Biomod/2011/TeamJapan/Sendai/Results/Atomic Force Microscope: Difference between revisions

Revision as of 03:07, 30 October 2011

<html>

      .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;}

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>

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

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="  " 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>

 <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>

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", "ＭＳＰゴシック", Osaka, "ヒラギノ角ゴ Pro W3"; color: #333333; margin:0px; padding:0px; }

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*/

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*/ }

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*/

navbar{

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

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; }

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; }

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*/ }

navbar a{

     color:#ffffFF;/*メニューボタンの文字の色*/

display:block; }

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*/

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; }

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; }

side h3 a {

     color:#ffffff;

font-weight:normal; }

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; }

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*/ }

side ul{

    list-style-type:none;

padding-left:2px; }

side li{

padding-left:15px;　/*文字の左端からの位置*/ }

side li a{

    color:#333333;/*サイドの文字色*/
    width:180px;
    display:block;

}

side .ad_list li{

    background-image:none;

padding-left:0; }

/*右側メイン部分の設定*/

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; }

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; }

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; }

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>

Atomic Force Microscope

Method for checking the structure　

We use AFM(Atomic Force Microscope) for checking structure. If you don't know about AFM, please check this page.

Observation 2D and 3D structure

Triangular prism 2D structure

Figure 1. caDNAno design: 2D view of origami unfolded body

Figure 1 is our design of 2D structure. Before checking 3D strucuture, we confirmed 2D strucure with AFM since the check was easy.
Figure 2 is AFM picture of 2D strucure.

The size of the structure is (67nm)×(23nm).
Compared to our design(60×20), it is similar to the size.
This indicates that 2D structure is almost the same as our design.

We used cutting M13 made by PCR.
The excessive arrangement of M13 has decreased very much.
The portion which is high is based on m13 in which only a few remained.

Condition
・M13:staples= 1:10(ratio of concentration)
・Mg2+ concentration 12.5 mM
・anealing time:3 hours
・Buffer:Tris-HCl
・cutting M13

We confirmed the size of 2D structure in this experiment.
Next experiment, we took 2D structure into consideration and checked 3D structure.
[m13noncutと並列画像で比較]

Triangular prism 3D structure

Figure 3 is our design of 3D structure and Figure.4 shows the triangular prism 3D structure in AFM.
As compared to the figure of 2D structure, there are some differences.
We can see the folded structure in figure.4.
This folding was caused by two edging stables.
There are two sticky ends in both ends of the 2D structure.
In figure.4, the shape seemed to be like triangle because the 3D structure could be linked only one sticky end.
So the 3D structure could be not stable and could be collapsed by electrostatic attractive force between structures and mica surface with Mg2+ ion.
The length of the side is almost equal to the design. So we could make 3D structures.
Scale bar is 200nm.

Condition
・M13:staples= 1:10(ratio of concentration)
・Mg2+ concentration 12.5 mM
・anealing time:3 hours
・Buffer:Tris HCl
・cutting M13

detail:Observation 2D and 3D structure

Observation Field　

Figure 5 is design of Field.Figure 4 is AFM picture of Field.
According to this picture, M13 of redundant was also observed.
The size of Field in AFM picture is similar to that of design.
Therefore we success to observe Field.
Scale bar is 100nm.

Condition
・M13:staples= 1:10(ratio of concentration)
・Mg2+ concentration 12.5 mM
・anealing time:3 hours
・Buffer:Tris-HCl

Observation structure on the Field

Triangular prism 2D structure on the Field　

丸とかで構造体を囲むとわかりやすい？」
　 We happened to observe the 2D structure attaching the field using AFM.
In the sample, there ought to be only robots (2D structures which couldn't be folded and 3D structures ) but several fields were observed in this sample.
We supposed that the contamination occurred.
We scanned this field attached 2D structure about 10 times.
But the structure didn't go away. Next, we raised the scanning speed and the structure went away.
So this structure could attached to the field by hybridization.
There seems to be the possibility that robots attach the field.
Scale bar : 200 nm

Condition
・M13:staples= 1:10(ratio of concentration)
・Mg2+ concentration 12.5 mM
・anealing time:3 hours
・Buffer:Tris-HCl

Condition for the robots to attach the fields

『Flow chart of experiments to bind the robots and fields』

detail:Observation struture+field

　Observation diary　

We wrote the observation diary for AFM. If you want to check it, please click Observation diary.

@@ Line 21: / Line 21: @@
-Figure 1 is our design of 2D structure. Before checking 3D strucuture, We confirm 2D strucure with AFM since the check was easy.<br/>
+Figure 1 is our design of 2D structure. Before checking 3D strucuture, we confirmed 2D strucure with AFM since the check was easy.<br/>
 Figure 2 is AFM picture of 2D strucure.<br/>
-The size of AFM picture is (67nm)×(23nm).<br/>
+The size of the structure is (67nm)×(23nm).<br/>
 Compared to our design(60×20), it is similar to the size.<br/>
-This shows that 2D strucuture is almost the same as our design.<br/>
+This indicates that 2D structure is almost the same as our design.<br/>

Biomod/2011/TeamJapan/Sendai/Results/Atomic Force Microscope: Difference between revisions

Revision as of 03:07, 30 October 2011

Contents

Method for checking the structure

Observation 2D and 3D structure

Triangular prism 2D structure

Triangular prism 3D structure

Observation Field

Observation structure on the Field

Triangular prism 2D structure on the Field

Condition for the robots to attach the fields

Observation diary

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

research

Tools