基礎ゼミチーム/basic seminar team/experiment result: Difference between revisions

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<h2 id="wiki-mode2">Experiment result</h2>
<h2 id="wiki-mode2">Experiment result</h2>
<div class="text">
<div class="text">
*Tar = Target DNA<br>
*in illuste, target = Target DNA<br>
*S1,S2,S3 = Selector1,Selector2,Selector3
 




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<h3 id="title-1">2012/08/09</h3>
<h3 id="title-1">2012/08/09</h3>
<img src="http://openwetware.org/images/thumb/8/8e/20120809.jpg/800px-20120809.jpg" width="620px"><br>
<img src="http://openwetware.org/images/thumb/8/8e/20120809.jpg/800px-20120809.jpg" width="620px"><br>
<!--
 
<div id="marker">1+4</div><div id="marker">1+3</div><div id="marker">1+2+3+4</div><div id="marker">1+2+3</div><div id="marker">1+2</div><div id="marker">4</div><div id="marker">3</div><div id="marker">2</div><div id="marker">1</div><div id="marker">マーカー</div><br>
-->
<div id="kind">10% acrylamide gel</div><br>
<div id="kind">10% acrylamide gel</div><br>
<div id="ul">
<div id="ul">
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result
result
<ul>
<ul>
<li>Selector 2 and 3, each Selector seemed to hybridize with the target</li>
<li>Each Selector seemed to hybridize with the target</li>
</ul>
</ul>
</div>
</div>
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<h3 id="title-1">2012/08/17</h3>
<h3 id="title-1">2012/08/17</h3>
<img src="http://openwetware.org/images/thumb/a/aa/20120817.jpg/800px-20120817.jpg" id="photo" width="620px"><br>
<img src="http://openwetware.org/images/thumb/a/aa/20120817.jpg/800px-20120817.jpg" id="photo" width="620px"><br>
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<div id="kind">10% acrylamide gel</div>
<div id="kind">10% acrylamide gel</div>
<br>
<br>
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<h3 id="title-1">2012/08/20</h3>
<h3 id="title-1">2012/08/20</h3>
<img src="http://openwetware.org/images/thumb/0/0a/20120820_10-.jpg/800px-20120820_10-.jpg" id="photo" width="620px"><br>
<img src="http://openwetware.org/images/thumb/0/0a/20120820_10-.jpg/800px-20120820_10-.jpg" id="photo" width="620px"><br>
<!--
<div id="marker">Marker</div><div id="marker">Tar+S3</div><div id="marker">Tar+S2</div><div id="marker">Tar+S1+S2+S3</div><div id="marker">Tar+S1+S2</div><div id="marker">Tar+S1</div><div id="marker">S3</div><div id="marker">S2</div><div id="marker">S1</div><div id="marker">Tar</div><br>
-->
<div id="kind">10% acrylamide gel</div>
<div id="kind">10% acrylamide gel</div>
<br>
<br>


