基礎ゼミチーム/basic seminar team/experiment result

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<div id="head-1"> BIOMOD2012 Tohoku Team B </div>

<div id="head-under"></div>


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<div style="float:left;width:5px;height:30px;"> </div> <a href="http://openwetware.org/wiki/%E5%9F%BA%E7%A4%8E%E3%82%BC%E3%83%9F%E3%83%81%E3%83%BC%E3%83%A0/basic_seminar_team"><div id="HOME"> HOME </div></a> <a href="http://openwetware.org/wiki/%E5%9F%BA%E7%A4%8E%E3%82%BC%E3%83%9F%E3%83%81%E3%83%BC%E3%83%A0/basic_seminar_team/project"><div id="bottun"> Project </div></a> <a href="http://openwetware.org/wiki/%E5%9F%BA%E7%A4%8E%E3%82%BC%E3%83%9F%E3%83%81%E3%83%BC%E3%83%A0/basic_seminar_team/experiment_result"><div id="bottun"> Experiment </div></a> <a href="http://openwetware.org/wiki/%E5%9F%BA%E7%A4%8E%E3%82%BC%E3%83%9F%E3%83%81%E3%83%BC%E3%83%A0/basic_seminar_team/diary"><div id="bottun"> Diary </div></a> <a href="http://openwetware.org/wiki/%E5%9F%BA%E7%A4%8E%E3%82%BC%E3%83%9F%E3%83%81%E3%83%BC%E3%83%A0/basic_seminar_team/member"> <div id="bottun"> Team </div></a> <a href="http://openwetware.org/wiki/%E5%9F%BA%E7%A4%8E%E3%82%BC%E3%83%9F%E3%83%81%E3%83%BC%E3%83%A0/basic_seminar_team/link"> <div id="bottun"> Link </div></a> <br> <div id="under-line"> </div>


</div>



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<div id="line-title"> <font id="head">Experiment</font> </div> <div id="line2-5"></div> <div id="line3"></div>

<div id="line4"></div> <div id="line5"></div> <div id="line6"></div>

<div id="yohaku"></div>


<!-- 新　9月4日 -->

<div id="expe1"></div> <div id="expe2"></div> <div id="expe3">2012/09/04</div> <div id="expe4"></div> <div id="expe5"></div> <div id="expe6"></div> <div id="expe7"><img src="http://openwetware.org/images/thumb/2/27/20120904%2C100v%2C2h%2Cfrige.jpg/708px-20120904%2C100v%2C2h%2Cfrige.jpg" style="width:500px;float:left;margin:5px;">

<table> <tr><th>condition</th></tr> <tr><td>constant voltage 50V</td></tr> <tr><td>temparature:4℃(in refrigerate)</td></tr> <tr><td>the electrophoresis for 2 hours in a refrigerator</td></tr> <tr><td>SYBR Gold as a stain for 10 minutes</td></tr> <tr><td>1X TAE added to Mg2+ as a buffer</td></tr> </table>

<table> <tr><th>result</th></tr> <tr><td>The result was what we wanted completely.</td></tr> <tr><td>Target DNA hibridized to Selector 1</td></tr> <tr><td>Target DNA moved from Selector 1 to Selector2, and Selector 2 to Selector 3</td></tr> </table>

</div>


<!-- 新　8月30日 -->

<div id="expe1"></div> <div id="expe2"></div> <div id="expe3">2012/08/30</div> <div id="expe4"></div> <div id="expe5"></div> <div id="expe6"></div> <div id="expe7"><img src="http://openwetware.org/images/thumb/c/c7/20120830_%E2%91%A1.jpg/800px-20120830_%E2%91%A1.jpg" style="width:500px;float:left;margin:5px;">

<table> <tr><th>condition</th></tr> <tr><td>constant voltage 50V</td></tr> <tr><td>1X TAE added to Mg2+ as a buffer</td></tr> <tr><td>The room temperature was 33℃(4℃ in the refrigerator)</td></tr> <tr><td>the electrophoresis for 3.5 hours in a refrigerator</td></tr> <tr><td>SYBR Gold as a stain for 10 minutes</td></tr> </table>

