Biomod/2013/Titech/design: Difference between revisions

Revision as of 17:32, 27 October 2013

<!DOCTYPE> <html> <head> <title>project</title> <style type='text/css'> h1.firstHeading{display:none;}

jump-to-nav{display:none;}
siteSub{display:none;}
contentSub{display:none;}
column-one { display:none; width:0px;}
haikei{

         width:900px;

margin-right:200px; margin-left:330px;

                 margin-top:-290px;

background-color:#ffffff;

                 box-shadow:#000000 2px 2px, gray 5px 5px 5px 5px ;}

globalWrapper{background-color:green; display:none;}
column-content{background-color:yellow; display:none;}
bodyContent{display:none;}
column-one { display:none; width:0px;}

.OWWNBcpCurrentDateFilled {display: none;}

footer{margin-left:330px;; width:900px}

body{

 background-color:#ffffff;
 font-size:18px;
 font-family:arial;
text-decoration:none;
 }

h1{ text-align:left; font-style: italic; font-size:50px; text-decoration:none; }

h2{ font-style: italic; font-size:40px; text-align:center; text-decoration:none; }

haikei p span {

font-weight: bold; }

table{ border:1px black solid; } table tr td{ border:1px black solid; }

.fig{ font-weight:bold; font-size:20px; text-align:center; }

.itimojime{ font-size:36px; font-family:arial light; }

.menu{ text-decoration:none; font-family:Arial, Helvetica, sans-serif; list-style-type:none; display:block; position:fixed; } a.menu:link{ color:#4e90ff; } a.menu:visited{ color:#4e90ff; }

a.menu:active{ color:#4e90ff; } a.menu:hover{ font-size:24px; text-shadow:#e77070 2px 2px; }

bar{

list-style-type: none }

bar li {

text-decoration:none; } .risuto{ font-size:24px; } .risuto2{ font-size:18px; list-style-type: square; } </style> </head> <body> </div> </div> </div> </div> </div>

<p>&nbsp; </p>
   <p>&nbsp; </p>
   <p>&nbsp; </p>
   <p>&nbsp; </p>
<p>&nbsp; </p>
   <p>&nbsp; </p>
   <p>&nbsp; </p>
   <p>&nbsp; </p>

<div style="position:fixed;"float="left"> <ul id="bar"> <li class="risuto"><a href = "http://openwetware.org/wiki/Biomod/2013/Titech" class = "menu">Home</a></li> <li class="risuto"><a href = "http://openwetware.org/wiki/Biomod/2013/Titech/project" class = "menu">Project</a></li> <li class="risuto"><a href = "http://openwetware.org/wiki/Biomod/2013/Titech/design" class = "menu">Design</a></li> <li class="risuto"><span style="color:#4e90ff; font-family:Arial, Helvetica, sans-serif">Methods&Results</span>

            <ul><li class="risuto2"><a href="http://openwetware.org/wiki/Biomod/2013/Titech/methods&amp;results" class="menu">
            UV-Tuning Nano- Parasol</a></li>
                <li class="risuto2"><a href="http://openwetware.org/wiki/Biomod/2013/Titech/M%26R_Controlable_Optical_Makeup" class="menu">
            Controllable Optical Makeup</a></li></ul>

<li class="risuto"><a href = "http://openwetware.org/wiki/Biomod/2013/Titech/Achievements" class = "menu">Achievements</a></li> <li class="risuto"><a href = "http://openwetware.org/wiki/Biomod/2013/Titech/" class = "menu">supl.info </a></li> <li class="risuto"><a href = "http://openwetware.org/wiki/Biomod/2013/Titech/team" class = "menu">member</a></li> <li class="risuto"><a href = "http://openwetware.org/wiki/Biomod/2013/Titech/acknowledgement" class = "menu">Acknowledgement </a></li> </ul> </div>

<div id="haikei"> <a href="http://openwetware.org/wiki/Biomod">Biomod<a/>|<a href="http://openwetware.org/wiki/Biomod/2013">2013</a> <div style="width:900px"> <img src="https://upload.wikimedia.org/wikipedia/commons/3/34/%E3%81%A8%E3%81%A3%E3%81%B7%E3%81%8C.png" width="900"> </div>

