Biomod/2014/Kashiwa/Experiments

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   <li><a href="http://openwetware.org/wiki/Biomod/2014/Kashiwa"><img src="http://openwetware.org/images/e/ec/LogoKashiwa.png" onmouseover="this.src='http://openwetware.org/images/7/7a/Logo2Kashiwa.png'" onclick="this.src='http://openwetware.org/images/1/1d/Logo2.5.png'" onmouseout="this.src='http://openwetware.org/images/e/ec/LogoKashiwa.png'" height="80px" width="120px" name="def"></a>
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       <li><a href="http://openwetware.org/wiki/Biomod/2014/Kashiwa/Trial#1" onMouseOver="On('img1')" onMouseOut="Off()"><span style="font-size:12pt;">Design</span></a></li>
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</div> <br> <br> <br> <div class="page-back"><a href="#top"> <img src="http://openwetware.org/images/2/2a/Top1.gif" onmouseover="this.src='http://openwetware.org/images/f/f0/Top2.gif'" onmouseout="this.src='http://openwetware.org/images/2/2a/Top1.gif'" height="150px"/></a></div> </head>

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<div id="subContents"> <ul class="category"> <li><a href="#1"><h3>Experiments</h3></a></li> <li>The Receptor <ul> <li><a href="#1-1" title="CSS リファレンス一覧">Folding the Receptor</a></li> <li><a href="#1-2" title="Webデザインの一覧">Forming a Receptor dimer</a></li> <li><a href="#1-3" title="CSS ビギナー(初心者)向け一覧">Emitting the Initiator</a></li> <li><a href="#1-4" title="Photoshopの一覧">Embedding on the liposome</a></li></ul></li> <br> <li>The Motor <ul><li><a href="#2-1" title="(X)HTMLの一覧">Folding the Motor-Monomer</a></li> <li><a href="#2-2" title="Web関連情報の一覧">Forming the Motor-Polymer</a></li></ul></li> </ul> </ul> </div>

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<body> <a name="1"></a> <font face="Futura,Arial,Frutiger" font size="24px">EXPERIMENTS</font> <br> <br>

<TABLE BORDER="0" WIDTH="810px" CELLSPACING="0" CELLPADDING="30"> <TR> <TD align="center" BGCOLOR="#A9A9F5"> <span style="font-size:40px; color:#0A0A2A;">The Receptor</span> </TD> </TR> </TABLE> <br> <h1 class="title"><a name="background"> Direction</a></h1> <p class="paragraph">We planned to do experiments in several steps. First, we design the Receptor. Then, the following experiments are conducted in parallel. </p> <p class="paragraph">• Form the Receptor dimer by using thrombin. <br>• Emit the Polymerization Initiator by demerization. <br>• Embedding of Receptor on the liposome.</p> <br> <center><table><tr>

<table><tr> <td style="padding:0px 5px"><img src="http://openwetware.org/images/6/62/Experimentrece1.jpg" width="250px"></td> <td style="padding:0px 5px"><img src="http://openwetware.org/images/f/f4/Receptorstep2.jpg" width="250px"></td> <td style="padding:0px 5px"><img src="http://openwetware.org/images/4/4a/Experimentrece3.jpg" width="250px"></td> </tr></table></center> <a name="1-1"></a> <br> <p class="paragraph">Finally, after success in the experiments, we combine them to attain the dimerization and the Initiator emission on the liposome.</li> </p> <br> <h1 class="title"><a name="background"> Experiments</a></h1>

<h1 class="big"> Folding the Receptor</h1>

<p class="ex">Folding of the Receptor was confirmed by TEM and 1% agarose gel electrophoresis analysis. <br>The folded structure of the Receptor was clearly appeared in the TEM image.</p>

<h1 class="big"> Forming the Receptor dimer</h1>

<p class="ex">In this experiment, the dissociation constant (Kd) of thrombin and thrombin-binding aptamers was estimated. The purpose is to confirm the binding ability of each Aptamer (Aptamer A and B) with a thrombin before checking dimerization of the Receptor hetero-units. Binding of the aptamers with thrombin was analyzed with Native-PAGE.</p>