<table> <tr><th>result</th></tr> <tr><td>The result was what we had expected.</td></tr> <tr><td>Finally, Selector 1 hybridized with the target.</td></tr> </table>

</div>


<!-- 新　8月29日 -->

<div id="expe1"></div> <div id="expe2"></div> <div id="expe3">2012/08/29</div> <div id="expe4"></div> <div id="expe5"></div> <div id="expe6"></div> <div id="expe7"><img src="http://openwetware.org/images/thumb/4/4f/20120829_%E2%91%A1.jpg/800px-20120829_%E2%91%A1.jpg" style="width:500px;float:left;margin:5px;">

<table> <tr><th>condition</th></tr> <tr><td>1X TAE added to Mg2+ as a buffer</td></tr> <tr><td>The room temperature was 33℃ (4℃ in the refrigerator)</td></tr> <tr><td>the electrophoresis for 3.5 hours</td></tr> <tr><td>SYBR Gold as a stain for 10 minutes</td></tr> </table>

<table> <tr><th>result</th></tr> <tr><td>Selector 1 didn't hybridize with target. But the Other samples worked well.</td></tr> <tr><td>We will try again with cool buffer tomorrow.</td></tr> </table> </div>


<!-- 新　8月28日 -->

<div id="expe1"></div> <div id="expe2"></div> <div id="expe3">2012/08/28</div> <div id="expe4"></div> <div id="expe5"></div> <div id="expe6"></div> <div id="expe7"><img src="http://openwetware.org/images/thumb/5/5a/20120828_%E2%91%A1.jpg/800px-20120828_%E2%91%A1.jpg" style="width:500px;float:left;margin:5px;">

<table> <tr><th>condition</th></tr> <tr><td>constant voltage 50V</td></tr> <tr><td>1X TAE was added to Mg2+ as a buffer</td></tr> <tr><td>The room temperature was 33℃</td></tr> <tr><td>the electrophoresis for 3 hours</td></tr> <tr><td>SYBR Gold as a stain for 10 minutes</td></tr> </table>

<table> <tr><th>result</th></tr> <tr><td>We used the improved design DNA. Selector 1 didn't hybridize with the target, but the other results were what we had expected.</td></tr> <tr><td>The melting temperature of Selector 1 was lower than today's room temperature. And as for Selector 1, no hybridization occurred.</td></tr> <tr><td>Tomorrow we will do the experiment in a refrigerator.</td></tr> </table>

</div>


<!-- 新　8月24日 -->

<div id="expe1"></div> <div id="expe2"></div> <div id="expe3">2012/08/24</div> <div id="expe4"></div> <div id="expe5"></div> <div id="expe6"></div> <div id="expe7"><img src="http://openwetware.org/images/thumb/a/af/20120824_%E2%91%A1.jpg/791px-20120824_%E2%91%A1.jpg" style="width:500px;float:left;margin:5px;">

<table> <tr><th>condition</th></tr> <tr><td>constant voltage 50V</td></tr> <tr><td>1X TAE was added to Mg2+ as a buffer</td></tr> <tr><td>The room temperature was 28℃</td></tr> <tr><td>the electrophoresis for 3 hours</td></tr> <tr><td>SYBR Gold as a stain for 10 minutes</td></tr> </table>

<table> <tr><th>result</th></tr> <tr><td>Selector 1 seems to hybridize with itself.</td></tr> </table>

</div>

<!-- 新　8月22日 -->

<div id="expe1"></div> <div id="expe2"></div> <div id="expe3">2012/08/22</div> <div id="expe4"></div> <div id="expe5"></div> <div id="expe6"></div> <div id="expe7"><img src="http://openwetware.org/images/thumb/e/e3/20120822_%E2%91%A1.jpg/800px-20120822_%E2%91%A1.jpg" style="width:500px;float:left;margin:5px;">

<table> <tr><th>condition</th></tr> <tr><td>constant voltage 50V</td></tr> <tr><td>1X TAE was added to Mg2+ as a buffer</td></tr> <tr><td>The room temperature was 28℃</td></tr> <tr><td>the electrophoresis for 3 hours</td></tr> <tr><td>SYBR Gold as a stain for 10 minutes</td></tr> </table>

