Biomod/2012/TeamSendai/Design

From OpenWetWare
Revision as of 05:56, 27 October 2012 by Kazuki Hirahara (talk | contribs)
Jump to: navigation, search

<html> <head>

   <title>Team Sendai Top</title>
   <script type="text/javascript" src="http://code.jquery.com/jquery-latest.min.js"></script>
   <script type="text/javascript">
       $(function() {
         if ($.browser.msie && $.browser.version.substr(0,1)<7)
         {

$('li').has('ul').mouseover(function(){ $(this).children('ul').show(); }).mouseout(function(){ $(this).children('ul').hide(); })

         }
       });        
   </script>

<style>

body{ background-image:url(http://openwetware.org/images/7/78/Office.png); /*壁色と壁紙設定*/ background-repeat:repeat;/*繰り返さない場合はno-repeatに変更*/ font:"メイリオ", "MS Pゴシック", Osaka, "ヒラギノ角ゴ Pro W3"; color: #333333; margin:0px; padding:0px; }

  1. Container

{ Background-image: url(http://openwetware.org/images/6/62/Wall4.png); width: 960px; margin: auto; }

/* Main menu */

  1. menu

{ width: 100%; margin: 0; padding: 10px 0 0 0; list-style: none; background: #111; background: -moz-linear-gradient(#444, #111);

   background: -webkit-gradient(linear,left bottom,left top,color-stop(0, #111),color-stop(1, #444));	

background: -webkit-linear-gradient(#444, #111); background: -o-linear-gradient(#444, #111); background: -ms-linear-gradient(#444, #111); background: linear-gradient(#444, #111); -moz-border-radius: 50px; border-radius: 50px; -moz-box-shadow: 0 2px 1px #9c9c9c; -webkit-box-shadow: 0 2px 1px #9c9c9c; box-shadow: 0 2px 1px #9c9c9c; }

  1. menu li

{ float: left; padding: 0 0 10px 0; position: relative; line-height: 0; }

  1. menu a

{ float: left; height: 25px; padding: 0 25px; color: #999; text-transform: uppercase; font: bold 12px/25px Arial, Helvetica; text-decoration: none; text-shadow: 0 1px 0 #000; }

  1. menu li:hover > a

{ color: #fafafa; }

  • html #menu li a:hover /* IE6 */

{ color: #fafafa; }

  1. menu li:hover > ul

{ display: block; }

/* Sub-menu */

  1. menu ul

{

   list-style: none;
   margin: 0;
   padding: 0;    
   display: none;
   position: absolute;
   top: 35px;
   left: 0;
   z-index: 99999;    
   background: #444;
   background: -moz-linear-gradient(#444, #111);
   background: -webkit-gradient(linear,left bottom,left top,color-stop(0, #111),color-stop(1, #444));
   background: -webkit-linear-gradient(#444, #111);    
   background: -o-linear-gradient(#444, #111);	
   background: -ms-linear-gradient(#444, #111);	
   background: linear-gradient(#444, #111);
   -moz-box-shadow: 0 0 2px rgba(255,255,255,.5);
   -webkit-box-shadow: 0 0 2px rgba(255,255,255,.5);
   box-shadow: 0 0 2px rgba(255,255,255,.5);	
   -moz-border-radius: 5px;
   border-radius: 5px;

}

  1. menu ul ul

{

 top: 0;
 left: 150px;

}

  1. menu ul li

{

   float: none;
   margin: 0;
   padding: 0;
   display: block;  
   -moz-box-shadow: 0 1px 0 #111111, 0 2px 0 #777777;
   -webkit-box-shadow: 0 1px 0 #111111, 0 2px 0 #777777;
   box-shadow: 0 1px 0 #111111, 0 2px 0 #777777;

}

  1. menu ul li:last-child

{

   -moz-box-shadow: none;
   -webkit-box-shadow: none;
   box-shadow: none;    

}

  1. menu ul a

{

   padding: 10px;

height: 10px; width: 130px; height: auto;

   line-height: 1;
   display: block;
   white-space: nowrap;
   float: none;

text-transform: none; }

  • html #menu ul a /* IE6 */

{ height: 10px; }

  • first-child+html #menu ul a /* IE7 */

{ height: 10px; }

  1. menu ul a:hover

{

   background: #0186ba;

background: -moz-linear-gradient(#04acec, #0186ba); background: -webkit-gradient(linear, left top, left bottom, from(#04acec), to(#0186ba)); background: -webkit-linear-gradient(#04acec, #0186ba); background: -o-linear-gradient(#04acec, #0186ba); background: -ms-linear-gradient(#04acec, #0186ba); background: linear-gradient(#04acec, #0186ba); }

  1. menu ul li:first-child > a

{

   -moz-border-radius: 5px 5px 0 0;
   border-radius: 5px 5px 0 0;

