Team:KIT-Kyoto/Notebook/Protocol

From 2014.igem.org

(Difference between revisions)
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   <table class="materials">
   <table class="materials">
   <tr>
   <tr>
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     <th colspan="2">Buffer for KOD-FX-NEO</th>
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     <th>Buffer for KOD-FX-NEO</th>
 +
    <td>50μL</td>
   </tr>
   </tr>
   <tr>
   <tr>
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     <td>20μL</td>
     <td>20μL</td>
   </tr>
   </tr>
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   <tr>  
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   <tr>
     <td>Primer mix</td>
     <td>Primer mix</td>
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     <td>1μL</td>
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     <td>1.0μL</td>
   </tr>
   </tr>
   <tr>  
   <tr>  
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     <td>KOD-FX-NEO</td>
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    <td>Sample</td>
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     <td>2μL</td>
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    <td>0.5μL</td>
 +
  </tr>
 +
  <tr>
 +
     <td>KOD-FX-NEO (TOYOBO)</td>
 +
     <td>2.0μL</td>
   </tr>
   </tr>
   <tr>  
   <tr>  
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   <tr>  
   <tr>  
     <th>Total</th>
     <th>Total</th>
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     <th>50μL</th>  
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     <th>100μL</th>  
   </tr>
   </tr>
   </table>
   </table>
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   <strong>Procedure</strong>
   <strong>Procedure</strong>
   <ul class="procedure">
   <ul class="procedure">
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    <li>Bring the volume up forward primer to 100 pmol/μL with sterile dH2O
+
     <li>Add buffer, dNTP, primer mix, sample, KOD-FX-NEO and distilled water to an Eppendorf tube and mix  
-
    </li>
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     <li>Add 10 μL of this primer solution and 80 μL of H2O into another tube
+
-
    <br>Make 10 times dilution
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-
    </li>
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    <li>Use 1 μL primer mix for PCR
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-
    <br>Reaction composition is below
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     </li>
     </li>
 +
    <li>Clone
   </ul>
   </ul>
   <br>
   <br>

Revision as of 03:50, 23 September 2014

Protocol

LB Broth/ LB Medium

Materials

Tryptone final concentration: 1%(w/v)
Yeast extract final concentration: 0.5%(w/v)
Sodium chloride F.W. =58.44 final concentration: 1%(w/v)
5M Sodium hydroxide solution

Procedure
  • Dissolve tryptone (1.0 g), yeast extract (500 mg) and sodium chloride (1.0 g) in distilled water (90 ml)
  • Adjust pH to 7.0 by adding 20μL of 5M sodium chloride
  • Dilute solution with distilled water and bring volume to 100 ml
  • Autoclave

Note
  • Add antibiotics to medium at 1/1000

LB Agar

Materials

Agar powder final concentration: 1.5 %(w/v)
LB medium

Procedure
  • Add agar powder (6.0 g) to LB medium (400 ml)
  • Dissolve it by autoclaving
  • Stir up with magnetic stirrer
  • Cool it down to the room temperature in order to make it to gel form

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)
  • Dilute solution with distilled water and bring up volume to 100 ml
  • Sterilize by autoclave

Note
  • To make agar plate, add agar powder (final concentration: 1.5%) at procedure 1.

Main Culture

Materials

LB medium 100ml
IPTG 10μL
Sample 500μL

Procedure
  • Add samples to LB medium, cultivate at 37°C in shaken culture (120 rpm) until reaching a cell density of OD600 0.5A
  • Add IPTG (10 μL) to the sample (25 ml)
  • Cultivate at 37°C in shaken culture (120 rpm) for 3 hours

Note

Transformation (E.coli)

Materials

Sample 10μL
Competent cell 20μL

Procedure
  • Thaw the competent cells on ice
  • Add 10 μL of sample into thawed competent cells
  • Cool an Eppendorf tube, which contains competent cells and samples, with ice for one hour, then Heat shock the cells by immersion in pre-hearted water bath at 41°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
  • Seed 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

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
Phe-Chl
Cracking solution

Procedure
  • Dispense cracking solution (50 μL) each into Eppendorf 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
  • Check the bands by agar gel electrophoresis

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 and run the electrophoresis
  • Stop the electrophoresis when the BPB reaches 2/3 of the gel
  • Soak the gel in 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 Gel (%) 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

PCR

Materials

Buffer for KOD-FX-NEO 50μL
dNTP 20μL
Primer mix 1.0μL
Sample 0.5μL
KOD-FX-NEO (TOYOBO) 2.0μL
H2O 26.5μL
Total 100μL

Procedure
  • Add buffer, dNTP, primer mix, sample, KOD-FX-NEO and distilled water to an Eppendorf tube and mix
  • Clone

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

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