<img src="http://openwetware.org/images/thumb/f/f0/20120820_20%25_gel.jpg/776px-20120820_20%25_gel.jpg" id="photo" width="620px"><br>
<img src="http://openwetware.org/images/thumb/f/f0/20120820_20%25_gel.jpg/776px-20120820_20%25_gel.jpg" id="photo" width="620px"><br>
<!--
<div id="marker">Tar+S1</div><div id="marker">Tar+S3</div><div id="marker">Tar+S2</div><div id="marker">S3</div><div id="marker">S2</div><div id="marker">Tar+S1+S2</div><div id="marker">Tar+S1+S2+S3</div><div id="marker">S1</div><div id="marker">Tar</div><br>
-->
<div id="kind">20% acrylamide gel</div><br>
<div id="kind">20% acrylamide gel</div><br>
<div id="ul">
<div id="ul">
condition
condition
<ul>
<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 fridge( at 4 degrees)</li>
<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 stain the 10% gel with sybr gold</li>
<li>We do erectrophoresis in refrigerate （4℃） and constant voltage of 50v</li>
<li>We do erectrophoresis in refrigerate （4℃） and constant voltage of 50v</li>
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result
result
<ul>
<ul>
<li>As a result, the target hybridized with Selector2 in the lane of the target, Selector1, and 2. The target also hybridized with Selector3 in the lane of the target, Selector1, 2, and 3</li>
<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 Selecor2, and from Selector 2 to Selector 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, Selector1 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 Selector2</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, Selector1, 2, and 3, no band is around the place of single-stranded Selector1. So it's probable we forgot to put ???In the lane of the target, Selector1, 2, and 3, no band is around the place of single-stranded Selector1. So it's probable we forgot to put Selector 1</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>We don't make sure the target moved from Selector1 to Selector2. But we can probably say the target moved from Selector 2 to Selector3</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>
</ul>
</div>
</div>
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<h3 id="title-1">2012/8/21</h3>
<h3 id="title-1">2012/8/21</h3>
<img src="http://openwetware.org/images/thumb/9/94/20120821.jpg/800px-20120821.jpg" id="photo" width="620px"><br>
<img src="http://openwetware.org/images/thumb/9/94/20120821.jpg/800px-20120821.jpg" id="photo" width="620px"><br>
<!--
<div id="marker">Marker</div><div id="marker">Tar+S3</div><div id="marker">Tar+S2</div><div id="marker">Tar+S1+S2</div><div id="marker">Tar+S1</div><div id="marker">S3</div><div id="marker">S2</div><div id="marker">S1</div><div id="marker">Tar</div><br>
-->
<div id="kind">10% acrylamide gel</div><br>
<div id="kind">10% acrylamide gel</div><br>
<div id="ul">
<div id="ul">
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result
result
<ul>
<ul>
<li>As a result, in the lane of the target, Selector1, and 2, the band of Selector1 cannot be seen. And the band of Selector2 is seen at the same place as when it was single-stranded</li>
<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 Selector1 or 2</li>
   <li>The target didn't seem to attach either to Selector 1 or 2</li>
<li>So the selector1 and 2 aggregated with themselves or each other</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>
<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>
  </ul>
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result
result
<ul>
<ul>
<li>There were bands meaning  Tar+S1 and Tar+S2  hybridized each other</li>
<li>There were bands of sample mixed target and Selector 1, and target and Selector 2, hybridized each other</li>
<li>In S1+S3, there were both bands S1 only and S3 only so S1 and S3 don't interact 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 S2+S3, We could see a black band at one place</li>
<li>In sample mixed Selector 2 and Selector 3, We could see a black band at one place</li>
<li>Maybe S2's hairpin structure and S3's interacted each other.</li>
<li>Maybe Selector 2's hairpin structure and Selector 3's interacted each other.</li>
</ul>
</ul>
</div>
</div>
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<li>We used 1×TAE was added to Mg2+ as a buffer</li>
<li>We used 1×TAE was added to Mg2+ as a buffer</li>
<li>The room temperature is 28℃</li>
<li>The room temperature is 28℃</li>
<li>We did the electrophoresis for 3 hours.</li>
<li>We did the electrophoresis for 3 hours</li>
<li>We used SYBR Gold as a stain for 10 minutes.</li>
<li>We used SYBR Gold as a stain for 10 minutes</li>
</ul>
</ul>
result
result
<ul>
<ul>
<li>S1 seem to hybridised with itself.</li>
<li>Selector 1 seem to hybridised with itself</li>
</ul>
</ul>
</div>
</div>
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result
result
<ul>
<ul>
<li>We used new base sequence DNA and S1 didn’t hybridize with Target, but other results were what we want</li>
<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 S1 is lower than today’s room temperature , so didn’t hybridize</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>
<li>Tomorrow we will try in the refrigerator</li>
</ul>
</ul>
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condition
condition
<ul>
<ul>
<li>We used 1×TAE was added to Mg2+ as a buffer</li>
<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>The room temperature is 33℃(4℃ in the refrigerator)</li>
<li>We did the electrophoresis for 3.5 hours</li>
<li>We did the electrophoresis for 3.5 hours</li>
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result
result
<ul>
<ul>
<li>S1 didn’t hybridize with Target.　Other samples worked well</li>
<li>Selector 1 didn't hybridize with target. Other samples worked well</li>
<li>We will try again with cool buffer</li>
<li>We will try again with cool buffer</li>
</ul>
</ul>
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condition
condition
<ul>
<ul>
<li>We used 1×TAE was added to Mg2+ as a buffer</li>
<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>The room temperature is 33℃(4℃ in the refrigerator)</li>
<li>We did the electrophoresis for 3.5 hours</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>
<li>We used SYBR Gold as a stain for 10 minutes</li>
</ul>
</ul>
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<ul>
<ul>
<li>The result was what we want</li>
<li>The result was what we want</li>
<li>S1 hybridized with Target</li>
<li>Swlwctor 1 hybridized with target</li>
</ul>
</ul>
</div>
</div>

Revision as of 06:14, 2 September 2012

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  • in illuste, target = Target DNA<br>


<!-- 8月9日 -->


<div id="outer">

<h3 id="title-1">2012/08/09</h3> <img src="http://openwetware.org/images/thumb/8/8e/20120809.jpg/800px-20120809.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/a/aa/20120817.jpg/800px-20120817.jpg" id="photo" 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/0/0a/20120820_10-.jpg/800px-20120820_10-.jpg" id="photo" width="620px"><br> <div id="kind">10% acrylamide gel</div> <br>

<img src="http://openwetware.org/images/thumb/f/f0/20120820_20%25_gel.jpg/776px-20120820_20%25_gel.jpg" id="photo" 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/9/94/20120821.jpg/800px-20120821.jpg" id="photo" 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/0/0f/20120822.jpg/800px-20120822.jpg" id="photo" 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/3/3f/20120824.jpg/789px-20120824.jpg" id="photo" 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/8/87/20120828.jpg/800px-20120828.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/1/13/20120829.jpg/800px-20120829.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/4/41/20120830.jpg/800px-20120830.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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