Team:Kyoto/Protocol

From 2011.igem.org

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{{Kyoto_Foreground|active_page=notebook}}
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{{Kyoto_Foreground|active_page=method}}
{{Kyoto_Background}}
{{Kyoto_Background}}
{{Kyoto_WikiDesign}}
{{Kyoto_WikiDesign}}
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<!-- main -->
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='''Protocol'''=
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<div id="main">
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Listed below our protocol for this project.<br>
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We hope you find them useful!!
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= '''Protocol''' =
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<html><a name="cloning"></a></html>
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<!--TODO--
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<html>
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<ul>
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  <li>Medium</li>
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</ul>
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</html>
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-->
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=== Medium for drosophila ===
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::{| class="wikitable"
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|+ [http://www.biol.se.tmu.ac.jp/fly/www/standard-medium.html Medium for drosophila]
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! width="300" |Materials
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! width="300" |Methods
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|-
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|
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* water : 500 mL
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* dry yeast : 20 g
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* corn flour : 45 g
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* glucose : 50 g
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* agarose : 3.5~5 g
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* propionic acid : 1.5 mL
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* 10 % p-hydroxybenzoate in 70 % Eternol : 5 g
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|
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# Stir dry yeast and agarose with about two-thirds of water. Then, autoclave it.
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# Stir corn flour and glucose with the remaining water.
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# Stir 1 and 2, then autoclave it again.
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# after autoclave, add propionic acid and 10 % p-hydroxybenzoate in 70 % Eternol into it.■
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|}
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<br/>
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===M9 medium===
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[[File:Cloning.PNG|link=https://2011.igem.org/Team:Kyoto/Cloning|Cloning]]<br>
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::{| class="wikitable"
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[[File:Medium.PNG|link=https://2011.igem.org/Team:Kyoto/Medium|Medium]]<br>
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! width="300" |Materials
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[[File:Measurement.PNG|link=https://2011.igem.org/Team:Kyoto/Measurement|Measurement]]
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! width="300" |Methods
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|-
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|
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* water : 1 L
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* Na2HPO4: 6 g
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* KH2PO4 : 3 g
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* NaCl : 0.5 g
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* NH4Cl : 1 g
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* 100 mM MgSO4 : 10 ml
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* 20 % glucose : 10 mL
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* 10 mM CaCl2 : 10 ml
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* 100 mM thiamine-HCl : 10 ml
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* 20 % casamino acid : 10 ml
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# Stir Na2HPO4, KH2PO4, NaCl and NH4Cl with water.
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# After autoclave, add 10 ml filter sterilized 100 mM MgSO4, 20 % glucose, 10 mM CaCl2, 100 mM thiamine-HCl.
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# If you need, add 10 ml filter sterilized 20 % casamino acid.
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|}
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<br/>
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===LB medium===
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::{| class="wikitable"
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! width="300" |Materials
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! width="300" |Methods
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|-
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|
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* water : 1 L
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* Tryptone: 10 g
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* Yeast extract : 5 g
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* NaCl : 10 g
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* Agar : 15g
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# Stir Tryptone, Yeast extract and NaCl with water.
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# If you make LB plates, add agar.
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# Autoclave.
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|}
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<br/>
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===SOB medium===
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::{| class="wikitable"
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! width="300" |Materials
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! width="300" |Methods
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|-
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|
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* water : 100 mL
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* Tryptone: 2 g
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* Yeast extract : 0.5 g
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* 5 M NaCl : 200 ul
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* 3 M KCl : 84 ul
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* 1 M MgSO4 : 1 ml
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* 1 M MgCl2 : 1 ml
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# Stir Tryptone and Yeast extract with water.
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# Add 200 ul 5 M NaCl and 84 ul 3 M KCl.
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# After autoclave, add 1 ml filter sterilized 10 mM MgSO4 and 10 mM MgCl2.
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|}
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<br/>
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===SOC medium===
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::{| class="wikitable"
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! width="300" |Materials
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! width="300" |Methods
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|-
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|
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* SOB : 100 ml
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* 2 M glucose: 1 ml
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# Add 2 M glucose to 100 ml SOB.