<table> <tr><th>result</th></tr> <tr><td>The target and Selector 1, and the target and Selector 2, seemed to hybridize.</td></tr> <tr><td>In the lane of Selector 1 and Selector 3, single-stranded Selector 1 and Selector 3 were seen. So Selector 1 and Selector 3 don't interact with each other.</td></tr> <tr><td>In the lane of Selector 2 and Selector 3, We could see a black band at one place.</td></tr> <tr><td>Maybe Selector 2's and Selector3's hairpin structure interacted with each other.</td></tr> </table>

</div>


<!-- 新　8月21日 -->

<div id="expe1"></div> <div id="expe2"></div> <div id="expe3">2012/08/21</div> <div id="expe4"></div> <div id="expe5"></div> <div id="expe6"></div> <div id="expe7"><img src="http://openwetware.org/images/thumb/b/be/20120821_%E2%91%A1.jpg/800px-20120821_%E2%91%A1.jpg" style="width:500px;float:left;margin:5px;">

<table> <tr><th>condition</th></tr> <tr><td>constant voltage 50V</td></tr> <tr><td>1X TAE was added to Mg2+ as a buffer</td></tr> <tr><td>The room temperature was 28℃</td></tr> <tr><td>the electrophoresis for 3 hours</td></tr> <tr><td>SYBR Gold as a stain for 10 minutes</td></tr> <tr><td>We did electrophoresis at 50V in a fridge (at 4 ℃)</td></tr> <tr><td>To get the target to move between Selectors, we waited one hour before the next step</td></tr> </table>

<table> <tr><th>result</th></tr> <tr><td>As a result, in the lane of the target, Selector 1, and 2, the band of Selector 1 couldn't be seen. And the band of Selector 2 was seen at the same place as when it was single-stranded.</td></tr> <tr><td>The target didn't seem to attach either to Selector 1 or 2.</td></tr> <tr><td>So Selector 1 and 2 aggregated with themselves or each other.</td><tr> <tr><td>As the 20% gel is difficult to see the result and it takes a long time, We'll use only the 10% gel from now on.</td></tr> </table>

</div>

<!-- 新　8月20日 -->

<div id="expe1"></div> <div id="expe2"></div> <div id="expe3">2012/08/20</div> <div id="expe4"></div> <div id="expe5"></div> <div id="expe6"></div> <div id="expe7"><img src="http://openwetware.org/images/thumb/5/5d/20120820_10-_%E2%91%A1.jpg/800px-20120820_10-_%E2%91%A1.jpg" style="width:500px;float:left;margin:5px;"><br><img src="http://openwetware.org/images/thumb/a/af/201120820_20-_%E2%91%A1.jpg/767px-201120820_20-_%E2%91%A1.jpg" style="width:500px;float:left;margin:5px;">

<table> <tr><th>condition</th></tr> <tr><td>constant voltage 50V</td></tr> <tr><td>1X TAE was added to Mg2+ as a buffer</td></tr> <tr><td>The room temperature was 28℃</td></tr> <tr><td>the electrophoresis for 3 hours</td></tr> <tr><td>SYBR Gold as a stain for 10 minutes</td></tr> <tr><td>We did electrophoresis at 50V in a fridge (at 4 ℃)</td></tr> <tr><td>To get the target to move between Selectors, we waited one hour before the next step</td></tr> </table>

<table> <tr><th>result</th></tr> <tr><td>The target hybridized with Selector 2 in the lane of the target, Selector 1, and 2. The target also hybridized with Selector 3 in the lane of the target, Selector 1, 2, and 3.</td></tr> <tr><td>From this result, it's possible that Target DNA moved from Selector 1 to Selecor 2, and from Selector 2 to Selector 3.</td><tr> <tr><td>However, in the lane of the target, Selector 1 and 2, the band of the target and Selector 1 was also clear. So we cannot decide the target actually moved from Selector 1 to Selector 2.</td></tr> <tr><td>In the lane of the target, Selector 1, 2, and 3, no band was around the place of single-stranded Selector 1. Probably we forgot to put Selector 1.</td></tr> <tr><td>Today we don't make sure the target moved from Selector 1 to Selector 2. But it's likely the target moved from Selector 2 to Selector 3.</td></tr> </table>