<h2><b>〈UV-Tuning Nano-Parasol〉</b></h2> <p>    Our nano-scale parasol is made of gold nanoparticles and DNA. The DNA portion of the nano-parasol connects with model cells upon UV exposure, and the nanoparticle portion absorbs UV light. Design details are described below. For constructing a cosmetic biomolecular system to control your suntan condition, we set the following target functions as the component of this system.</p>

The UV-Tuning Nano-Parasol system can <div style="font-weight:bold;"> <ol> <li> convert the information of the total amount of UV exposure into the amount of DNA signal (<strong class="blue">UV-DNA converter</strong>).</li>

<li> perform threshold processing of the amount of DNA signal (<strong class="blue">Threshold processor</strong>).</li>

<li> connect the nano-parasols onto the surface of model cells according to the threshold processing of DNAsignal (<strong class="blue">Nano-parasol</strong>).</li>

<li> put the nano-parasols out of skin cells automatically when UV irradiation stops(<strong class="blue">Reset mechanism</strong>).</li> </ol> </div>

<p>  </p> <h2>1. UV-DNA converter</h2> <p> </p> <div align="center"> <img src="https://upload.wikimedia.org/wikipedia/commons/thumb/7/7c/Design10-25_UV%E5%90%B9%E3%81%8D%E5%87%BA%E3%81%97.png/800px-Design10-25_UV%E5%90%B9%E3%81%8D%E5%87%BA%E3%81%97.png" width="600"> </div>

<P>    By using a DNA containing azobenzene that changes its isomer type from <I>trans</I> to <I>cis</I> upon UV irradiation, we designed a UV-DNA converter. The isomerization of azobenzene destabilizes the double-stranded structure formed by complementary DNA strands. In Fig. 1. (a), Converter complex in the double-stranded form          　transforms into single strands upon UV exposure, and thus, releases a DNA signal. The amount of DNA signal released by UV-DNA converter corresponds to the total amount of UV exposure.</P>

<p> </p> <div align="center"> <img src="https://upload.wikimedia.org/wikipedia/commons/thumb/2/25/Design10-25_%E3%81%82%E3%81%9E%E3%81%B9%E3%82%93%E3%81%9C%E3%82%93%E3%81%8B%E3%81%84%E3%82%8A%E3%81%84%E3%81%84%E3%81%84.png/800px-Design10-25_%E3%81%82%E3%81%9E%E3%81%B9%E3%82%93%E3%81%9C%E3%82%93%E3%81%8B%E3%81%84%E3%82%8A%E3%81%84%E3%81%84%E3%81%84.png" width="600"> </div> <p><strong>Fig. 1. UV-DNA converter. DNA dissociation due to the <i>trans-to-cis</i><br>           transformation of azobenzenes.</strong></p> <p>  </p>

<h2>2. Threshold processor</h2> <p>  </p> <div align="center"> <img src="https://upload.wikimedia.org/wikipedia/commons/thumb/5/5f/Design10-22%E9%96%BE%E5%80%A4%E5%90%B9%E3%81%8D%E5%87%BA%E3%81%97.png/800px-Design10-22%E9%96%BE%E5%80%A4%E5%90%B9%E3%81%8D%E5%87%BA%E3%81%97.png" width="600"></div>

<p>  </p> <p>    The DNA signal released from the UV-DNA converter triggers a release of Linker strand to crosslink a nano-parasol onto a model cell. We introduced threshold processing into this process. As a consequence, the attachment of nano-parasols onto model skin cells, is programmed to start only when the amount of UV exposure exceeds the predefined threshold. The toehold-mediated strand exchange of the DNA signal with a Threshold complex occurs earlier than that with a Linker-output complex (Fig. 2). Therefore, the release of the Linker strands occurs after the strand exchange between the DNA signal and a Threshold complex. By changing the amount of Threshold complex, you can arbitrarily set the threshold value for UV sensing.</p> <p>  </p>

