Biomod/2011/TeamJapan/Sendai/Strategy

From OpenWetWare
Jump to navigationJump to search

<html>

<style rel="stylesheet" type="text/css"> 

      .clear {clear:both;}
 #verticalmenu {

/*this .CSS is inspired by http://www.javascriptkit.com/ */ font-family: "Comic Sans MS" , "Brush Script MT",serif, sans-serif, monospace, cursive, fantasy; list-style:none;}

  1. verticalmenu a:hover {

color: #aa1d1d; /* color when the click is over the main menu text-transform: uppercase; font-size: 10px; */


}

a:visited { color:#00a5ea; text-decoration: none }

.glossymenu, .glossymenu li ul{ list-style-type: none; margin: 0; padding: 0; width: 250px; /*WIDTH OF MAIN MENU ITEMS*/ border: 1px solid black; list-style:none; }

.glossymenu li{ position: relative; }

.glossymenu li a{ background: white url(http://openwetware.org/images/a/a7/Glossyback2.jpg) repeat-x bottom left; font: bold 17px Verdana, Helvetica, sans-serif; color: white; display: block; width: auto; padding: 10px 0; padding-left: 10px; text-decoration: none; }

.glossymenu li ul{ /*SUB MENU STYLE*/ position: absolute; width: 200px; /*WIDTH OF SUB MENU ITEMS*/

left: 0; top: 0; display: none; }

.glossymenu li ul li{ float: left; }

.glossymenu li ul a{ width: 190px; /*WIDTH OF SUB MENU ITEMS - 10px padding-left for A elements */ }

.glossymenu .arrowdiv{ position: absolute; right: 2px; background: transparent url(http://openwetware.org/images/6/69/Arrow.gif) no-repeat center right; }

.glossymenu li a:visited, .glossymenu li a:active{ color: white; }

.glossymenu li a:hover{ background-image: url(http://openwetware.org/images/5/50/Glossyback.jpg); }

/* Holly Hack for IE \*/

  • html .glossymenu li { float: left; height: 1%; }
  • html .glossymenu li a { height: 1%; }

/* End */

</style>

<script type="text/javascript">

/***********************************************

  • CSS Vertical List Menu- by JavaScript Kit (www.javascriptkit.com)
  • Menu interface credits: http://www.dynamicdrive.com/style/csslibrary/item/glossy-vertical-menu/
  • This notice must stay intact for usage
  • Visit JavaScript Kit at http://www.javascriptkit.com/ for this script and 100s more
                                                                                              • /

var menuids=new Array("verticalmenu") //Enter id(s) of UL menus, separated by commas var submenuoffset=-2 //Offset of submenus from main menu. Default is -2 pixels.

function createcssmenu(){ for (var i=0; i<menuids.length; i++){ 

 var ultags=document.getElementById(menuids[i]).getElementsByTagName("ul")
   for (var t=0; t<ultags.length; t++){
   var spanref=document.createElement("span")

spanref.className="arrowdiv" spanref.innerHTML="&nbsp;&nbsp;" ultags[t].parentNode.getElementsByTagName("a")[0].appendChild(spanref) 

   ultags[t].parentNode.onmouseover=function(){
   this.getElementsByTagName("ul")[0].style.left=this.parentNode.offsetWidth+submenuoffset+"px"
   this.getElementsByTagName("ul")[0].style.display="block"
   }
   ultags[t].parentNode.onmouseout=function(){
   this.getElementsByTagName("ul")[0].style.display="none"
   }
   }
 }

} if (window.addEventListener) window.addEventListener("load", createcssmenu, false) else if (window.attachEvent) window.attachEvent("onload", createcssmenu) </script>

<table border="0" align="center" vertical-align: middle;> <tr> 

 <td>

<ul id="verticalmenu" class="glossymenu"> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Sendai">Home</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Sendai/Strategy">Strategy</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Sendai/Design">Design</a></li> <li><a href="#">Experiments</a> 

   <ul>
   <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Sendai/Results/Electrophoresis">Electrophoresis</a> 
   <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Sendai/Results/Atomic_Force_Microscope">AFM</a> 
   </ul>

</li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Sendai/Computational_design/Simulation" >Simulation</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Sendai/Notes">Notes</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Sendai/Team">Team</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Sendai/Resources">Resources</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Sendai/Sitemap">Sitemap</a></li>


</ul> </td> 

 <td>

<img src="http://openwetware.org/images/0/07/3D_sendai.png" width="650"> </td> </tr> </table> </html> <html> <head> <style type="text/css">

  1. content {padding-left: 10px;width: 970px;}}

h3 {font-decoration: none;} h1.firstHeading {display: none; } </style> </head> </html>

<html> <style rel="stylesheet" type="text/css"> /*このスタイルシートの著作権はテンプレート工房TAKEにあります*/ /*ページのレイアウト用css*/

body{ background:#F5F5DC; /*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. contents{
     width:900px;

margin:0 auto; background-color: #FFFFFF ;/*コンテンツ内の背景(サイズをぴったりにすること）*/ background-repeat:repeat-y; /*縦に繰り返し*/ border:solid 1px #666666;/*サイトに枠を付ける設定,色の変更可*/ 

     position:relative;
     font-size:80%;