</div>


<!-- 新　8月17日 -->

<div id="expe1"></div> <div id="expe2"></div> <div id="expe3">2012/08/17</div> <div id="expe4"></div> <div id="expe5"></div> <div id="expe6"></div> <div id="expe7"><img src="http://openwetware.org/images/thumb/e/e3/20120817_%E2%91%A1.jpg/800px-20120817_%E2%91%A1.jpg" style="width:500px;float:left;margin:5px;">

<table> <tr><th>condition</th></tr> <tr><td>constant voltage 100V</td></tr> <tr><td>1X TAE as a buffer</td></tr> <tr><td>The room temperature was 28℃</td></tr> <tr><td>SYBR Gold as a stain for 10 minutes</td></tr> <tr><td>the electrophoresisin a fridge (at 4 ℃)</td></tr> <tr><td>To get the target to move between Selectors, we waited 50 minutes before the next step</td></tr> </table>

<table> <tr><th>result</th></tr> <tr><td>The materials diffused and the bands weren't clear, because we forgot to put the 15μl buffer of 1.25 % concentration of Mg2+ to samples.</td></tr> </table>

</div>


<!-- 新　8月9日 -->

<div id="expe1"></div> <div id="expe2"></div> <div id="expe3">2012/08/09</div> <div id="expe4"></div> <div id="expe5"></div> <div id="expe6"></div> <div id="expe7"><img src="http://openwetware.org/images/thumb/e/e3/20120809_%E2%91%A1.jpg/800px-20120809_%E2%91%A1.jpg" style="width:500px;float:left;margin:5px;">

<table> <tr><th>condition</th></tr> <tr><td>1X TAE as a buffer</td></tr> <tr><td>The room temperature was 28℃</td></tr> <tr><td>SYBR Gold as a stain for 10 minutes</td></tr> <tr><td>We did electrophoresis at constant voltage 100V in a fridge (at 4 ℃)</td></tr> <tr><td>To get the target to move between Selectors, we waited 30 minutes before the next step</td></tr> </table>

<table> <tr><th>result</th></tr> <tr><td>We used 10% and 20 % acrylamide gel for the electrophoresis.</td></tr> <tr><td>We stained the 10% gel with midori green, but the gel wasn't stained clearly(the picture is not here).</td></tr> <tr><td>The above picture is the 20% gel stained with SYBR gold.</td></tr> </table>

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<!--


<div id="outer"> <h3 id="t0i0t:le-1">2012/09/04</h3> <img src="http://openwetware.org/images/thumb/2/27/20120904%2C100v%2C2h%2Cfrige.jpg/708px-20120904%2C100v%2C2h%2Cfrige.jpg" width="620px"> <div id="kind">10% acrylamide gel</div><br> <div id="ul"> condition <ul> <li>constant voltage 50V</li> <li>We used 1X TAE added to Mg2+ as a buffer.</li> <li>The room temperature was 25℃(6℃ in the refrigerator).</li> <li>We did the electrophoresis for 2 hours in a refrigerator.</li> <li>We used SYBR Gold as a stain for 10 minutes.</li> </ul> result <ul> <li>The result was what we wanted completely.</li> <li>Target DNA hibridized to Selector 1</li> <li>Target DNA moved from Selector 1 to Selector2, and Selector 2 to Selector 3</li>

</ul> </div> </div>

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<div id="outer"> <h3 id="title-1">2012/08/30</h3> <img src="http://openwetware.org/images/thumb/c/c7/20120830_%E2%91%A1.jpg/800px-20120830_%E2%91%A1.jpg" width="620px"> <div id="kind">10% acrylamide gel</div><br> <div id="ul"> condition <ul> <li>We used 1X TAE added to Mg2+ as a buffer.</li> <li>The room temperature was 33℃(4℃ in the refrigerator).</li> <li>We did the electrophoresis for 3.5 hours in a refrigerator.</li> <li>We used SYBR Gold as a stain for 10 minutes.</li> </ul> result <ul> <li>The result was what we had expected.</li> <li>Finally, Selector 1 hybridized with the target.</li> </ul> </div> </div> --> <!--

