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{{Team:HokkaidoU_Japan/CSS}} | {{Team:HokkaidoU_Japan/CSS}} | ||
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− | < | + | <html> |
− | < | + | <head> |
− | + | <style type="text/css"> | |
− | + | .ka-soru { | |
+ | cursor: pointer | ||
+ | } | ||
− | + | .ichi{ | |
− | + | position: absolute; | |
− | + | left: 30px; | |
− | + | } | |
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− | < | + | </style> |
− | + | ||
− | + | ||
− | + | </head> | |
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− | < | + | <body> |
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<br> | <br> | ||
− | < | + | <img src="https://static.igem.org/mediawiki/2016/2/29/T--HokkaidoU_Japan--protocols.png" alt="Protcols"> |
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+ | <div align="right"><a href="https://2016.igem.org/Team:HokkaidoU_Japan/Notebook"><span class="big">Notebook</span></a></div> | ||
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− | < | + | <div class="ichi"> |
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<br> | <br> | ||
− | < | + | <h1 onClick="hyoji1()"><span class="ka-soru">PCR</span></h1> |
− | < | + | |
− | + | ||
− | </ | + | |
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− | < | + | <div id="disp1"> |
− | < | + | <span class="nomal2"> |
− | + | Use KOD -Plus- Neo (TOYOBO CO.,LTD) as polymerase. Mix PCR solutions and run the PCR machine in a program which is detailed below. | |
− | + | ||
− | + | ||
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− | + | ||
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− | + | ||
− | <tr align="center" | + | <table> |
− | <td | + | <tr align="center"> |
− | <td | + | <th>Solution</th> |
− | <td | + | <td>template DNA</td> |
− | </tr> | + | <td>Primer-F 10 µM</td> |
+ | <td>Primer-R 10 µM</td> | ||
+ | <td>MgSO<sub>4</sub></td> | ||
+ | <td>dNTPs</td> | ||
+ | <td>10x Buffer</td> | ||
+ | <td>KOD Plus Neo</td> | ||
+ | <td>DW</td> | ||
+ | <td>Total</td> | ||
+ | </tr> | ||
+ | <tr align="center"> | ||
+ | <th>Volume (µL)</th> | ||
+ | <td>1</td> | ||
+ | <td>1</td> | ||
+ | <td>1</td> | ||
+ | <td>3</td> | ||
+ | <td>5</td> | ||
+ | <td>5</td> | ||
+ | <td>1</td> | ||
+ | <td>33</td> | ||
+ | <td>50</td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | Thermal protocol is following | ||
+ | <h2>2STEP Cycle (Tm value > 63°C)</h2> | ||
+ | <table> | ||
+ | <tr align="center"> | ||
+ | <th>Sequence</th><th>Temp. (°C)</th><th>Time (sec)</th> | ||
+ | </tr> | ||
+ | <tr align="center"> | ||
+ | <td>1</td><td>94</td><td>120</td> | ||
+ | </tr> | ||
+ | <tr align="center"> | ||
+ | <td>2</td><td>98</td><td>10</td> | ||
+ | </tr> | ||
+ | <tr align="center"> | ||
+ | <td>3</td><td>68</td><td>30 / 1kbp</td> | ||
+ | </tr> | ||
+ | <tr align="center"> | ||
+ | <td>4</td><td>4</td><td>Hold</td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | Cycle: sequence 2~3 × (25~45) | ||
− | <tr align="center | + | <h2>3STEP Cycle (Tm value < 63°C)</h2> |
− | < | + | <table> |
− | < | + | <tr align="center"> |
− | </td> | + | <th>Sequence</th><th>Temp. (°C)</th><th>Time (sec)</th> |
− | <td | + | </tr> |
− | < | + | <tr align="center"> |
− | </td> | + | <td>1</td><td>94</td><td>120</td> |
− | <td | + | </tr> |
− | < | + | <tr align="center"> |
− | </td> | + | <td>2</td><td>98</td><td>10</td> |
− | </tr> | + | </tr> |
− | + | <tr align="center"> | |
− | <tr align="center | + | <td>3</td><td>Tm</td><td>30</td> |
− | <td | + | </tr> |
− | < | + | <tr align="center"> |
− | < | + | <td>4</td><td>68</td><td>30 / 1kbp</td> |
− | </tr> | + | </tr> |
+ | <tr align="center"> | ||
+ | <td>5</td><td>4</td><td>Hold</td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | Cycle: sequence 2~4 × (25~45) | ||
− | <tr align="center" | + | <h2>STEP DOWN</h2> |
− | <td | + | <table> |
− | < | + | <tr align="center"> |
− | </td> | + | <th>Sequence</th><th>Temp. (°C)</th><th>Time (sec)</th> |
− | <td | + | </tr> |
− | < | + | <tr align="center"> |
− | </td> | + | <td>1</td><td>94</td><td>120</td> |
− | <td | + | </tr> |
− | < | + | <tr align="center"> |
− | </td> | + | <td>2</td><td>98</td><td>10</td> |