}


/*ヘッダー部分の設定*/

  1. header{

background-image:url(http://openwetware.org/images/c/c4/TeamSendai-logo3.png) ;/*ヘーダー*/ background-repeat:repeat-x; /*縦に繰り返し*/ background-position:top right; height:140px; /*ヘーダーの高さ*/ }

  1. header p {

font-size: 26px; 

       color:#333333;

padding-top: 15px; padding-left: 20px; }


/*上部メニューボタンの設定*/

  1. navbar{
     background-color:#FFFFFF; 
     width: 100%;
     height:40px;
     position:margine;
     top:100px;
     left:0px;
     border-top:solid 1px #FFFFFF;
     border-bottom:solid 1px #FFFFFF; 
     }


  1. navbar ul{
         margin:0;

padding:0; list-style-type:none; font-family:Arial, Helvetica, sans-serif; font-size: 12px; line-height:40px; letter-spacing:2px; }

  1. navbar li{
     background-color:#000099;  /*上部メニューのボタンの背景*/

float:left; width:146px; /*メニューボタンの幅*/ text-align:center; padding:0; border-right:solid 1px #ffffff; }

  1. navbar ul a:hover{
  	background-color:#0033cc;	/*メニューボタンにカーソルが来た時に背景*/

width:146px; /*メニューボタンの幅*/ }

  1. navbar a{
     color:#ffffFF;/*メニューボタンの文字の色*/

display:block; }

  1. navbar a:hover{
  color:#999999; /*メニューの文字がカーソルが来た時、この色に変わる*/
  }



/*サイドメニューの設定*/

  1. side{

background-color:#ddffff; 

     width:220px;/*サイドの幅（変更するときはコンテンツ背景も変更すること）*/

position:margin; top:600px;/*上からの位置*/ left:12px; }

  1. side h3 {

font-size: 90%; border: double 3px #FFFFFF; color:#ffffff; text-align: center; background-color:#999999; 

     width:190px;

line-height: 30px; margin-top: 10px; margin-left: 5px; margin-bottom: 5px; }

  1. side h3 a {
     color:#ffffff;

font-weight:normal; }

  1. side ul{
     font-size:100%;

line-height:220%; /*サイドの文字と文字の行間設定*/ background-color: #ddffff; margin:0px; padding-left:10px; }

  1. side ul a:hover {
     width:180px;

background-color: #99ffff; /*サイドのカーソルオーバー時の背景色*/ color: #999999; /*サイドのカーソルオーバー時の文字色*/ }

  1. side ul{
    list-style-type:none;

padding-left:2px; }

  1. side li{

padding-left:15px;　/*文字の左端からの位置*/ }

  1. side li a{
    color:#333333;/*サイドの文字色*/
    width:180px;
    display:block;

}

  1. side .ad_list li{
    background-image:none;

padding-left:0; }



/*右側メイン部分の設定*/

  1. main{
     width:630px;
     padding-top:15px;
     margin-left:240px;

}



/*下部のフッター部分の設定*/ address{ font-size:80%; font-style:normal; text-align:center; padding-top:5px; }

address{ 

     background-color:#000066;
     color:#ffffff;
         width:882px;

padding-bottom:10px; border:none; } address a{ 

     color:#ff9999;

}


/*文字の設定*/ h1{ font-size:60%; letter-spacing: 2px; padding-left:10px; margin: 0px; }

h1 a{ 

     color:#FFFFFF;

font-weight:normal; }


h2{ 

     font-size:140%;

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-size:120%;

border: solid 1px #111111; 

       color:#ffffff;

background-color:#4682B4 ; line-height: 30px; padding-left:10px; margin-top: 10px; margin-bottom: 1px; }

p{ 

     font-size:90%;/*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*/ }


/*リンク文字の設定*/ a{ 

    color:#000099;
     text-decoration:none;

} a:hover { color: #FF0000;/*リンクの文字の上にマウスが来た時この色に変わる*/ text-decoration: none; }

  1. purple{
     font-size:120%;

border: solid 1px #111111; 

       color:#ffffff;

background-color:#9370DB; line-height: 40px; padding-left:10px; margin-top: 10px; margin-bottom: 1px; }

h5{ 

     font-size:120%;

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; }

</style> </html>

Project summary

Designing a molecular robot is one of the most interesting and challenging targets in biomolecular design. This year, two teams from Japan and one from Denmark propose the first “molecular race” over a defined track made with DNA origami. We are now making a molecular robot for the race.

Our molecular robot and its mechanism for movement are based on the molecular spider developed by Lund et al. (Nature, 2010). In the original design, the spider body consisted of the streptavidin protein, and three DNA-based legs are attached to it. The walking movement of the spider is random, thus the robot must be controlled by means of the patterned course on the Origami.