<div id="outer"> <h3 id="title-1">2012/08/29</h3> <img src="http://openwetware.org/images/thumb/4/4f/20120829_%E2%91%A1.jpg/800px-20120829_%E2%91%A1.jpg" width="620px"> <div id="kind">10% acrylamide gel</div><br> <div id="ul"> condition <ul> <li>We used 1X TAE added to Mg2+ as a buffer.</li> <li>The room temperature was 33℃ (4℃ in the refrigerator).</li> <li>We did the electrophoresis for 3.5 hours.</li> <li>We used SYBR Gold as a stain for 10 minutes.</li> </ul> result <ul> <li>Selector 1 didn't hybridize with target. But the Other samples worked well.</li> <li>We will try again with cool buffer tomorrow.</li> </ul> </div>

</div> -->

<!--

<div id="outer"> <h3 id="title-1">2012/08/28</h3> <img src="http://openwetware.org/images/thumb/5/5a/20120828_%E2%91%A1.jpg/800px-20120828_%E2%91%A1.jpg" width="620px"> <div id="kind">10% acrylamide gel</div> <br> <div id="ul"> condition <ul> <li>The voltage of electrophoresis was cv 50v.</li> <li>We used 1X TAE was added to Mg2+ as a buffer.</li> <li>The room temperature was 33℃.</li> <li>We did the electrophoresis for 3 hours.</li> <li>We used SYBR Gold as a stain for 10 minutes.</li> </ul> result <ul> <li>We used the improved design DNA. Selector 1 didn't hybridize with the target, but the other results were what we had expected.</li> <li>The melting temperature of Selector 1 was lower than today's room temperature. And as for Selector 1, no hybridization occurred.</li> <li>Tomorrow we will do the experiment in a refrigerator.</li> </ul> </div>

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<div id="outer"> <h3 id="title-1">2012/08/24</h3> <img src="http://openwetware.org/images/thumb/a/af/20120824_%E2%91%A1.jpg/791px-20120824_%E2%91%A1.jpg" width="620px"> <div id="kind">10% acrylamide gel</div> <br> <div id="ul"> condition <ul> <li>The voltage of electrophoresis was 50v by constant voltage.</li> <li>We used 1X TAE was added to Mg2+ as a buffer.</li> <li>The room temperature was 28℃.</li> <li>We did the electrophoresis for 3 hours.</li> <li>We used SYBR Gold as a stain for 10 minutes.</li> </ul> result <ul> <li>Selector 1 seems to hybridize with itself.</li> </ul> </div> </div> --> <!-- <div id="outer"> <h3 id="title-1">2012/08/22</h3> <img src="http://openwetware.org/images/thumb/e/e3/20120822_%E2%91%A1.jpg/800px-20120822_%E2%91%A1.jpg" width="620px"> <div id="kind">10% acrylamide gel</div> <br> <div id="ul"> condition <ul> <li>The voltage of electrophoresis was 50v by constant voltage.</li> <li>We used 1X TAE added to Mg2+ as a buffer.</li> <li>The room temperature was 28℃.</li> <li>We did the electrophoresis for 3 hours.</li> <li>We used SYBR Gold as a stain for 10 minutes.</li> </ul> result <ul> <li>The target and Selector 1, and the target and Selector 2, seemed to hybridize.</li> <li>In the lane of Selector 1 and Selector 3, single-stranded Selector 1 and Selector 3 were seen. So Selector 1 and Selector 3 don't interact with each other.</li> <li>In the lane of Selector 2 and Selector 3, We could see a black band at one place.</li> <li>Maybe Selector 2's and Selector3's hairpin structure interacted with each other.</li> </ul> </div> </div>

