufferⅢ and gel then shake it gently
- Soak the membrane on ethanol then soak it in BufferⅢ and percolate
- 2, 1, 3 Whatman papers (all in the same size) on BufferⅠ, BufferⅡ, BufferⅢ respectively. wet the surface of the blotter
- Blot at the constant current of membrane's area ×2.5 mA
- Dye the membrane with Ponceau S for 5 minutes rinse it with distilled water and scan it
- Shake and wash with PBS-TS (3 minutes ×3 times)
- Put the membrane in a hybridization bag add PBS-S antiglutathione S-transferase and shake it for one hour at room temperature
- Shake and wash with PBS-T twice (5 min/10 min)
- Shake and wash with PBS twice (5 min/5 min)
- Add one drip of 3 Peroxidase Stain Kits and distilled water
- Scan it
Reagent
- BufferⅠ: bring to 300 ml with Tris base 10.9g, MetOH60ml/H2O
- BufferⅡ: bring to 300 ml with Tris base 0.9g, MetOH60ml/H2O
- BufferⅢ: bring to 300 ml with Tris base 0.91g, Boric acid10.5mg, MetOH60ml/H2O
- PBS-S: PBS with 1% SkimMilk
- PBS-T: PBS with 0.05% Tween20
- PBS-TS: PBS with 0.05% Tween20+1% SkimMilk
LB Broth/ LB Medium
Materials
Tryptone | final concentration: 1%(w/v) |
Yeast Extract | final concentration: 0.5%(w/v) |
NaCl | final concentration: 1%(w/v) |
5M NaOH |
Procedure
- Dissolve Tryptone (1.0 g), Yeast Extract (500 mg) and NaCl (1.0 g) in distilled water (90 ml)
- Adjust pH to 7.0 by adding 20μL of 5M NaOH
- Fill up to 100 ml with distilled water
- Autoclave
Note
- To make agar plate, add agar powder at the final concentration of 2 %(w/v) in Procedure 2
YPD Broth/YPD Medium
Materials
Peptone | final concentration: 2%(w/v) |
Yeast extract | final concentration: 1%(w/v) |
Glucose | final concentration: 2%(w/v) |
Procedure
- Dissolve peptone (2.0 g), yeast extract (1.0 g) and glucose (2.0 g) to distilled water (90 ml)
- Fill up to 100 ml with distilled water
- Sterilize by autoclave
Note
- To make agar plate, add agar powder (final concentration: 2.0%) at procedure 1.