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|}
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<br/>
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===Buffer TB===
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::{| class="wikitable"
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! width="300" |Materials
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! width="300" |Methods
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|-
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|
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* water : 200 ml
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* PIPES : 3 g
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* CaCl2・2H2O : 0.22 g
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* 3 M KCl : 8.315 ml
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* KOH
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* MnCl2・4H2O : 1.09 g
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# Stir PIPES and CaCl2・2H2O with 100 ml water.
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# Add 8.315 ml 3 M KCl.
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# Add KOH and adjust pH 6.8.
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# Add MnCl2・4H2O.
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# Add water up to 200 ml.
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# Filter sterilize
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|}
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===DNS reaegnt===
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::{| class="wikitable"
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! width="300" |Materials
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! width="300" |Methods
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|-
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* 4.5% NaOH : 30 ml
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* 1% DNS : 88 ml
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* Rochelle salt : 25.5 g
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* 10% NaOH : 2.2 ml
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* Phenol : 1 g
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* Water : 7.8 ml
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* NaHCO3 : 0.69 g
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# Add 1% DNS 88ml and Rochelle salt 25.5 g to 4.5% NaOH 30 ml (A solution)
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# Add Phenol 1 g and water 7.8 ml to 10% NaOH 2.2 ml (B solution)
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# Add NaHCO3 6.9g to B solution 6.9 ml
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# Add A solution 118ml to B solution 6.9 ml
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# Leave 2 days
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# Store in brown bottle
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|}
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以下昨年度のコピペのため一部変更必要
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===Standard PCR===
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<ol>
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<li> Dilute template DNA. If the concentration of DNA is 2-100ng/&micro;L, transfer 1&micro;L to a clean tube and add 99&micro;L MilliQ.</li>
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<li> Dilute Primer. If the concentration of Primer is X&micro;M, dilute primer X timers and transfer 1&micro;L to a clean tube and add 99&micro;L MilliQ.</li>
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<li> Mix the following.
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  <ol>
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  <li> For use of KOD plus ver2:
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{|
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|-
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|25mM MgSO4
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|3&micro;L
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|-
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|2mM dNTPs
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|5&micro;L
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|-
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|10xBuffer for KOD plus ver.2
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|5&micro;L
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|-
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|Template DNA  (5ng/&micro;L)
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|5&micro;L
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|-
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|Primer Forward (10&micro;M)
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|1.5&micro;L
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|-
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|Primer Reverse (10&micro;M)
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|1.5&micro;L
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|-
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|KOD plus ver.2
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|1&micro;L
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|-
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|MilliQ
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|28&micro;L
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|-
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|Total
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|50&micro;L
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|}
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  </li>
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  <li> For use of KOD FX:
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{|
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|-
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|2mM dNTPs
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|10&micro;L
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|-
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|2xBuffer for KOD FX
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|25&micro;L
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|-
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|Template DNA
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|5&micro;L
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|-
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|Primer Forward (10&micro;M)
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|1.5&micro;L
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|-
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|Primer Reverse (10&micro;M)
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|1.5&micro;L
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|-
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|KOD FX
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|1&micro;L
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|-
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|MilliQ
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|6&micro;L
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|-
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|Total
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|50&micro;L
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|}
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  </li>
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  </ol>
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</li>
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<li> (If amplification is not succeeded, try at 4.5 or 6.0&micro;L 25mM MgSO4.)</li>
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<li> Let stand for 2min at 94&#x2103;.</li>
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<li> 25-40 cycles for 10s at 98&#x2103;, for 30s at Tm-5&#x2103;, and for 1min (1min for 1kb) at 68&#x2103; (Tm is temparature at which primer will dissolve).</li>
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<li> At 15&#x2103; forever. </li>
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<li> Agarose Gel Electrophoresis for confirmation.</li>
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</ol>
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===Screening PCR===
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<ol><li> Mix the following (Do on PCR Bench).
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<dl><dt> 10x PCR buffer (TAKARA)</dt><dd> 40&micro;L
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</dd><dt> 2.5mM dNTP</dt><dd> 8&micro;L
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</dd><dt> Primer-1 (10pmol/&micro;L)</dt><dd> 8&micro;L
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</dd><dt> Primer-2 (10pmol/&micro;L)</dt><dd> 8&micro;L
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</dd><dt> Ex Taq HS (TAKARA)</dt><dd> 1.6&micro;L
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</dd><dt> MilliQ&nbsp;</dt><dd> 334&micro;L (to total 400&micro;L)
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</dd></dl>
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</li><li> Dispense 25&micro;L to 15 tubes.