<p><strong>Fig. 2. Threshold processor.</strong></p>

<p>  </p> <h2>3. Nano- parasol</h2> <p>  </p> <div align="center"> <img src="https://upload.wikimedia.org/wikipedia/commons/thumb/1/12/Design10-22%E7%B4%B0%E8%83%9E%E3%81%AB%E4%BB%98%E3%81%8F%E5%90%B9%E3%81%8D%E5%87%BA%E3%81%97.png/800px-Design10-22%E7%B4%B0%E8%83%9E%E3%81%AB%E4%BB%98%E3%81%8F%E5%90%B9%E3%81%8D%E5%87%BA%E3%81%97.png" width="600"> <img src="https://upload.wikimedia.org/wikipedia/commons/thumb/c/cf/Design_10-25_%E3%83%A2%E3%83%87%E3%83%AB%E5%8C%96.png/800px-Design_10-25_%E3%83%A2%E3%83%87%E3%83%AB%E5%8C%96.png" width="400"> <img src="https://upload.wikimedia.org/wikipedia/commons/thumb/3/3b/Design_10-25_%E8%8F%AF%E5%83%91%E3%81%95%E3%82%8C%E3%82%8B%E6%BC%AB%E7%94%BB%28c%29.png/800px-Design_10-25_%E8%8F%AF%E5%83%91%E3%81%95%E3%82%8C%E3%82%8B%E6%BC%AB%E7%94%BB%28c%29.png" width="600"> </div>

<p><strong>Fig. 3. Nano-parasol. <br>         (a)</strong> A Nano-parasol system to model the attachment to a skin cell. <br> <strong>         (b)</strong> Attachment procedure of the Nano-parasol triggered by a DNA signal.</p> <p>  </p>

<p>    For prooving our main concept in this summer project, we designed a model experiment, in which the crosslinking among three complementary nucleic acid strands and a polystyrene micro bead were adopted instead of the crosslinking among a Port DNA, an aptamer-containing crosslinker and a marker protein on the cell surface and a skin cell, respectively (Fig. 3. (a)). </p>

<p>    After the threshold processing, the DNA signal triggers the release of the Linker strand from the Linker-output complex if there remains the DNA signal in the single-stranded form (Fig. 3. (b)). Then, the Linker strand crosslinks between a Handle DNA attached to a gold nanoparticle and a Port DNA as a model of the cellular membrane protein. Therefore, in response to the DNA signal released according to UV exposure, the nano-parasols connect to the model cells and shade UV light. </p>

<p>  </p> <h2>4. Reset mechanism</h2> <p>  </p> <div align="center"> <img src="https://upload.wikimedia.org/wikipedia/commons/thumb/b/ba/Design10-22%E5%A4%96%E3%82%8C%E3%82%8B%E5%90%B9%E3%81%8D%E5%87%BA%E3%81%97.png/799px-Design10-22%E5%A4%96%E3%82%8C%E3%82%8B%E5%90%B9%E3%81%8D%E5%87%BA%E3%81%97.png" width="600"> </div> <img src="https://upload.wikimedia.org/wikipedia/commons/thumb/a/ac/Design_10-25_RNaseH%E3%81%AB%E3%82%88%E3%82%8B%E5%88%86%E8%A7%A3%E5%8F%8D%E5%BF%9C.png/800px-Design_10-25_RNaseH%E3%81%AB%E3%82%88%E3%82%8B%E5%88%86%E8%A7%A3%E5%8F%8D%E5%BF%9C.png" width="450">        

<p><strong> Fig. 4. Reset mechanism <br>          (a)</strong> Detachment of the Nano-parasol due to the Linker degradation by RNaseH. <br>          <strong>(b)</strong> The single-stranded RNA portion of the Linker-output complex <br>       this portion is not degraded by RNaseH. </p> <p>  </p>

<p>    In the present system, we added a small amount of RNaseH which specifically degrades a RNA strand in a hybridized double strand of complementary DNA and RNA strands. Therefore, the release of the Linker strand and its degradation competitively occurs, and thus, UV-Tuning Nano-Parasol system can be automatically reset without the continuous UV exposure (Fig. 4). Note here that, the RNA portion of the Linker strand is in the double-stranded form only when it crosslinks the nano-parasol and the model cell by hybridization between DNA and RNA strands. Before its use, the RNA portion of the Linker strand, bound within the Linker-output complex, forms a loop structure and is not be degraded by RNaseH. </p>

<p>    If there is not the Reset mechanism, the nano-parasols keep connecting with model cells and in the next day, it absorbs UV even if the amount of UV exposure doesn’t exceeds the threshold. The Reset mechanism allows the nano-parasols to detach from the cells in the evening for keeping your favorite suntan condition. In the next day, nano-parasols start their operation again according to the threshold defined by users. </p>