− | </tr> | + | </tr> |
+ | <tr align="center"> | ||
+ | <td>3</td><td>74</td><td>30 / 1kbp</td> | ||
+ | </tr> | ||
+ | <tr align="center"> | ||
+ | <td>4</td><td>98</td><td>10</td> | ||
+ | </tr> | ||
+ | <tr align="center"> | ||
+ | <td>5</td><td>72</td><td>30</td> | ||
+ | </tr> | ||
+ | <tr align="center"> | ||
+ | <td>6</td><td>98</td><td>10</td> | ||
+ | </tr> | ||
+ | <tr align="center"> | ||
+ | <td>7</td><td>70</td><td>30</td> | ||
+ | </tr> | ||
+ | <tr align="center"> | ||
+ | <td>8</td><td>98</td><td>10</td> | ||
+ | </tr> | ||
+ | <tr align="center"> | ||
+ | <td>9</td><td>68</td><td>30</td> | ||
+ | </tr> | ||
+ | <tr align="center"> | ||
+ | <td>10</td><td>68</td><td>420</td> | ||
+ | </tr> | ||
+ | <tr align="center"> | ||
+ | <td>11</td><td>4</td><td>Hold</td> | ||
+ | </tr> | ||
− | |||
</table> | </table> | ||
− | <br | + | Cycle: |
+ | <br>sequence 2~3 × 5 | ||
+ | <br>sequence 4~5 × 5 | ||
+ | <br>sequence 6~7 × 5 | ||
+ | <br>sequence 8~9 × 15 | ||
− | < | + | </span> |
− | < | + | </div> |
+ | <script> | ||
+ | document.getElementById("disp1").style.display="none"; | ||
+ | var displaying=0; | ||
+ | function hyoji1() | ||
+ | { | ||
+ | if (displaying==0) | ||
+ | { | ||
+ | document.getElementById("disp1").style.display="block"; | ||
+ | displaying=1; | ||
+ | } | ||
+ | else | ||
+ | { | ||
+ | document.getElementById("disp1").style.display="none"; | ||
+ | displaying=0; | ||
+ | } | ||
+ | } | ||
+ | </script> | ||
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− | < | + | <h1 onClick="hyoji2()"><span class="ka-soru">PCR Purification</span></h1> |
− | < | + | <div id="disp2"> |
− | < | + | <span class="nomal2"> |
− | < | + | FastGene<sup>TM</sup> Gel/PCR Extraction kit (Nippon Genetics Co., Ltd) |
+ | <br>Purification of PCR products | ||
+ | </span> | ||
− | + | </div> | |
− | < | + | <script> |
+ | document.getElementById("disp2").style.display="none"; | ||
+ | var displaying=0; | ||
+ | function hyoji2() | ||
+ | { | ||
+ | if (displaying==0) | ||
+ | { | ||
+ | document.getElementById("disp2").style.display="block"; | ||
+ | displaying=1; | ||
+ | } | ||
+ | else | ||
+ | { | ||
+ | document.getElementById("disp2").style.display="none"; | ||
+ | displaying=0; | ||
+ | } | ||
+ | } | ||
+ | </script> | ||
− | < | + | <h1 onClick="hyoji3()"><span class="ka-soru">Digestion</span></h1> |
− | < | + | <div id="disp3"> |
+ | <span class="nomal2"> | ||
+ | Mix the following reagents in PCR tube. | ||
+ | <table> | ||
+ | <tr align="center"> | ||
+ | <th>Solution</th> | ||
+ | <td>DNA</td> | ||
+ | <td>RE1 10 U/µL</td> | ||
+ | <td>RE2 10 U/µL</td> | ||
+ | <td>Appropriate buffer</td> | ||
+ | <td>Total</td> | ||
+ | </tr> | ||
+ | <tr align="center"> | ||
+ | <th>Volume (µL)</th> | ||
+ | <td>16</td> | ||
+ | <td>1</td> | ||
+ | <td>1</td> | ||
+ | <td>2</td> | ||
+ | <td>20</td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | <table> | ||
+ | <tr align="center"> | ||
+ | <th>Sequence</th><th>Temp. (°C)</th><th>Time (min)</th> | ||
+ | </tr> | ||
+ | <tr align="center"> | ||
+ | <td>1</td><td>37</td><td>120</td> | ||
+ | </tr> | ||
+ | <tr align="center"> | ||
+ | <td>2</td><td>65</td><td>15</td> | ||
+ | </tr> | ||
+ | <tr align="center"> | ||
+ | <td>3</td><td>4</td><td>Hold</td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </span> | ||
+ | </div> | ||
− | < | + | <script> |
− | + | document.getElementById("disp3").style.display="none"; | |
− | + | var displaying=0; | |
+ | function hyoji3() | ||
+ | { | ||
+ | if (displaying==0) | ||
+ | { | ||
+ | document.getElementById("disp3").style.display="block"; | ||
+ | displaying=1; | ||
+ | } | ||
+ | else | ||
+ | { | ||
+ | document.getElementById("disp3").style.display="none"; | ||
+ | displaying=0; | ||
+ | } | ||
+ | } | ||
+ | </script> | ||
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− | < | + | <h1 onClick="hyoji4()"><span class="ka-soru">Ligation</span></h1> |
− | < | + | <div id="disp4"> |
− | + | <span class="nomal2"> | |
− | + | Mix the following reagents in 0.2 mL PCR tube. Use DNA Ligation Kit Mighty Mix (Takara Bio Inc.) which contains ligase and buffer. | |