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</li><li> Pick a single colony and transfer it to each tubes.
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</li><li> Suspend the colony.
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</li><li> Let stand for 10min at 90&#x2103;.
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</li><li> 35 cycles for 30s at 94&#x2103;, for 30s 55&#x2103;, and for 1min at 72&#x2103;.
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</li><li> Let stand for 4min at 72&#x2103;.
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</li><li> Add 5mL Loading Buffer to the tubes.
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</li><li> Agalose Gel Electrophoresis for confirmation.
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</li><li> Negative Control: Use nothing.
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</li><li> Positive Control: Use a colony that will yield a product with this primers.
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</li></ol>
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===Mutagenesis (Point mutation, Deletion, Insertion)===
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<ol><li> Mix the following.
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<dl><dt> 10xBuffer</dt><dd> 5&micro;L
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</dd><dt> 2mM dNTP</dt><dd> 5&micro;L
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</dd><dt> Primer Forward (10&micro;M)</dt><dd> 1.5&micro;L
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</dd><dt> Primer Reverse (10&micro;M)</dt><dd> 1.5&micro;L
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</dd><dt> Template Plasmid (50ng/&micro;L)</dt><dd> 1&micro;L
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</dd><dt> KOD plus ver.2</dt><dd> 1&micro;L
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</dd><dt> MilliQ</dt><dd> 35&micro;L
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</dd><dt> Total</dt><dd> 50&micro;L
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</dd></dl>
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</li><li> Prepare control: instead of KOD plus ver.2, add 1&micro;L MilliQ.
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</li><li> Let stand for 2min at 94&#x2103;.
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</li><li> X cycles (1 cycle for 1kb) for 10s at 98&#x2103; and for Ymin (1min for 1kb) at 68&#x2103;.
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</li><li> Hold at 4&#x2103;.
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</li><li> Take 25&micro;L of the solutions into fresh tubes.
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</li><li> Add 1&micro;L <i>Dpn</i>I (10U/&micro;L).
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</li><li> Let stand for 1h at 37&#x2103;.
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</li><li> Agarose gel electrophoresis, using 5&micro;L of the solution for confirmation.
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</li><li> Mix the following.
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<dl><dt> Sample</dt><dd> 2&micro;L
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</dd><dt> Ligation high</dt><dd> 5&micro;L
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</dd><dt> T4 Polynucleotide Kinase (5U/&micro;L)</dt><dd> 1&micro;L
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</dd><dt> MilliQ</dt><dd> 7&micro;L
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</dd><dt> Total</dt><dd> 15&micro;L
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</dd></dl>
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</li><li> Let stand for 1h at 16&#x2103;.
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</li><li> Transformation, using 10&micro;L of the solution.
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</li></ol>
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===PCR Purification===
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<ol><li> Use Wizard SV Gel and PCR Clean-Up System by Promega.
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</li><li> Combine 1 part sample (PCR product) with one part Membrane Binding Solution (e.g. 50&mu;l sample+ 50&mu;l).
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</li><li> Apply the solution to the column, and let stand for 1min.
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</li><li> Centrifuge for 1min at 13000rpm. Discard the flow-through.
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</li><li> Add 700&micro;l Membrane Wash Solution.
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</li><li> Centrifuge for 1min and discard the through.
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</li><li> Add 500&mu;l Membrane Wash Solution.
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</li><li> Centrifuge for 5min and discard the through.
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</li><li> Place the column in a clean tube.
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</li><li> Add 60&micro;l MilliQ to the center of each column, let stand for 1min.
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</li><li> Centrifuge for 1min at 13000rpm.
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</li><li> Discard the column.
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</li></ol>
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===Solubilization of Antibiotics===
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# Mix the following (Final concentration is 50mg/mL).
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#* Ampicillin:
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#*; Ampicillin: 1.0g
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#*; MilliQ: 20mL
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#* Kanamycin:
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#*; Kanamycin: 0.5g
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#*; MilliQ: 10mL
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# Dispense 1.1mL of the solution into 1.5mL tubes.