}

  1. menu ul li:first-child > a:after

{

   content: '';
   position: absolute;
   left: 30px;
   top: -8px;
   width: 0;
   height: 0;
   border-left: 5px solid transparent;
   border-right: 5px solid transparent;
   border-bottom: 8px solid #444;

}

  1. menu ul ul li:first-child a:after

{

   left: -8px;
   top: 12px;
   width: 0;
   height: 0;
   border-left: 0;	
   border-bottom: 5px solid transparent;
   border-top: 5px solid transparent;
   border-right: 8px solid #444;

}

  1. menu ul li:first-child a:hover:after

{

   border-bottom-color: #04acec; 

}

  1. menu ul ul li:first-child a:hover:after

{

   border-right-color: #04acec; 
   border-bottom-color: transparent; 	

}


  1. menu ul li:last-child > a

{

   -moz-border-radius: 0 0 5px 5px;
   border-radius: 0 0 5px 5px;

}

/* Clear floated elements */

  1. menu:after

{ visibility: hidden; display: block; font-size: 0; content: " "; clear: both; height: 0; }

  • html #menu { zoom: 1; } /* IE6 */
    first-child+html #menu { zoom: 1; } /* IE7 */

/* 目次 */ div#mokuji {width: 960px; margin-left: auto; margin-right: auto; background-color: #f5f5dc}

div#mokuji h2 { background-color: # f5f5dc; font-size: 1.50em; color: #000000; line-height: 45px; padding-left: 12px; margin-bottom: 0}

div#mokuji h3 {border-bottom:solid 3px #66aa66; font-size: 1.50em; line-height: 22px; padding-left: 12px; margin-top: 30px; margin-bottom: 0; clear: both}


ol#mokuji {font-size: 1.00em; margin-left: 0; padding-left: 0}


/*文字の設定*/ h1{ font-family: 'Times New Roman', 'Times', serif; font-size: 2.00em; letter-spacing: 2px; padding-left:10px; margin: 0px; }


h2{ font-family: 'Times New Roman', 'Times', serif;

     	font-size:1.8em;

border-left: 10px solid #000066;

         	border-bottom:solid 1px #000099;/*文字の下に線を入れる設定*/
         	width:900px;

padding-left: 5px; color:#333333; margin-top: 15px; margin-bottom: 5px; }

h3{ font-family: 'Times New Roman', 'Times', serif;

     font-size:1.60em;
       color:# 333333;

}

p{

   	font-family: 'Times New Roman', 'Times', serif  	font-size:1.40em;/*全体の文字サイズ*/

line-height:150%;/*全体で使う、文字と文字の行間*/

         	margin-left:5px;

}

p img{

    	float:left;
        	margin-top:5px;  /*写真の左にスペースを空ける*/

margin-left:5px; /*写真の左にスペースを空ける*/ margin-right:10px; /:写真と文字の間隔*/ }


h5{

     font-size:1.60em;

border: solid 1px #111111;

       color:#ffffff;

background-color:#FFA500; line-height: 30px; padding-left:10px; margin-top: 10px; margin-bottom: 1px; }

h6{

     font-size:120%;

border: solid 1px #111111;

       color:#ffffff;

background-color:#006400; line-height: 30px; padding-left:10px; margin-top: 10px; margin-bottom: 1px; }

  1. red{
     font-size:120%;

border: solid 1px #111111;

       color:#ffffff;

background-color:#DC143C; line-height: 40px; padding-left:10px; margin-top: 10px; margin-bottom: 1px; }

  1. blue{
     font-size:120%;

border: solid 1px #111111;

       color:#ffffff;

background-color:#191970; line-height: 40px; padding-left:10px; margin-top: 10px; margin-bottom: 1px; }

  1. pop {

width: 50%; margin: 0px; float: left; }

  1. pop h2 {

width: 90%; margin: 0px; float: left; }

  1. pop p {

width: 90%; margin: 0px; float: left; }


/*topに戻る*/

  1. ttop {position:fixed;bottom:140px;left:auto;margin:0 0 0 960px; /* マージン:上 右 下 左 */width:41px;height:390px;background:url(http://openwetware.org/images/e/ed/Cellgate.gif) no-repeat left bottom;}/* IE6以下用 */* html #ttop {margin:0 0 -390px 0;position:relative;bottom:490px; /* 上で設定した ttopの高さ390px+下100px */left:960px;}#ttop:hover {background:url(http://openwetware.org/images/a/a7/029.png) no-repeat left bottom;/* 画像の高さによって適当に調整 */}a.page_top {display:block;width:41px;height:390px;}