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− | + | ||
+ | <table> | ||
+ | <tr align="center"> | ||
+ | <th>Solution</th><td>Vector DNA</td><td>Insert DNA</td><td>DW</td><td>Mighty Mix</td><td>Total</td> | ||
+ | </tr> | ||
+ | <tr align="center"> | ||
+ | <th>Volume (µL)</th><td>1</td><td>2</td><td>2</td><td>5</td><td>10</td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | Thermal protocol is following | ||
+ | <table> | ||
+ | <tr align="center"> | ||
+ | <th>Sequence</th><th>Temp. (°C)</th><th>Time (min)</th> | ||
+ | </tr> | ||
+ | <tr align="center"> | ||
+ | <td>1</td><td>16</td><td>30</td> | ||
+ | </tr> | ||
+ | <tr align="center"> | ||
+ | <td>2</td><td>65</td><td>10</td> | ||
+ | </tr> | ||
+ | <tr align="center"> | ||
+ | <td>3</td><td>4</td><td>Hold</td> | ||
+ | </tr> | ||
+ | </table> | ||
</span> | </span> | ||
− | |||
</div> | </div> | ||
− | < | + | <script> |
− | + | document.getElementById("disp4").style.display="none"; | |
− | + | var displaying=0; | |
− | + | function hyoji4() | |
+ | { | ||
+ | if (displaying==0) | ||
+ | { | ||
+ | document.getElementById("disp4").style.display="block"; | ||
+ | displaying=1; | ||
+ | } | ||
+ | else | ||
+ | { | ||
+ | document.getElementById("disp4").style.display="none"; | ||
+ | displaying=0; | ||
+ | } | ||
+ | } | ||
+ | </script> | ||
+ | <h1 onClick="hyoji5()"><span class="ka-soru">Electrophoresis</span></h1> | ||
+ | <div id="disp5"> | ||
<span class="nomal2"> | <span class="nomal2"> | ||
− | < | + | <ol> |
− | < | + | <li>Put gel into electrophoresis tank.</li> |
− | + | <li>Pour 2x TBE buffer into the tank to soak gel.</li> | |
− | + | <li>Add 5 µL of EtBr into cathode.</li> | |
− | + | <li>Pre-migration for 30 min at 100 V.</li> | |
− | + | <li>Apply DNA solutions with 6x loading dye and ladder.</li> | |
− | + | <li>Start electrophoresis at 100 V.</li> | |
− | < | + | <li>Stop at appropriate time. |
− | + | </ol> | |
− | < | + | |
</span> | </span> | ||
− | |||
− | |||
− | < | + | </div> |
− | + | <script> | |
− | + | document.getElementById("disp5").style.display="none"; | |
− | + | var displaying=0; | |
− | + | function hyoji5() | |
− | + | { | |
− | </ | + | if (displaying==0) |
+ | { | ||
+ | document.getElementById("disp5").style.display="block"; | ||
+ | displaying=1; | ||
+ | } | ||
+ | else | ||
+ | { | ||
+ | document.getElementById("disp5").style.display="none"; | ||
+ | displaying=0; | ||
+ | } | ||
+ | } | ||
+ | </script> | ||
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+ | <h1 onClick="hyoji6()"><span class="ka-soru">Gel Extraction</span></h1> | ||
+ | <div id="disp6"> | ||
<span class="nomal2"> | <span class="nomal2"> | ||
− | + | FastGene<sup>TM</sup> Gel/PCR Extraction kit (Nippon Genetics Co., Ltd) | |
− | < | + | <br>DNA extraction from gel |
</span> | </span> | ||
+ | </div> | ||
+ | <script> | ||
+ | document.getElementById("disp6").style.display="none"; | ||
+ | var displaying=0; | ||
+ | function hyoji6() | ||
+ | { | ||
+ | if (displaying==0) | ||
+ | { | ||
+ | document.getElementById("disp6").style.display="block"; | ||
+ | displaying=1; | ||
+ | } | ||
+ | else | ||
+ | { | ||
+ | document.getElementById("disp6").style.display="none"; | ||
+ | displaying=0; | ||
+ | } | ||
+ | } | ||
+ | </script> | ||
− | |||
− | < | + | <h1 onClick="hyoji7()"><span class="ka-soru">Ethanol precipitation</span></h1> |
− | < | + | <div id="disp7"> |
− | < | + | <span class="nomal2"> |
− | < | + | <ol> |
− | </ | + | <li>Add 1/10 volume of NaOAc, and 5/2 of 100% ethanol.</li> |
+ | <li>Leave it at room temperature for 5 min.</li> | ||
+ | <li>Centrifuge at 15,000 rpm for 15 min at 25°C.</li> | ||
+ | <li>Remove supernatant and add 600 µL of 70% ethanol.</li> | ||
+ | <li>Centrifuge at 15,000 rpm for 5 min at 25°C.</li> | ||
+ | <li>Remove supernatant and dry up at room temperature with light sheilding.</li> | ||
+ | <li>Suspend with 10 µL of TE.</li> | ||
+ | </ol> | ||
− | < | + | </span> |
− | < | + | </div> |
− | < | + | <script> |
− | + | document.getElementById("disp7").style.display="none"; | |
− | + | var displaying=0; | |
− | + | function hyoji7() | |
− | + | { | |
− | + | if (displaying==0) | |
− | + | { | |
