Team:KIT-Kyoto/Notebook/Protocol

From 2014.igem.org

(Difference between revisions)
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    <ul class="slidemenu">
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    <li class="btn">
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      <a href="">PCR
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      </a>
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      </li>
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    <ul class="slidemenu">
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       <a href="">LB medium
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       <a href="">AGE
       <a href="">AGE
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      </a>
 
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      </li>
 
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      <a href="">PCR
 
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   <div class="main-contents">
   <div class="main-contents">
   <h1>Protocol</h1>
   <h1>Protocol</h1>
 +
<!--PCR-->
 +
  <div class="accordion">
 +
  <div class="scroll">
 +
  </div>
 +
  <h2><a href="javascript:void(0);">PCR</a></h2>
 +
  <div class="ac">
 +
  <p class="sentence">
 +
  <strong>Materials</strong>
 +
  <table class="materials">
 +
  <tr>
 +
    <td>Buffer for KOD-FX-NEO</td>
 +
    <td>50μL</td>
 +
  </tr>
 +
  <tr>
 +
    <td>dNTP</td>
 +
    <td>20μL</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Primer mix</td>
 +
    <td>1.0μL</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Template DNA</td>
 +
    <td>0.5μL</td>
 +
  </tr>
 +
  <tr>
 +
    <td>KOD-FX-NEO (TOYOBO)</td>
 +
    <td>2.0μL</td>
 +
  </tr>
 +
  <tr>
 +
    <td>H2O</td>
 +
    <td>26.5μL</td>
 +
  </tr>
 +
  <tr>
 +
    <th>Total</th>
 +
    <th>100μL</th>
 +
  </tr>
 +
  </table>
 +
  <br>
 +
  <strong>Procedure</strong>
 +
  <ul class="procedure">
 +
    <li>Add buffer, dNTP, primer mix, Template DNA, KOD-FX-NEO and distilled water to an Eppendorf tube and mix
 +
    </li>
 +
    <li>Place the PCR tubes into the PCR machine and set the program
 +
  </ul>
 +
  <br>
 +
<strong>PCR Profiles for KOD-FX-NEO</strong>
 +
  <table class="materials">
 +
  <tr>
 +
    <td>Predenature</td>
 +
    <td>Denature</td>
 +
    <td>Annealing</td>
 +
    <td>Extension</td>
 +
    <td>Final Extension</td>
 +
  </tr>
 +
  <tr>
 +
    <td>98.0°C KOD-FX-NEO</td>
 +
    <td>98.0°C</td>
 +
    <td>51.0°C</td>
 +
    <td>68.0°C</td>
 +
    <td>68.0°C</td>
 +
  </tr>
 +
  <tr>
 +
    <td>2 minutes</td>
 +
    <td>10 seconds</td>
 +
    <td>30 seconds</td>
 +
    <td>1 minutes</td>
 +
    <td>2 minutes</td>
 +
  </tr>
 +
  <tr>
 +
    <td>1 cycle</td>
 +
    <td>30 cycles</td>
 +
    <td></td>
 +
    <td></td>
 +
    <td>1 cycle</td>
 +
  </tr>
 +
  </table>
 +
 
 +
</p>
 +
</div>
 +
</div>
 +
<!--PCR終わり-->
<!-- LB Brothプロトコル -->
<!-- LB Brothプロトコル -->
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</div>
</div>
<!--AGE終わり-->
<!--AGE終わり-->
-
 
-
<!--PCR-->
 
-
  <div class="accordion">
 
-
  <div class="scroll">
 
-
  </div>
 
-
  <h2><a href="javascript:void(0);">PCR</a></h2>
 
-
  <div class="ac">
 
-
  <p class="sentence">
 
-
  <strong>Materials</strong>
 
-
  <table class="materials">
 
-
  <tr>
 
-
    <td>Buffer for KOD-FX-NEO</td>
 
-
    <td>50μL</td>
 
-
  </tr>
 
-
  <tr>
 
-
    <td>dNTP</td>
 
-
    <td>20μL</td>
 
-
  </tr>
 
-
  <tr>
 
-
    <td>Primer mix</td>
 
-
    <td>1.0μL</td>
 
-
  </tr>
 
-
  <tr>
 
-
    <td>Template DNA</td>
 
-
    <td>0.5μL</td>
 
-
  </tr>
 
-
  <tr>
 
-
    <td>KOD-FX-NEO (TOYOBO)</td>
 
-
    <td>2.0μL</td>
 
-
  </tr>
 
-
  <tr>
 
-
    <td>H2O</td>
 
-
    <td>26.5μL</td>
 
-
  </tr>
 
-
  <tr>
 
-
    <th>Total</th>
 
-
    <th>100μL</th>
 
-
  </tr>
 
-
  </table>
 
-
  <br>
 
-
  <strong>Procedure</strong>
 
-
  <ul class="procedure">
 
-
    <li>Add buffer, dNTP, primer mix, Template DNA, KOD-FX-NEO and distilled water to an Eppendorf tube and mix
 
-
    </li>
 
-
    <li>Place the PCR tubes into the PCR machine and set the program
 
-
  </ul>
 
-
  <br>
 
-
<strong>PCR Profiles for KOD-FX-NEO</strong>
 
-
  <table class="materials">
 
-
  <tr>
 
-
    <td>Predenature</td>
 
-
    <td>Denature</td>
 
-
    <td>Annealing</td>
 
-
    <td>Extension</td>
 
-
    <td>Final Extension</td>
 
-
  </tr>
 
-
  <tr>
 
-
    <td>98.0°C KOD-FX-NEO</td>
 
-
    <td>98.0°C</td>
 
-
    <td>51.0°C</td>
 
-
    <td>68.0°C</td>
 
-
    <td>68.0°C</td>
 
-
  </tr>
 
-
  <tr>
 
-
    <td>2 minutes</td>
 
-
    <td>10 seconds</td>
 
-
    <td>30 seconds</td>
 
-
    <td>1 minutes</td>
 
-
    <td>2 minutes</td>
 
-
  </tr>
 
-
  <tr>
 
-
    <td>1 cycle</td>
 
-
    <td>30 cycles</td>
 
-
    <td></td>
 
-
    <td></td>
 
-
    <td>1 cycle</td>
 
-
  </tr>
 
-
  </table>
 
-
 
 
-
</p>
 
-
</div>
 
-
</div>
 
-
<!--PCR終わり-->
 
<!--Ligation-->
<!--Ligation-->

Revision as of 09:20, 30 September 2014

Protocol

PCR

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 Profiles 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

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)
  • 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 and cultivate (37℃, 120 rpm) until reaching a cell density of OD600 = 0.5
  • Add IPTG (10 μL) to the medium (25 ml)
  • Further cultivation for 3 hours


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

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

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

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