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<h3 id="title-1">2012/8/21</h3> <img src="http://openwetware.org/images/thumb/b/be/20120821_%E2%91%A1.jpg/800px-20120821_%E2%91%A1.jpg" width="620px"><br> <div id="kind">10% acrylamide gel</div><br> <div id="ul"> condition <ul> <li>We did electrophoresis with the same condition as yesterday, except that we didn't make the lane of the target, Selector1, 2, and 3.</li> </ul> result <ul> <li>As a result, in the lane of the target, Selector 1, and 2, the band of Selector 1 couldn't be seen. And the band of Selector 2 was seen at the same place as when it was single-stranded.</li> 

 <li>The target didn't seem to attach either to Selector 1 or 2.</li>

<li>So Selector 1 and 2 aggregated with themselves or each other.</li> <li>As the 20% gel is difficult to see the result and it takes a long time, We'll use only the 10% gel from now on.</li> 

</ul>

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<div id="outer"> <h3 id="title-1">2012/08/20</h3> <img src="http://openwetware.org/images/thumb/5/5d/20120820_10-_%E2%91%A1.jpg/800px-20120820_10-_%E2%91%A1.jpg" width="620px"><br> <div id="kind">10% acrylamide gel</div> <br>

<img src="http://openwetware.org/images/thumb/a/af/201120820_20-_%E2%91%A1.jpg/767px-201120820_20-_%E2%91%A1.jpg" width="620px"><br> <div id="kind">20% acrylamide gel</div><br> <div id="ul"> condition <ul> <li>To get the target to move between Selectors, we waited one hour before the next step today. We did electrophoresis at 50V in a fridge (at 4 ℃).</li> <li>We stain the 10% gel with SYBR gold.</li> <li>The bands in the 20% gel were warped, and we couldn't get any sufficient result.</li> <li>The following is about the electrophoresis of the 10% gel.</li> </ul> result <ul> <li>The target hybridized with Selector 2 in the lane of the target, Selector 1, and 2. The target also hybridized with Selector 3 in the lane of the target, Selector 1, 2, and 3.</li> <li>From this result, it's possible that Target DNA moved from Selector 1 to Selecor 2, and from Selector 2 to Selector 3.</li> <li>However, in the lane of the target, Selector 1 and 2, the band of the target and Selector 1 was also clear. So we cannot decide the target actually moved from Selector 1 to Selector 2.</li> <li>In the lane of the target, Selector 1, 2, and 3, no band was around the place of single-stranded Selector 1. Probably we forgot to put Selector 1.</li> <li>In the lane of the target, Selector 1, 2, and 3, no band was around the place of single-stranded Selector 1. Probably we forgot to put Selector 1.</li> <li>Today we don't make sure the target moved from Selector 1 to Selector 2. But it's likely the target moved from Selector 2 to Selector 3.</li> </ul> </div> </div> --> <!-- <div id="outer"> <h3 id="title-1">2012/08/17</h3> <img src="http://openwetware.org/images/thumb/e/e3/20120817_%E2%91%A1.jpg/800px-20120817_%E2%91%A1.jpg" width="620px"><br> <div id="kind">10% acrylamide gel</div> <br> <div id="ul"> condition <ul> <li>In order to get the target to move between Selectors, we waited 50 minutes before the next step.</li> 

</ul>

result <ul> 

 <li>The materials diffused and the bands weren't clear, because we forgot to put the 15μl buffer of 1.25 % concentration of Mg2+ to samples.</li>
 </ul>

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<h3 id="title-1">2012/08/09</h3> <img src="http://openwetware.org/images/thumb/e/e3/20120809_%E2%91%A1.jpg/800px-20120809_%E2%91%A1.jpg" width="620px"><br>

<div id="kind">10% acrylamide gel</div><br> <div id="ul"> condition <ul> <li>We used 10% and 20 % acrylamide gel for the electrophoresis.</li> <li>We stained the 10% gel with midori green, but the gel wasn't stained clearly(the picture is not here).</li> <li>The above picture is the 20% gel stained with SYBR gold.</li> </ul> result <ul> <li>Each Selector seemed to hybridize with the target.</li> </ul> </div>

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<div id="yohaku"></div>


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