To win the race, we want to substantially improve the robot performance. For this purpose, we make the whole structure of our robot with DNA, which allows us to design arbitrary geometry of the body. Also, we can assign different base sequence to each leg and scaffold on the field. These new parameters give us freedom to optimize our robot design.

We have been developing a stochastic dynamics simulation model in order to evaluate the movement of different types of molecular robots, searching for the optimal design. In the final report, we will show our optimal design and the experimental results including walking motion of the robot captured by a video-rate AFM.

Molecular Robot Race

Rules

Our molecular robot race is based on the following rules:

  • The task for the molecular robot is to move from the start region to the goal region as fast as possible.
  • The field is placed on a cleaved mica surface using counter ion method.
  • No restriction is defined for the solution environment, as long as the field and the movement of robot are observable by fast scanning AFM.
  • No restriction is defined as a material for the robot.
Figure 1. Parameters, start point and goal point of the molecular race


Our strategy

We want to get to the goal in a more efficient way. This involves a more faster robot.
Now, what should you do to make a robot arrive at the goal more quickly?

First, let us think the problem at the macroscopic scale.. what makes an athlete win the competition?
<html> <OL> <LI> Striding with longer legs </LI> <LI> Reducing useless motions such as deviating from the route </LI> <LI> Increasing steps rate </LI> </OL> </html>

Analogously, at the molecular scale:
<html> <OL> <LI> Increasing the body’s size and legs</LI> <LI> Suppressing the random motion</LI> <LI> Improving the DNAzyme activity mechanism</LI> </OL> </html>

But, how to achieve these solutions?
<html> <OL> <LI> Making a larger robot body than streptavidin by using DNA origami method </LI> <LI> Using a special combination of DNA sequences for the legs and substrate to reduce random motion </LI> </OL> </html>

Project

Designing the molecular robot

Figure 2. 3D view of origami folded body

The body of our molecular robot has the shape of a triangular prism. Previous to BIOMOD2011, we have never made any DNA structure. Therefore, we thought it difficult to make a 3D structure and more than that to view it.

One of the problems in visualizing this kind of structure arise from the fact that an AFM observation is done from the top of the sample surface. So, in the case of the triangular prism we may not be able to know whether what we detect is our desire structure or not.

Under the previous circumstances, we decided to make a 2D structure: a development view taken from the structure of a triangular prism. Figure 1 and figure 2 show our 2D structure design using caDNAno and its assembled view, respectively. We planned that if both ends of the 2D structure are connected by double strands between the green and red staple (Figure 3), then, our proposed structure is complete.

Figure 3. caDNAno design: 2D view of origami unfolded body

http://openwetware.org/images/9/9f/CADNano-prismBody2.png

Figure 4. caDNAno design: Schematic design of M13mp18 (thin line colored sky-blue) and staples


Our robot moving mechanism

We considered our robot to move along a specific direction just by rolling. Our initial plan consisted in attaching the two same legs, of three different kinds, to each edge of the triangular prism. But, our simulation predicts that we could get a better performance just by solely using one kind of legs instead of using three kinds. So, we believe that our future work would comprise the experiment of one leg type for the robot, thus, improving the robot efficiency.

Procedure for cutting DNA

Figure 5. M13 cutting animation

For producing the robot body we used the viral M13mp18 DNA single strand (M13) as scaffold. But we only used 1,108 bases of 7,249 bases ([1]), then having a leftover of around the 84% of the whole M13 sequence. In this situation we thought about cutting the part of M13 that we needed. Our first attempt was to extract the necessary part of M13 by reproducing M13 with polymerase chain reaction. But we failed. So we changed the method for cutting the M13 with now using restriction enzyme. Therefore, we found that the restriction enzyme method is an easy way to get and can cut near 1,108 bases. Then, we later successfully checked by electrophoresis whether the M13 sequence was properly cut.

How to cut M13

3D DNA nanostructure　

  • Electrophoresis

First, we carried out electrophoresis (EP) in order to check whether the structure was correctly made. We did EP only for the M13 and did annealing for the sample mix of M13 and staples, and analyzed the difference of length between the bands. We used agarose as gel.

  • Atomic force microscope

After successfully constructed the structure by EP, we observed the annealed sample by high-speed AFM. First, we observed the 2D structure. Second, as the first stage was success we proceeded to check the 3D structure.

Verification of our structure and field from the mix sample

When we carried out annealing, we added a more quantity of staples than M13s. Therefore, we tried to get rid of the over staples from sample. Because of the excess of staples, we can hardly distinguish between body structure and field.

We have three methods to separate the excess staples from sample:

  • PEG (polyethylene glycol) precipitation([2])
  • Freez'N squeeze ([3])
  • Micro spin column by S-400HR ([4])

These methods could remove the excess staples, however it is not sure to take safely the body structure from solution.

Retrieved from "https://openwetware.org/mediawiki/index.php?title=Biomod/2011/TeamJapan/Sendai/Strategy&oldid=556791"