基礎ゼミチーム/basic seminar team/experiment result: Difference between revisions
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<img src="http://openwetware.org/images/thumb/2/27/20120904%2C100v%2C2h%2Cfrige.jpg/708px-20120904%2C100v%2C2h%2Cfrige.jpg" width="620px"> | <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="kind">10% acrylamide gel</div><br> |
Revision as of 19:59, 6 September 2012
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<div id="head-1"> BIOMOD2012 Tohoku Team B </div>
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<div style="float:left;width:5px;height:30px;">
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<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">
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Project
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<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
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Team
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<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">
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Link
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<br>
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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>
<!--
<div id="expe1"></div> <div id="expe2"></div> <div id="expe3">2012/09/05</div> <div id="expe4"></div> <div id="expe5"></div> <div id="expe6"></div> <div id="expe7"><img src="" style="width:400px;float:left;"> content <ul> <li>---</li> </ul> result <ul> <li>---</li> <ul> -->
<!-- 9月4日 -->
<div id="outer"> <h3 id="title-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>
<!-- 8月30日 -->
<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>
<!-- 8月29日 --> <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>
<!-- 8月28日 -->
<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>
</div>
<!-- 8月24日 -->
<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>
<!-- 8月22日 -->
<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>
<!-- 8月21日 -->
<div id="outer">
<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>
</div>
</div>
<!-- 8月20日 -->
<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>
<!-- 8月17日 --> <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>
</div> </div>
<!-- 8月9日 -->
<div id="outer">
<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>
</div>
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<div id="yohaku"></div>
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