− | + | document.getElementById("disp7").style.display="block"; | |
− | </ | + | displaying=1; |
+ | } | ||
+ | else | ||
+ | { | ||
+ | document.getElementById("disp7").style.display="none"; | ||
+ | displaying=0; | ||
+ | } | ||
+ | } | ||
+ | </script> | ||
− | < | + | <h1 onClick="hyoji8()"><span class="ka-soru">Colony PCR</span></h1> |
− | + | <div id="disp8"> | |
− | < | + | <span class="nomal2"> |
− | < | + | <table> |
− | <tr align="center" | + | <tr align="center"> |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
+ | <th>Solution</th> | ||
+ | <td>DNA</td> | ||
+ | <td>Kapa-Taq (Taq polymerase)</td> | ||
+ | <td>EX-F primer 10 µM</td> | ||
+ | <td>PS-R primer 10 µM</td> | ||
+ | <td>Total</td> | ||
+ | </tr> | ||
+ | <tr align="center"> | ||
+ | <th>Volume (µL)</th> | ||
+ | <td>4.2</td> | ||
+ | <td>5</td> | ||
+ | <td>0.4</td> | ||
+ | <td>0.4</td> | ||
+ | <td>10</td> | ||
+ | </tr> | ||
</table> | </table> | ||
− | |||
− | < | + | <table> |
− | + | <tr align="center"> | |
− | < | + | <th>Sequence</th><th>Temp. (°C)</th><th>Time (sec)</th> |
+ | </tr> | ||
+ | <tr align="center"> | ||
+ | <td>1</td><td>94</td><td>120</td> | ||
+ | </tr> | ||
+ | <tr align="center"> | ||
+ | <td>2</td><td>94</td><td>30</td> | ||
+ | </tr> | ||
+ | <tr align="center"> | ||
+ | <td>3</td><td>68</td><td>60 / 1kbp</td> | ||
+ | </tr> | ||
+ | <tr align="center"> | ||
+ | <td>4</td><td>4</td><td>Hold</td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | Cycles: sequence 2~3 × 25~45 | ||
</span> | </span> | ||
+ | </div> | ||
+ | <script> | ||
+ | document.getElementById("disp8").style.display="none"; | ||
+ | var displaying=0; | ||
+ | function hyoji8() | ||
+ | { | ||
+ | if (displaying==0) | ||
+ | { | ||
+ | document.getElementById("disp8").style.display="block"; | ||
+ | displaying=1; | ||
+ | } | ||
+ | else | ||
+ | { | ||
+ | document.getElementById("disp8").style.display="none"; | ||
+ | displaying=0; | ||
+ | } | ||
+ | } | ||
+ | </script> | ||
− | < | + | <h1 onClick="hyoji9()"><span class="ka-soru">Sequencing</span></h1> |
+ | <div id="disp9"> | ||
+ | <span class="nomal2"> | ||
+ | <table> | ||
+ | <tr align="center"> | ||
+ | <th>Solution</th> | ||
+ | <td>5 x Sequencing Buffer</td> | ||
+ | <td>primer 1 µM</td> | ||
+ | <td>template DNA</td> | ||
+ | <td>Ready Reaction Premix</td> | ||
+ | <td>DW</td> | ||
+ | <td>Total</td> | ||
+ | </tr> | ||
+ | <tr align="center"> | ||
+ | <th>Volume (µL)</th> | ||
+ | <td>1.5</td> | ||
+ | <td>1.5</td> | ||
+ | <td>1</td> | ||
+ | <td>1</td> | ||
+ | <td>5</td> | ||
+ | <td>10</td> | ||
+ | </tr> | ||
+ | </table> | ||
− | + | <table> | |
− | <tr align="center | + | <tr align="center"> |
− | < | + | <th>Sequence</th><th>Temp. (°C)</th><th>Time (sec)</th> |
− | </tr> | + | </tr> |
− | + | <tr align="center"> | |
− | <tr align="center | + | <td>1</td><td>96</td><td>10</td> |
− | <td | + | </tr> |
− | < | + | <tr align="center"> |
− | </td> | + | <td>2</td><td>50</td><td>5</td> |
+ | </tr> | ||
+ | <tr align="center"> | ||
+ | <td>3</td><td>60</td><td>240</td> | ||
+ | </tr> | ||
+ | <tr align="center"> | ||
+ | <td>4</td><td>4</td><td>Hold</td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | Cycle: sequence 2~4 × 25 | ||
+ | <h2>Ethanol precipitation</h2> | ||
+ | <table> | ||
+ | <tr align="center"> | ||
+ | <th>Solution</th> | ||
+ | <td>PCR product</td> | ||
+ | <td>DW</td> | ||
+ | <td>3M NaOAc</td> | ||
+ | <td>Glycogen</td> | ||
+ | <td>100% EtOH</td> | ||
+ | </tr> | ||
+ | <tr align="center"> | ||
+ | <th>Volume (µL)</th> | ||
+ | <td>10</td> | ||
+ | <td>10</td> | ||
+ | <td>2</td> | ||
+ | <td>1</td> | ||
+ | <td>50</td> | ||
+ | </tr> | ||
</table> | </table> | ||
− | < | + | <ol> |
+ | <li>Centrifuge at 15,000 rpm for 15 min at room temprature.</li> | ||
+ | <li>Remove supernatant, add 100 µL of 70% EtOH and tap tubes by finger.</li> | ||
+ | <li>Centrifuge at 15,000 rpm for 10 min at room temprature.</li> | ||
+ | <li>Remove supernatant and dry up at room temperature.</li> | ||
+ | <li>Resuspend the pellet to HiDi formamide and remove to 96-well plate.</li> | ||
+ | <li>Set the plate and start electrophoresis.</li> | ||
+ | </ol> | ||
