基礎ゼミチーム/basic seminar team/experiment result: Difference between revisions
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<h1 id="wiki-mode1"><strong><font color="#DC143C">BIOMOD2012 Tohoku Team B</font></strong></h1>
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<h2 id="wiki-mode2">Experiment result</h2>
<div class="text">
- In illustration, target = Target DNA<br>
- In illustration, numbers are time when the sample was put in since first samples were put in
<!-- 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 use 10% and 20 % acrylamide gel in erectrophoresis</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>
<!-- 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 let the target 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 15μl buffer containg 1.25 % concentration of Mg2+ to samples</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 let the target move between Selectors, we waited one hour before the next step today. We did electrophoresis at 50V in a refrigerate( at 4 degrees)</li> <li>We stain the 10% gel with sybr gold</li> <li>We do erectrophoresis in refrigerate (4℃) and constant voltage of 50v</li> <li>The bands in the 20% gel were warped and we couldn't get the sufficient result</li> <li>The following statement is about the electrophoresis in the 10% gel</li> </ul> result <ul> <li>As a result, 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, Target DNA may be able to move from Selector 1 to Selecor 2, and from Selector 2 to Selector 3</li> <li>In the lane of the target, Selector 1 and 2, the band of the target and Selector1 and the band of the target and Selector 2 are both clear. So we have some doubts to say 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 is around the place of single-stranded Selector 1. So it's probable we forgot to put it</li> <li>In the lane of the target, Selector 1, 2, and 3, no band is around the place of single-stranded Selecto r1. So it's probable we forgot to put Selector 1</li> <li>We don't make sure the target moved from Selector 1 to Selector 2. But we can probably say the target moved from Selector 2 to Selector 3</li> </ul> </div> </div>
<!-- 8月21日 -->
<div id="outer">
<hr> <p> <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 prepare 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 cannot be seen. And the band of Selector 2 is 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 the Selector 1 and 2 aggregated with themselves or each other</li> <li>As the 20% gel is difficult to get the result and it takes a long time to, We'll use only the 10% gel from now on</li>
</ul>
</div> </p> <hr>
</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 is 50v by constant voltage</li> <li>We used 1×TAE added to Mg2+ as a buffer</li> <li>The room temperature is 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>There were bands of sample mixed target and Selector 1, and target and Selector 2, hybridized each other</li> <li>In sample mixed Selector 1 and Selector 3, there were both bands Selector 1 only and Selector 3 only so Selector 1 and Selector 3 don't interact each other</li> <li>In sample mixed Selector 2 and Selector 3, We could see a black band at one place</li> <li>Maybe Selector 2's hairpin structure and Selector 3's interacted each other.</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 is 50v by constant voltage</li> <li>We used 1×TAE was added to Mg2+ as a buffer</li> <li>The room temperature is 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 seem to hybridised with itself</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 is cv 50v</li> <li>We used 1×TAE was added to Mg2+ as a buffer</li> <li>The room temperature is 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 new base sequence DNA and Selector 1 didn't hybridize with target, but other results were what we want</li> <li> Tm of Selector 1 is lower than today's room temperature, so didn't hybridize</li> <li>Tomorrow we will try in the refrigerator</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 was added to Mg2+ as a buffer</li>
<li>The room temperature is 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. Other samples worked well</li>
<li>We will try again with cool buffer</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 was added to Mg2+ as a buffer</li> <li>The room temperature is 33℃(4℃ in the refrigerator)</li> <li>We did the electrophoresis for 3.5 hours in the refrigerator</li> <li>We used SYBR Gold as a stain for 10 minutes</li> </ul> result <ul> <li>The result was what we want</li> <li>Swlwctor 1 hybridized with target</li> </ul> </div> </div>
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