<br>

<p class="ex">We could confirm that aptamers bind to thrombin based on these two results. First, there are bands on the upper of that of aptamer's in the lanes (added aptamers 20 or 10 times as much as thrombin) of the left electrophoresis figure. Second, in fig.2, the bands of aptamers are weaker in the lanes (added thrombin 50 or 25 times as much as aptamers) than the other lanes, and we attributed these results to the formation of the complexes of thrombin and aptamers. In addition, the Kd of aptamers and thrombin is estimated about 50-300nM by measuring the intensity of band with the software (Image J).</p>

<h1 class="big"> Emitting the Initiator</h1>

<p class="ex">We confirmed whether the strand displacement mechanism was worked, and confirm the release of Polymerization Initiator. Also, we optimized the sequence by examine the effect of mismatch ratio of the strands.</p> <p class="ex">We used the following abbreviation; <br>J: Non-modified single strands <br>J’: Biotin modified single strands <br> (J is completely complimentary to J’) <br>Ini: Initiator (The percentage of mismatch to J is 5, 20 and 40%) <br>Cy5-modified Streptavidin (SA) </p>

<p class="ex"><b>Figure1 native-PAGE stained by EtBr. <br>J: Non-modified single strands <br>J’: Biotin modified single strands. Completely complement to J. <br>Ini XX%: Initiator. Partially complement to J with XX% mismatch introduced. <br>SA: Cy5-modified streptavidin.</b></p>

<div class="left"><img src="http://openwetware.org/images/9/93/Emission_of_ini_5%25.jpg"><img src="http://openwetware.org/images/c/c2/Emission_of_ini_20%25.jpg"></div> <p class="ex"><b>Figure2 The ratio of released Initiator to the whole Initiator, with 5 % mismatch introduced sequence. The result showed that little Initiator was released with this condition.</b></p> <p class="ex"><b>Figure3 The ratio of released Initiator to the whole Initiator, with 20 % mismatch introduced sequence. The result showed that Initiators were released with this condition.</b></p>

<p class="ex">Based on this experiment, the displacement of hybridized strand, and the release of Initiator was confirmed. Initiators were hardly released when the percentage of mismatch is 5 %, while with 20 % mismatch Initiators were released. For 40 % mismatch sequence, the band of released Initiator and that of original Initiator - J hybridized duplex were hardly distinguishable. To overcome this problem, it might be better to use fluorescently labeled strands.</p>

<h1 class="big"> Embedding on the liposome</h1>

<br>

<p class="ex">In order to certify the penetration of the Receptors to liposomes, a flotation assay was conducted.</p> <p class="ex">In preparation for a floation assay, cholesterol oligomers were hybridized to the Receptors for penetration. The hybridization was confirmed by 1% agarose gel electrophoresis analysis.</p>

<br>

<p class="ex">In flotation assay, we divided mixture with the Receptors and the liposomes to a few fractions, each of them was analyzed by fluorescence spectrophotometer and 1% agarose gel electrophoresis. This assay showed the distribution of liposomes and the Receptors, therefore we can distinguish the Receptor embedded into the liposomes from the free Receptors floating in solution.</p>

<br>

<p class="ex"><b>The fluorescence intensity of NileRed in each fraction (NileRed dyes the membrane of liposomes.)</b></p> <p class="ex">The result of fluorescence spectrophotometer (JASCO, FP-6500) showed that liposome distributed mostly in fraction 3.</p>

<br> <p class="ex"><b>The ratios of the Receptor in each fraction were analyzed by the density of band.</b></p> <p class="ex">In sample1 (cholesterol + / liposome +), the ratio of the Receptor in fraction3 was a bit larger than that in fraction2. In contrast, in sample 2, 3 and 4, the ratio of the Receptor in fraction3 was smaller than that in fraction2. As liposomes were mostly seen in fraction3 in both sample 1 and 3, and the ratio of the Receptor in each fraction was different only in sample1, we concluded that this difference was caused by penetration of the Receptor to liposomes.</p>