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# Store in the -20&#x2103; freezer.
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===Transformation===
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# Unfreeze conpitent cells on ice.
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# Dry a plate by letting the plate upside down and partly open in incubator.
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# Add 1&micro;L DNA solution and 20&micro;L compitent cells to 1.5mL tube, let stand for 30min on ice. If few colony is observed, increase the amount of the compitent cells or DNA, but make the amount of DNA not to get over that of the compitent cells.
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# Heatshock for 60s at 42&#x2103;.
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# Let stand for 2min on ice.
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# Culture for 1h in preculture medium (LB or SOC medium), and plate by using spreader. Do not heat spreader too much because e.coli will dead for heat.
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===Miniprep===
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# Use QIAprep Spin Miniprep Kit Cat. No. 27104 by QIAGEN
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# Pick a single colony from a freshly streaked selective plate and inoculate a culture of about 3mL LB medium containing the appropriate selective antibiotic.
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# Incubate at 170rpm for 8h at 37&#x2103; with vigorous shaking.
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# Transfer a half of the culture to a tube.
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# Harvest the bacterial cells by centrifugation at 14,000g for 1min at 4&#x2103;. Remove the medium by decanting.
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# Transfer the half of the culture to same tube and harvest as same. Remove the medium by pippetting.
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# Resuspend pelleted bacterial cells in 250&micro;L Buffer P1 and mix thoroughly by pippeting.
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# Add 250&micro;L Buffer P2 and mix thoroughly by inverting the tube gently 4-6 times.
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# Add 350&micro;L Buffer N3 and mix immediately and thoroughly by inverting the tube 4-6 times.
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# Centrifuge for 10min at 14,000g at 4&#x2103;.
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# Apply the supernatants from step 10 to the QIAprep spin column by pipetting.
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# Centrifuge for 10s in a table-top microcentrifuge. Discard the flow-through.
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# Wash the QIAprep spin column by adding 0.5mL Buffer PB and centrifuging for 10s in a table-top microcentrifuge. Discard the flow-through.
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# Wash QIAprep spin column by adding 0.65mL Buffer PeE and centrifuging fo 10s in a table-top microcentrifuge.
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# Discard the flow-through, and centrifuge for and additional 1min to remove residual wash buffer.
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# Place the QIAprep column in a clean tube. To elute DNA, add 50&micro;L water to the center of each QIAprep spin column, let stand for 1min, and centrifuge for 1min.
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# Discard the QIAprep spin column.
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# Measure the concentration of DNA by using eppendorf BioPhotometer plus.
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# Restriction Digestion.
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# Agarose Gel Electrophoresis for Confirmation.
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===Ethanol Precipitation===
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# Use Ethachinmate (NIPPON GENE、312-01791).
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# Add 3.3 &micro;L of 3M Sodium Acetate (attached with Ethachinmate) into 100&micro;L of DNA solution.
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# Add 1&micro;L of Ethachinmate.
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# Vortex.
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# Add ethanol, 200-250&micro;L.
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# Vortex. 
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# Centrifuge at 12000xg for 5min.
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# Precipitation.
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===RNA Extraction===
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# Use　ISOGEN－LS（NIPPON　GENE,311-02621）
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# Add 1mL ISOGEN-LS to sample and vortex.
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# Store for 5min on ice.
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# Add 250&micro;L chloroform and shake vigorously for 15 sec.
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# Store for 3min. on ice.
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# Centrifuge 17400xg for 10min. at 4&#x2103;.
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# Transfer aqueous phase to another tube and add 0.8 volume isopropanol.
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# Store for 10min.  on ice.
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# Centrifuge 17400xg for 10min. at 4&#x2103;.
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# Discard the supernatant .
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# Add 800&micro;L 80% ethanol and vortex.
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# Centrifuge 7500xg for 5min. at 4&#x2103;.
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# Discard the supernatant .
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# Dry briefly.
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# Dissolve in nuclease-free water.
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</div>
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<!-- end of main -->
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Latest revision as of 02:26, 6 October 2011

Protocol

Listed below our protocol for this project.
We hope you find them useful!!

Cloning
Medium
Measurement

Retrieved from "http://2011.igem.org/Team:Kyoto/Protocol"