</style> </head>


<body> <div id="Container"> <!-- Menu --> <ul id="menu"> <li><a href="http://openwetware.org/wiki/Biomod/2012/Tohoku/Team_Sendai ">Home</a></li> <li><a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Idea ">Project</a></li> <li><a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Design">Design</a> </li> <li><a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Simulation">Simulation</a> </li> <li> <a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Experiment ">Experiment</a> </li> <li> <a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Future Application">Future Application</a> </li> <li> <a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Diary">Diary</a> </li> <li> <a href=" http://openwetware.org/wiki/Biomod/2012/TeamSendai/Team ">Team</a> </li> <li> <a href=" http://openwetware.org/wiki/Biomod/2012/Tohoku/Team Sendai/header"></a> </li>

</ul>

<div id="ttop"> <a href="#top" class="page_top" onfocus="this.blur();" onclick="scrollTo(0,0); return false;" title="Top"></a></div>

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


Cell-gate

Designtopcellgate.png

The left figure gives our project "Cell-gate" outliine. Our project is divided into major three parts, Gate, Porter, and Membrane. Gate is Cell-gate itself.  Porter is function to transport the target inside and outside cell membrane.  Membrane is liposome which is model of cell membrane. We divided our project into above three group and did experiment. On this page, we give you the description how we determined our robot design.

Design

Design of Gate

Size / Structure

The Gate has to connect inside and outside of the cell. So we decided to apply a hexagonal cylinder nanostructure made of DNA origami.

We refer "A logic-gated nanorobot for targeted transport of molecular payloads" (SM Douglas, I Bachelet, GM Church - Science Signalling, 2012) for the hexagonal cylinder structure of DNA origami.

Next, we made a simulation in order to examine the size of the structure. The size of the cylinder must be small enough not to pass freely through anything. However, it must be large enough to pass through the desired product. The gate which made of DNA origami has negative electric charge. So if the gate is too small, target can't enter the Gate. According to simulation, our Gate size determined 24*24*33nm. This size is suitable to transport the target.

DNA origami

We used caDNAno to design the hexagonal cylinder structure.

スライド15.jpg スライド16.jpg Cadnanogazou.png


Potential Barrier

Potential graph.jpg Our Gate is made of DNA, so it has negative electric charge. Single stranded DNA has negative electric charge, too. Here is a graph about potential energy of the cylinder.(藤原さんに頂いた下のグラフ載せる。) GATE size means the length of the Gate. If the potential energy is high, it is difficult for single stranded DNAs to enter the Gate. If the radius of the Gate is 1.5 times larger than now design, potential energy decreases and to enter the Gate is easier. So our Gate is well designed.


Design of Porter

Principle

Perportergifkoyama.gif

There are essentially two problems for making CELL-GATE.

    How to pull the target DNA into GATE ?
    How to pass the target through GATE ?

To solve these problems, we propose a nano-system made of ssDNA and named it Porter. Porter stands in line in GATE, pulls the target DNA, and transports it.

This idea is supported by GATE simulation, which shows that target DNA can not enter GATE by itself. So, the work of PORTER is to pull and bring the target DNA inside GATE.

We designed PORTER having some loop structures when it hybridizes with the target. Porter has some complementary sequences to the target here and there. So after the target attaches to Porter, Porter shrinks, or in other words it pulls the target DNA. Finally the target enter GATE.

The inner Porter has more complementary sequences to the target and has higher bonding energy than from the one at the entrance of Gate. This design enables the target to move to the inner Porter because of the combination stability. In experiment, we apply the sequences below.


スクリーンショット 2012-10-27 20.32.50.png

These are the sequences for electrophoresis, and correspond to only a part of the actual Porter sequence. These are sequences that are complementary to the target. When planted in the gate, Porter has spacer sequences of 10 nucleotides length at its foot in addition to the sequences above; this is to reduce the Coulomb force produced by the wall of GATE.


Simulation

We compared the ability to catch the target of Porter with that of toehold structure.

How to implement

Cell model

Cholesterol

We also have the aim of this GATE insert in the cell membrane, it can not sting in the cell membrane of normal hexagonal cylinder. However, We can create a cylinder with a different structure by exchanging some staple. We have designed a simple cylinder first,and I have to be attached anywhere in the structure to replace the staple. We can later add functionality to an existing structure using this method. We thought that to have an affinity for lipid membrane with the DNA that can be modified cholesterol on the side of the cylinder by this method. In addition, we have also designed DNA-like beard at the entrance of the cylinder. We expect the effect of electrostatically repel force with DNA which are not intended. Our cylinder is small,so we designed the cylinder to connect to each other and be long in order to easily confirmed using AFM. By replacing the staple, this structure is also removably.
スクリーンショット 2012-10-15 1.11.25.png スクリーンショット 2012-10-15 1.11.35.png スクリーンショット 2012-10-15 1.22.38.png