Team:KIT-Kyoto/Notebook/Protocol

From 2014.igem.org

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     <li>Remove isopropyl alcohol gently so that the pellet will not break
     <li>Remove isopropyl alcohol gently so that the pellet will not break
     </li>
     </li>
-
     <li>Add 1,000μL of 75% ethanol and centrifuge at 14,500 rpm for 5 minutes at 4°C
+
     <li>Add 1,000 μL of 75% ethanol and centrifuge at 14,500 rpm for 5 minutes at 4°C
     </li>
     </li>
     <li>Dry it by aspirator for 10 minutes
     <li>Dry it by aspirator for 10 minutes
     </li>
     </li>
-
     <li>Add 25μL of distilled H2O and mix
+
     <li>Add 25 μL of distilled H2O and mix
     </li>
     </li>
   </ul>
   </ul>

Revision as of 10:37, 14 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 13,000 rpm then throw away the filter paper
  • Add buffer 5 and centrifuge for 1 minute at 13,000 rpm 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 Primer Design
Lot.No Oligo Base Number Sequence
T14F190235 pGEX6P-2F1 30 CACACAGGAACTAGTATTCATGTCCCCTAT
T14F190236 pGEX6P-2F2 30 GGATCTGGAAGTTCTGTTCCACTAGTCCCT
T14F190237 pGEX6P-2R 29 TCATCACCGAAACGCTCGAGGCAGATCGT


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

Restriction Digest

Materials

DNA sample 6μL
Buffer 1μL
Restriction Enzyme 0.5μL
Distilled water 2.5μL

Procedure
  • Add all materials to a tube and mix them gently
  • Incubate at 37˚C for the enzyme reaction for 15 minutes


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 (100 V) and run the electrophoresis
  • Stop the electrophoresis when the BPB reaches 2/3 of the gel
  • Soak the gel in EtBr (ethidium bromide) solution 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

DNA RefinementⅠ

Materials

DNA sample 200μL
distilled H2O 400μL
CH3COONa 50μL
Phe/Chl 700μL
Isopropyl alcohol 750μL
75% Ethanol 1000μL

Procedure
  • Add materials (DNA, H2O, CH3COONa, and Phe/Chl) to sample tube and vortex
  • Centrifuge at 14,500 rpm for 10 minutes at room temperature
  • Transfer the supernatant to a new sample tube
  • Add 750 μL of isopropyl alcohol to the sample tube and vortex
  • Centrifuge at 14,500 rpm for 10 minutes at 4°C
  • Remove isopropyl alcohol gently so that the pellet will not break
  • Add 1,000 μL of 75% ethanol and centrifuge at 14,500 rpm for 5 minutes at 4°C
  • Dry it by aspirator for 10 minutes
  • Add 25 μL of distilled H2O and mix

Note
  • Phe/Chl composition Phenol:Chloroform:Isoamyl alcohol=25:24:1

Ligation

Materials

DNA sample 5μL
DNA ligase (Ligation High from Nippon gene) 5μL

Procedure
  • Mix DNA sample and DNA ligase in a sample tube gently
  • Ligation for 15 minutes 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 Reagent,10X: Samples=1:9 and extract protein for 15 minutes at room temperature

Protein Extraction (Saccharomyces cerevisiae)

Materials

Glass Beads
50 mM potassium phosphate buffer (pH6.8)
SDS sample buffer

Procedure
  • Harvest yeast cells by centrifuge at 3,000 rpm for 4 minutes at room temperature
  • Wash cells once with potassium phosphate buffer
  • Cool down the sample tube on ice for 1 minute
  • Add the same amount of glass beads as the sample then add 20 μL of potassium phosphate buffer and mix
  • Disrupt the cells by FastPrep 24 (MP Biochemicals) for 45 seconds at speed 4.5
  • Cool down the sample tube on ice for 1 minute
  • Add 80 µl of potassium phosphate buffer, cool it down and centrifuge for 5 minutes at 14,500 rpm at 4°C
  • Transfer 40 µl of the supernatant and mix with 8 µl of SDS sample buffer
  • Treat the sample with heat for 5 minutes at 100˚C

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 (Nacalai Tesque) 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 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 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.

SD Medium

Materials

Yeast nitrogen base 0.67%(w/v)
Glucose 2% (w/v)
Adenine 0.004% (w/v)
Histidine 0.002% (w/v)
Leucine 0.006% (w/v)
Lysine 0.003% (w/v)
Methionine 0.002% (w/v)
Tryptophan 0.004% (w/v)

Procedure
  • Dissolve yeast nitrogen base (6.7 g), adenine (40 mg), histidine (20 mg), leucine (60 mg), lysine (30mg), tryptophan (40mg) and methionine (20mg) into 40 ml of distilled H2O, and then fill up to 50 ml with H2O.
  • Dissolve glucose (20.0 g) into 40 ml of distilled H2O, and then fill up to 50 ml with H2O.
  • Sterilize each solution by autoclave.
  • Mix solutions after cooling it down.

Note
  • Autoclave glucose and agar plate separately from other materials