+ | </span> | ||
+ | </div> | ||
+ | <script> | ||
+ | document.getElementById("disp9").style.display="none"; | ||
+ | var displaying=0; | ||
+ | function hyoji9() | ||
+ | { | ||
+ | if (displaying==0) | ||
+ | { | ||
+ | document.getElementById("disp9").style.display="block"; | ||
+ | displaying=1; | ||
+ | } | ||
+ | else | ||
+ | { | ||
+ | document.getElementById("disp9").style.display="none"; | ||
+ | displaying=0; | ||
+ | } | ||
+ | } | ||
+ | </script> | ||
+ | <h1 onClick="hyoji10()"><span class="ka-soru">Competent Cells</span></h1> | ||
+ | <div id="disp10"> | ||
+ | <span class="nomal2"> | ||
+ | <ol> | ||
+ | <li>Thaw original competent cells on ice.</li> | ||
+ | <li>Add 5 µL of original competent cells to 2 mL of LB.</li> | ||
+ | <li>Incubate the cells for 16 hrs at 37°C.</li> | ||
+ | <li>Add 5 µL, 50 µL, and 500 µL of original cells to 100 mL of LB.</li> | ||
+ | <li>Incubate the cells at 130 rpm at 20°C, until OD<sub>600</sub> reach 0.5.</li> | ||
+ | <li>Take 50 mL of incubated cells to two different culture tubes and centrifuge them at 3,000 rpm for 20 min at 4°C.</li> | ||
+ | <li>Remove supernatant and add 75 mL of TB to each tube.</li> | ||
+ | <li>Bring them to a one tube and centrifuge at 3,000 rpm for 20 min at 4°C.</li> | ||
+ | <li>Remove supernatant and add 32 mL of TB.</li> | ||
+ | <li>Add 32 µL of DMSO 10 times.</li> | ||
+ | <li>Take 50 µL and freeze with liquid nitrogen.</li> | ||
+ | </ol> | ||
+ | </span> | ||
+ | </div> | ||
+ | <script> | ||
+ | document.getElementById("disp10").style.display="none"; | ||
+ | var displaying=0; | ||
+ | function hyoji10() | ||
+ | { | ||
+ | if (displaying==0) | ||
+ | { | ||
+ | document.getElementById("disp10").style.display="block"; | ||
+ | displaying=1; | ||
+ | } | ||
+ | else | ||
+ | { | ||
+ | document.getElementById("disp10").style.display="none"; | ||
+ | displaying=0; | ||
+ | } | ||
+ | } | ||
+ | </script> | ||
+ | <h1 onClick="hyoji11()"><span class="ka-soru">Transformation</span></h1> | ||
+ | <div id="disp11"> | ||
+ | <span class="nomal2"> | ||
+ | <ol> | ||
+ | <li>Add plasmid to thawed competent cells on ice.</li> | ||
+ | <li>Incubate on ice for 30 min.</li> | ||
+ | <li>Add to LB.</li> | ||
+ | <li>Incubate the cells for 2 hrs at 37°C.</li> | ||
+ | <li>Spread 300 µL of the culture onto plate with LB and appropriate antibiotics.</li> | ||
+ | <li>Incubate the plate(s) at 37°C for 16~20 hrs.</li> | ||
+ | </ol> | ||
+ | </span> | ||
+ | </div> | ||
+ | <script> | ||
+ | document.getElementById("disp11").style.display="none"; | ||
+ | var displaying=0; | ||
+ | function hyoji11() | ||
+ | { | ||
+ | if (displaying==0) | ||
+ | { | ||
+ | document.getElementById("disp11").style.display="block"; | ||
+ | displaying=1; | ||
+ | } | ||
+ | else | ||
+ | { | ||
+ | document.getElementById("disp11").style.display="none"; | ||
+ | displaying=0; | ||
+ | } | ||
+ | } | ||
+ | </script> | ||
+ | <h1 onClick="hyoji12()"><span class="ka-soru">Mini-prep</span></h1> | ||
+ | <div id="disp12"> | ||
<span class="nomal2"> | <span class="nomal2"> | ||
+ | FastGene<sup>TM</sup> Plasmid mini kit (Nippon Genetics Co., Ltd) | ||
+ | <br>fast / standard / low copy protocol | ||
+ | </span> | ||
+ | </div> | ||
+ | <script> | ||
+ | document.getElementById("disp12").style.display="none"; | ||
+ | var displaying=0; | ||
+ | function hyoji12() | ||
+ | { | ||
+ | if (displaying==0) | ||
+ | { | ||
+ | document.getElementById("disp12").style.display="block"; | ||
+ | displaying=1; | ||
+ | } | ||
+ | else | ||
+ | { | ||
+ | document.getElementById("disp12").style.display="none"; | ||
+ | displaying=0; | ||
+ | } | ||
+ | } | ||
+ | </script> | ||
− | + | <h1 onClick="hyoji13()"><span class="ka-soru">Streaking (Single colony isolation)</span></h1> | |
− | + | <div id="disp13"> | |
− | < | + | <span class="nomal2"> |
− | < | + | <ol> |
− | + | <li>Pick the colony with an inoculating loop from the agar plate.</li> | |
− | + | <li>Drag the loop across on a new agar plate.</li> | |
− | + | <li>Resterilize the loop and drag it across again.</li> | |
− | + | <li>Repeat method 3.</li> | |
− | + | </ol> | |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | </ | + | |
</span> | </span> | ||
</div> | </div> | ||
+ | <script> | ||
+ | document.getElementById("disp13").style.display="none"; | ||
+ | var displaying=0; | ||
+ | function hyoji13() | ||
+ | { | ||
+ | if (displaying==0) | ||
+ | { | ||
+ | document.getElementById("disp13").style.display="block"; | ||
+ | displaying=1; | ||
+ | } | ||
+ | else | ||
+ | { | ||
+ | document.getElementById("disp13").style.display="none"; | ||
+ | displaying=0; | ||
+ | } | ||
+ | } | ||
+ | </script> | ||
− | < | + | <h1 onClick="hyoji14()"><span class="ka-soru">PEG precipitation</span></h1> |
− | <div> | + | <div id="disp14"> |
− | < | + | <span class="nomal2"> |
− | + | <ol> | |
+ | <li>Add 13 µL of PEG to 20 µL of product(s).</li> | ||
+ | <li>Leave it at room temperature for 1 hr.</li> | ||
+ | <li>Centrifuge at 15,000 rpm for 20 min at 4°C.</li> | ||
+ | <li>Remove supernatant and add 100 µL of 70% ethanol.</li> | ||
+ | <li>Centrifuge at 15,000 rpm for 2 min at 4°C.</li> | ||
+ | <li>Remove supernatant and dry up at room temperature with light sheilding.</li> | ||
+ | <li>Suspend with 10 µL of TE.</li> | ||
+ | </ol> | ||
+ | </span> | ||
+ | </div> | ||
+ | <script> | ||
+ | document.getElementById("disp14").style.display="none"; | ||
+ | var displaying=0; | ||
+ | function hyoji14() | ||
+ | { | ||
+ | if (displaying==0) | ||
+ | { | ||
+ | document.getElementById("disp14").style.display="block"; | ||
+ | displaying=1; | ||
+ | } | ||
+ | else | ||
+ | { | ||
+ | document.getElementById("disp14").style.display="none"; | ||
+ | displaying=0; | ||
+ | } | ||
+ | } | ||
+ | </script> | ||
+ | <h1 onClick="hyoji15()"><span class="ka-soru">Gel Free System</span></h1> | ||
+ | <div id="disp15"> | ||
<span class="nomal2"> | <span class="nomal2"> | ||
− | < | + | <h2>Preparation of biotinylated DNA fragments</h2> |
+ | Use KOD -Plus- Neo (TOYOBO CO.,LTD) as polymerase and 5'-biotinylated primers. Mix PCR solutions and run the PCR machine in a program which is detailed below. | ||
− | <table | + | <table> |
− | + | <tr align="center"> | |
− | + | <th>Solution</th> | |
− | + | <td>template DNA</td> | |
− | + | <td>5'-biotinylated 100-UP primer 10 µM</td> | |
− | + | <td>5'-biotinylated 200-DN primer 10 µM</td> | |
+ | <td>MgSO<sub>4</sub></td> | ||
+ | <td>dNTPs</td> | ||
+ | <td>10x Buffer</td> | ||
+ | <td>KOD Plus Neo</td> | ||
+ | <td>DW</td> | ||
+ | <td>Total</td> | ||
+ | </tr> | ||
+ | <tr align="center"> | ||
+ | <th>Volume (µL)</th> | ||
+ | <td>1</td> | ||
+ | <td>1.5</td> | ||
+ | <td>1.5</td> | ||
+ | <td>3</td> | ||
+ | <td>5</td> | ||
+ | <td>5</td> | ||
+ | <td>1</td> | ||
+ | <td>32</td> | ||
+ | <td>50</td> | ||
+ | </tr> | ||
</table> | </table> | ||
+ | Thermal protocol is following | ||
+ | <h2>2STEP Cycle (Tm value > 63°C)</h2> | ||
+ | <table> | ||
+ | <tr align="center"> | ||
+ | <th>Sequence</th><th>Temp. (°C)</th><th>Time (sec)</th> | ||
+ | </tr> | ||
+ | <tr align="center"> | ||
+ | <td>1</td><td>94</td><td>120</td> | ||
+ | </tr> | ||
+ | <tr align="center"> | ||
+ | <td>2</td><td>98</td><td>10</td> | ||
+ | </tr> | ||
+ | <tr align="center"> | ||
+ | <td>3</td><td>68</td><td>30 / 1kbp</td> | ||
+ | </tr> | ||
+ | <tr align="center"> | ||
+ | <td>4</td><td>4</td><td>Hold</td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | Cycle: sequence 2~3 × (25~45) | ||
− | < | + | <h2>Preparation of magnetic beads</h2> |
+ | <ol> | ||
+ | <li>Mix 2 µL of magnetic beads (SiMAG-Streptavidin) and 48 µL of TE by vibration using sonic-toothbrush.</li> | ||
+ | <li>Collect the beads by attracting them to one side in 0.2 mL polypropylene tube using neodymium magnet.</li> | ||
+ | <li>Remove supernatant.</li> | ||
+ | </ol> | ||
+ | <h2>Fixation to magnetic beads</h2> | ||
+ | <ol> | ||
+ | <li>Add 3 µL of PCR product (0.48 pmol) and 7 µL of TE to beads.</li> | ||
+ | <li>Mix by vibration using sonic-toothbrush.</li> | ||
+ | <li>Collect the beads using magnet.</li> | ||
+ | <li>Remove supernatant containing excess amount of free DNA fragment.</li> | ||
+ | </ol> | ||
− | < | + | <h2>Double restriction digestion</h2> |
− | + | <ol> | |