<h1 class="title"><a name="background"> Next Steps</a></h1> <p class="paragraph">In these experiments, we achieved to construct the Receptors and insert them into the liposomes. The very basics of others, formation of the Receptor dimers and emission of the Initiator, were also confirmed. Therefore, we are planning to approach the ones following for next steps. </p> <p class="paragraph">• Confirm the more advanced mechanism of forming the Receptor dimers and emitting the Initiator. <br>• Examine conditions for dimerization of the Receptor heterounits on the liposomes, may need changes in design of the Receptor.</p>

<a name="2"> </a> <br> <br> <br> <br> <TABLE LEFTMARGIN="-10px" BORDER="0" WIDTH="810px" CELLSPACING="0" CELLPADDING="30"> <TR> <TD align="center" BGCOLOR="#A9A9F5"> <span style="font-size:40px; color:#0A0A2A;">The Motor Monomer</span> </TD> </TR> </TABLE> <br> <h1 class="title"><a name="background"> Direction</a></h1> <br> <p class="paragraph">We planned to do experiments in several steps. First, we design the Motor-Monomer and assay the formation of a simple Motor-Polymer. Then, the following experiments are conducted in parallel.</p> <p class="paragraph">• Control the initiation of the polymerization (forming ring structures and ring-opening polymerization). <br>• Put the Motor-Monomers into the liposome.</p>

<a name="2-1"></a> <p class="paragraph">Finally, after success in the experiments, we combine them to attain the polymerization in the liposome.</p> <br><br><br><br>

<h1 class="title"><a name="background"> Experiments</a></h1>

<h1 class="big"> Folding the Motor-Monomer</h1>

<p class="ex">The assembly condition of the Motor-Monomer was optimized with concentration of MgCl<sub>2</sub>, annealing temperature and the ratio of staples to scaffold. The resulting structure was analyzed by agarose gel electrophoresis.</p>

<br>

<p class="ex">Multimers (e.g. dimers) appeared at lower temperature, so optimum temperature of annealing was 55.0℃.</p>

<div class="left"><img src="http://openwetware.org/images/3/32/Koala_002.jpg" height="300px"><img src="http://openwetware.org/images/4/43/Monomer_mgcl2.JPG"></div> <p class="ex">(Annealing temperature : 55.0℃, M13 : staples = 1 : 2) <br>The band of monomer at 16mM is bending and its migration distance is different from the one of MoN. It shows that the Monomers were not annealed correctly at 16 mM. There seemed to be little difference at other concentration, so optimum concentration of MgCl<sub>2</sub> was the range 10 to 14mM.</p>

<p class="ex">(Annealing temperature : 55.0℃, MgCl<sub>2</sub> : 10mM) <br>At the ratio of 6 and 8 a band of a monomer is weak and migrating distance was shorter than the one of monomer. As the graph showed, the ratio of dimer to monomer was low in lane 1 and 2, so optimum ratio of staples to scaffold was 2 or 4.</p>

<a name="2-2"></a> <p class="ex">Folding of the Motor-Monomer was corroborated by agarose gel electrophoresis analysis. The folding, however, was not verified by TEM. We considered it was because of hollow structures of the Motor-Monomers.</p>

<h1 class="big"> Forming the Motor-Polymer</h1>

<p class="paragraph"><b>MoN: The Motor-Monomers with no arm    negative control: mixture of both inactivated MoX and MoY</b></p>

<br>

<p class="ex">In this experiment, the effect of the number of arm on polymerization was examined. Two samples, one has three arms extruded from the body and the other has one, was compared. The Monomers comprise two similar structures, the Motor-Monomer X and the Motor-Monomer Y. The polymerization was confirmed by mixing the Monomer X and the Monomer Y.</p>

<p class="ex">The ratio of dimers of three arms monomers roughly increased with time, while the ratio did not change significantly for one arm monomers. It confirmed the polymerization of the Monomers with three arms.</p>

<p class="ex">The Monomer concentration was optimized.</p> <p class="ex">The ratio of dimers was high at high monomer concentration of three arms monomers, while for one arm monomers, the ratio was not different from that of monomer only condition. It meant Polymerization of three arms monomers proceeds efficiently at high concentration of monomers in solution.</p>

<h1 class="title"><a name="background"> Next Steps</a></h1> <br>

<br> <br> <h1 class="title">Reference</h1> <font size="2">

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