<p>  </p> <h2><b>〈Controllable Optical Makeup〉</b></h2> <p>  </p> <div align="center"> <img src="https://upload.wikimedia.org/wikipedia/commons/thumb/2/25/Design_10-22%E3%82%AA%E3%83%91%E3%83%BC%E3%83%AB%E3%81%AE%E3%83%96%E3%83%A9%E3%83%83%E3%82%B0%E3%83%AA%E3%83%95%E3%83%AC%E3%82%AF%E3%82%B7%E3%83%A7%E3%83%B3.png/800px-Design_10-22%E3%82%AA%E3%83%91%E3%83%BC%E3%83%AB%E3%81%AE%E3%83%96%E3%83%A9%E3%83%83%E3%82%B0%E3%83%AA%E3%83%95%E3%83%AC%E3%82%AF%E3%82%B7%E3%83%A7%E3%83%B3.png" width="500"> </div>

<p>    Our optical makeup system provides structural colors as a novel category of colors for makeup. The structural color is the color originating from the interference of light from substance’s structure. The representative examples of structural color are the outer shells of insects, the surfaces of Compact Discs and opal, known as the birthstone for October. When you observe the surface of precious opal jewelry by a Scanning Electron Microscope (SEM), you may find that SiO<sub>2</sub> nanoparticles is forming an ordered crystal structure. This ordered crystal structure makes a Bragg reflection and interferences light. In the present system, we also utilize gold nanoparticles and DNA for constructing ordered crystal structures by connecting them together via DNA hybridization. </p>

<p>    For establishing a cosmetic biomolecular system that can light you up with a variety of structural colors according to your tastes, we set the following target functions as the component of this system. </p> <p>  </p>

<div align="center"> <img src="https://upload.wikimedia.org/wikipedia/commons/thumb/9/9b/Design_10-251%E3%81%A82.png/800px-Design_10-251%E3%81%A82.png" width="600"> </div> <p> The Controllable Optical Makeup system can </p>

<div style="font-weight:bold;"> <ol> <li>make the crystal structure that expresses structural color by precisely arraying gold nanoparticles in three dimensions (<strong class="blue">Particle crystallizer</strong>).</li> <li> change the structural color, that is determined according to the distance of particles, by altering the length of DNA for connecting particles (<strong class="blue">Color variation</strong>)</li> </ol> </div>

<p>  </p> <h2>1. Particle crystallizer</h2> <p>  </p> <div align="center"> <img src="https://upload.wikimedia.org/wikipedia/commons/thumb/5/5b/Design_10-25_%E6%A7%8B%E9%80%A0%E8%89%B2%E5%90%B9%E3%81%8D%E5%87%BA%E3%81%97.png/800px-Design_10-25_%E6%A7%8B%E9%80%A0%E8%89%B2%E5%90%B9%E3%81%8D%E5%87%BA%E3%81%97.png" width="600"> </div>

<div style="width:400px;float:right;margin-top:40px;" > <img src="https://upload.wikimedia.org/wikipedia/commons/thumb/9/92/Resolt_and_Method_%E9%87%91%E3%83%8A%E3%83%8E%E6%9E%B6%E6%A9%8B.png/800px-Resolt_and_Method_%E9%87%91%E3%83%8A%E3%83%8E%E6%9E%B6%E6%A9%8B.png" width="400px" > <p><strong>Fig. 5.1. Composition of A crystallizer DNA complex.</strong></p> </div>

<p>    We designed a crystallization system, in which gold nanoparticles are precisely arrayed via hybridization of Crystallizer DNA complexes, by following the method developed by Robert J. macfarlane <br> et al. A Crystallizer DNA complex consists of the longer strand and the shorter strand, which binds to the middle region of the longer strand to form a stiff double-stranded structure for allowing precise positioning. One end of the longer strand in the Crystallizer DNA complex hybridizes with the Handle DNA attached to the nanoparticle, and the other end having a self-complementary sequence hybridizes with the same end of another Crystallizer DNA complex (Fig. 5.1). </p>

<p>    Upon hybridization of the Crystallizer DNA complexes, the nanoparticles firstly form non-crystalline aggregates. And then, by subjecting the nanoparticles to an annealing process, the particles reposition themselves to form the thermodynamically most stable crystal structure .In the case of the present study,a face-centered cubic (fcc) structure, in which the particles are situated at each apex and the center of each face, would be formed (Fig. 5.2.(a)). The resulted three-dimensional crystal structure of gold nanoparticles makes the Bragg reflection by interfering with light, and expresses the structural color (Fig. 5.2.(b)). Consequently, the crystal structure formed by our optical makeup system is expected to express the structural color like a precious Opal jewelry. </p>