+ | <li>Add Digestion Premix containing 1 µL of 10x RE solution, 8 µL of DW and each 0.5 µL of restriction endonuclease, <I>Xba</I>I and <I>Spe</I>I, to the beads.</li> | ||
+ | <li>Mix by pumping using pipette.</li> | ||
+ | <li>Incubate at 37 °C for 30 min.</li> | ||
+ | <li>Collect the beads using magnet.</li> | ||
+ | <li>Obtain supernatant containing digested DNA fragment.</li> | ||
+ | <li>Purify the supernatant by ethanol precipitation.</li> | ||
+ | </ol> | ||
</span> | </span> | ||
− | |||
</div> | </div> | ||
− | < | + | </div> |
<br> | <br> | ||
− | < | + | <br> |
− | < | + | <script> |
− | + | document.getElementById("disp15").style.display="none"; | |
+ | var displaying=0; | ||
+ | function hyoji15() | ||
+ | { | ||
+ | if (displaying==0) | ||
+ | { | ||
+ | document.getElementById("disp15").style.display="block"; | ||
+ | displaying=1; | ||
+ | } | ||
+ | else | ||
+ | { | ||
+ | document.getElementById("disp15").style.display="none"; | ||
+ | displaying=0; | ||
+ | } | ||
+ | } | ||
+ | </script> | ||
− | + | ||
− | + | ||
− | </ | + | </body> |
</div> | </div> | ||
− | </div> | + | </div> <!-- 2016contents 閉じる --> |
− | + | ||
− | <!-- 2016contents 閉じる --> | + | |
<!--begin footer--> | <!--begin footer--> | ||
<br> | <br> | ||
Line 418: | Line 841: | ||
</div> | </div> | ||
<!--background--> | <!--background--> | ||
− | |||
</html> | </html> |
Revision as of 17:38, 19 October 2016
Team:HokkaidoU Japan
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Cycles: sequence 2~3 × 25~45
Cycle: sequence 2~4 × 25
Thermal protocol is following
Cycle: sequence 2~3 × (25~45)
![Protcols](https://static.igem.org/mediawiki/2016/2/29/T--HokkaidoU_Japan--protocols.png)
PCR
Use KOD -Plus- Neo (TOYOBO CO.,LTD) as polymerase. Mix PCR solutions and run the PCR machine in a program which is detailed below.
Thermal protocol is following
Cycle: sequence 2~3 × (25~45)
Cycle: sequence 2~4 × (25~45)
Cycle:
sequence 2~3 × 5
sequence 4~5 × 5
sequence 6~7 × 5
sequence 8~9 × 15
Solution | template DNA | Primer-F 10 µM | Primer-R 10 µM | MgSO4 | dNTPs | 10x Buffer | KOD Plus Neo | DW | Total |
---|---|---|---|---|---|---|---|---|---|
Volume (µL) | 1 | 1 | 1 | 3 | 5 | 5 | 1 | 33 | 50 |
2STEP Cycle (Tm value > 63°C)
Sequence | Temp. (°C) | Time (sec) |
---|---|---|
1 | 94 | 120 |
2 | 98 | 10 |
3 | 68 | 30 / 1kbp |
4 | 4 | Hold |
3STEP Cycle (Tm value < 63°C)
Sequence | Temp. (°C) | Time (sec) |
---|---|---|
1 | 94 | 120 |
2 | 98 | 10 |
3 | Tm | 30 |
4 | 68 | 30 / 1kbp |
5 | 4 | Hold |
STEP DOWN
Sequence | Temp. (°C) | Time (sec) |
---|---|---|
1 | 94 | 120 |
2 | 98 | 10 |
3 | 74 | 30 / 1kbp |
4 | 98 | 10 |
5 | 72 | 30 |
6 | 98 | 10 |
7 | 70 | 30 |
8 | 98 | 10 |
9 | 68 | 30 |
10 | 68 | 420 |
11 | 4 | Hold |
sequence 2~3 × 5
sequence 4~5 × 5
sequence 6~7 × 5
sequence 8~9 × 15
PCR Purification
FastGeneTM Gel/PCR Extraction kit (Nippon Genetics Co., Ltd)
Purification of PCR products
Purification of PCR products
Digestion
Mix the following reagents in PCR tube.
Solution | DNA | RE1 10 U/µL | RE2 10 U/µL | Appropriate buffer | Total |
---|---|---|---|---|---|
Volume (µL) | 16 | 1 | 1 | 2 | 20 |
Sequence | Temp. (°C) | Time (min) |
---|---|---|
1 | 37 | 120 |
2 | 65 | 15 |
3 | 4 | Hold |
Ligation
Mix the following reagents in 0.2 mL PCR tube. Use DNA Ligation Kit Mighty Mix (Takara Bio Inc.) which contains ligase and buffer.
Thermal protocol is following
Solution | Vector DNA | Insert DNA | DW | Mighty Mix | Total |
---|---|---|---|---|---|
Volume (µL) | 1 | 2 | 2 | 5 | 10 |
Sequence | Temp. (°C) | Time (min) |
---|---|---|
1 | 16 | 30 |
2 | 65 | 10 |
3 | 4 | Hold |
Electrophoresis
- Put gel into electrophoresis tank.
- Pour 2x TBE buffer into the tank to soak gel.
- Add 5 µL of EtBr into cathode.
- Pre-migration for 30 min at 100 V.
- Apply DNA solutions with 6x loading dye and ladder.
- Start electrophoresis at 100 V.
- Stop at appropriate time.
Gel Extraction
FastGeneTM Gel/PCR Extraction kit (Nippon Genetics Co., Ltd)
DNA extraction from gel
DNA extraction from gel
Ethanol precipitation
- Add 1/10 volume of NaOAc, and 5/2 of 100% ethanol.
- Leave it at room temperature for 5 min.
- Centrifuge at 15,000 rpm for 15 min at 25°C.
- Remove supernatant and add 600 µL of 70% ethanol.
- Centrifuge at 15,000 rpm for 5 min at 25°C.
- Remove supernatant and dry up at room temperature with light sheilding.
- Suspend with 10 µL of TE.
Colony PCR
Solution | DNA | Kapa-Taq (Taq polymerase) | EX-F primer 10 µM | PS-R primer 10 µM | Total |
---|---|---|---|---|---|
Volume (µL) | 4.2 | 5 | 0.4 | 0.4 | 10 |
Sequence | Temp. (°C) | Time (sec) |
---|---|---|
1 | 94 | 120 |
2 | 94 | 30 |
3 | 68 | 60 / 1kbp |
4 | 4 | Hold |
Sequencing
Solution | 5 x Sequencing Buffer | primer 1 µM | template DNA | Ready Reaction Premix | DW | Total |
---|---|---|---|---|---|---|
Volume (µL) | 1.5 | 1.5 | 1 | 1 | 5 | 10 |
Sequence | Temp. (°C) | Time (sec) |
---|---|---|
1 | 96 | 10 |
2 | 50 | 5 |
3 | 60 | 240 |
4 | 4 | Hold |
Ethanol precipitation
Solution | PCR product | DW | 3M NaOAc | Glycogen | 100% EtOH |
---|---|---|---|---|---|
Volume (µL) | 10 | 10 | 2 | 1 | 50 |
- Centrifuge at 15,000 rpm for 15 min at room temprature.
- Remove supernatant, add 100 µL of 70% EtOH and tap tubes by finger.
- Centrifuge at 15,000 rpm for 10 min at room temprature.
- Remove supernatant and dry up at room temperature.
- Resuspend the pellet to HiDi formamide and remove to 96-well plate.
- Set the plate and start electrophoresis.
Competent Cells
- Thaw original competent cells on ice.
- Add 5 µL of original competent cells to 2 mL of LB.
- Incubate the cells for 16 hrs at 37°C.
- Add 5 µL, 50 µL, and 500 µL of original cells to 100 mL of LB.
- Incubate the cells at 130 rpm at 20°C, until OD600 reach 0.5.
- Take 50 mL of incubated cells to two different culture tubes and centrifuge them at 3,000 rpm for 20 min at 4°C.
- Remove supernatant and add 75 mL of TB to each tube.
- Bring them to a one tube and centrifuge at 3,000 rpm for 20 min at 4°C.
- Remove supernatant and add 32 mL of TB.
- Add 32 µL of DMSO 10 times.
- Take 50 µL and freeze with liquid nitrogen.
Transformation
- Add plasmid to thawed competent cells on ice.
- Incubate on ice for 30 min.
- Add to LB.
- Incubate the cells for 2 hrs at 37°C.
- Spread 300 µL of the culture onto plate with LB and appropriate antibiotics.
- Incubate the plate(s) at 37°C for 16~20 hrs.
Mini-prep
FastGeneTM Plasmid mini kit (Nippon Genetics Co., Ltd)
fast / standard / low copy protocol
fast / standard / low copy protocol
Streaking (Single colony isolation)
- Pick the colony with an inoculating loop from the agar plate.
- Drag the loop across on a new agar plate.
- Resterilize the loop and drag it across again.
- Repeat method 3.
PEG precipitation
- Add 13 µL of PEG to 20 µL of product(s).
- Leave it at room temperature for 1 hr.
- Centrifuge at 15,000 rpm for 20 min at 4°C.
- Remove supernatant and add 100 µL of 70% ethanol.
- Centrifuge at 15,000 rpm for 2 min at 4°C.
- Remove supernatant and dry up at room temperature with light sheilding.
- Suspend with 10 µL of TE.
Gel Free System
Preparation of biotinylated DNA fragments
Use KOD -Plus- Neo (TOYOBO CO.,LTD) as polymerase and 5'-biotinylated primers. Mix PCR solutions and run the PCR machine in a program which is detailed below.Solution | template DNA | 5'-biotinylated 100-UP primer 10 µM | 5'-biotinylated 200-DN primer 10 µM | MgSO4 | dNTPs | 10x Buffer | KOD Plus Neo | DW | Total |
---|---|---|---|---|---|---|---|---|---|
Volume (µL) | 1 | 1.5 | 1.5 | 3 | 5 | 5 | 1 | 32 | 50 |
2STEP Cycle (Tm value > 63°C)
Sequence | Temp. (°C) | Time (sec) |
---|---|---|
1 | 94 | 120 |
2 | 98 | 10 |
3 | 68 | 30 / 1kbp |
4 | 4 | Hold |
Preparation of magnetic beads
- Mix 2 µL of magnetic beads (SiMAG-Streptavidin) and 48 µL of TE by vibration using sonic-toothbrush.
- Collect the beads by attracting them to one side in 0.2 mL polypropylene tube using neodymium magnet.
- Remove supernatant.
Fixation to magnetic beads
- Add 3 µL of PCR product (0.48 pmol) and 7 µL of TE to beads.
- Mix by vibration using sonic-toothbrush.
- Collect the beads using magnet.
- Remove supernatant containing excess amount of free DNA fragment.
Double restriction digestion
- Add Digestion Premix containing 1 µL of 10x RE solution, 8 µL of DW and each 0.5 µL of restriction endonuclease, XbaI and SpeI, to the beads.
- Mix by pumping using pipette.
- Incubate at 37 °C for 30 min.
- Collect the beads using magnet.
- Obtain supernatant containing digested DNA fragment.
- Purify the supernatant by ethanol precipitation.