<p><strong>Fig. 5.2. Particle crystallizer. <br>          (a)</strong> Formation of fcc structure by Crystallizer DNA complexes. <br> <strong>         (b)</strong> Expression of the structural color by the particle crystallization.</p>

<p>  </p> <h2>2. Color variation</h2> <p>  </p>

<p>    If you can arbitrarily change the distance between nanoparticles, you will obtain a variety of structural color based on the Bragg reflection. In the present system, the distance between particles can be controlled by the length of the longer strand of the Crystallizer DNA complex, which connects the gold nanoparticles together. Note here that, the length of the short strand is uniform and the number of the short strands bound to the longer strands differs for the different structural color (Fig. 6).</p>

<p><strong>Fig. 6. Expression of the different structural color according to the length of <br>            the longer strand of the Crystallizer DNA complex.</strong></p>

<p>    For achieving a convenient color selection procedure for our cosmetic biomolecular system, we devised and designed a <strong>“Permutation color-directing system”</strong> to efficiently output the longer strands for the Crystallizer DNA complex of the different lengths in response to a small number of DNA inputs. In the Permutation color-directing system, <i>N !</i> outputs are encoded only with <i>N</i> inputs. In Fig. 7., we illustrate a three input example of the Permutation color-directing system. Each Output complex (X, Y, Z) corresponds to an Input DNA (A, B, C), respectively. Upon addition of Input-A, Output-X complex releases Output-X via toehold-mediated strand exchange (Fig. 7.1).</p>

<p>  </p> <div align="center"> <img src="https://upload.wikimedia.org/wikipedia/commons/thumb/a/a8/Design10-25_FIG7_1.png/799px-Design10-25_FIG7_1.png" width="600"> </div> <p><strong>Fig. 7.1. The correspondence of each Input DNA and Output-complex.</strong></p> <p>  </p>

<p>    Besides that, the existence of Input-A makes Input-C invalid via hybridization, which occurs faster than the strand exchange, since the 5’ portion of Input-A has a sequence complementary to the 3’ portion of Input-C. Similarly, Input-B and Input-C trigger the release of Output-Y and Output-Z and inactivate Input-A and Input-B, respectively (Fig. 7.2. (a)). As a consequence, the order of input addition directs the combination of released Output-DNAs. In this three input example, 3! = 6 combinations of Output-DNAs are directed by three Input-DNAs (Fig. 7.2. (b)).</p>

<p>  </p> <p><strong>Fig. 7.2. Permutation color-directing system. <br>          (a)</strong>Invalid Input-C by Input-A.<br>    <strong>      (b)</strong>3!=6combinationsofoutput-DNAs fromthree input-DNAs.</strong></p>

<p>    By connecting with logical AND gates to release the longer strands for the Crystallizer DNA complex, which is easily implemented by DNA, the Permutation color-directing system could direct the release of the longer strands of the different lengths as the final output of this system (Fig. 7.3). Therefore, you can efficiently choose the structural color according to the order of input addition.</p>

<div align="center"> <img src="https://upload.wikimedia.org/wikipedia/commons/thumb/4/48/Design10-25_FIG_7_3.png/800px-Design10-25_FIG_7_3.png" width="600"> </div> <p align="center"><strong>Fig. 7.3. <i>N!</i> kinds of colors from <i>N!</i> longer strands by <i>N!</i> Outputs-DNAs</strong></p>

</div> </div> </body> </html>

Biomod/2013/Titech/design: Difference between revisions

Revision as of 17:32, 27 October 2013

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

research

Tools

@@ Line 209: / Line 209: @@
-<p><strong>Fig. 2. Threshold processor.</strong></p>
 <p>&nbsp; </p>
 <p>&nbsp;&nbsp;&nbsp;
@@ Line 218: / Line 217: @@
 <img src="https://upload.wikimedia.org/wikipedia/commons/thumb/a/a1/Design_10-25_%E9%96%BE%E5%80%A4%E3%82%B2%E3%83%BC%E3%83%882.png/800px-Design_10-25_%E9%96%BE%E5%80%A4%E3%82%B2%E3%83%BC%E3%83%882.png" width="650">
 </div>
+<p><strong>Fig. 2. Threshold processor.</strong></p>
 <p>&nbsp; </p>