Difference between revisions of "Biomod/2013/Sendai/design"

From OpenWetWare
Jump to: navigation, search
Line 71: Line 71:
  
 
<h2 id=chain>Project goal</h2>
 
<h2 id=chain>Project goal</h2>
In Lipo-HANABI project we need to develop the following subsystems<br><br>
+
In Lipo-HANABI project, we need to develop the following two subsystems.<br><br>
  
 
i) Sensing system (1st stage): liposome disruption by temperature control. <br><br>
 
i) Sensing system (1st stage): liposome disruption by temperature control. <br><br>
Line 78: Line 78:
  
 
<h3 id=Flower>1st stage: Sensing system </h3>
 
<h3 id=Flower>1st stage: Sensing system </h3>
To make temperature-sensitive liposomes, we used lipids conjugated with NIPAM polymer.<br>
+
The purpose of 1st stage is to detect temperature change and release key molecules for the 2nd stage. This is achieved by temperature-sensitive liposomes containing the keys. To make the liposome, we used lipids conjugated with NIPAM polymer.<br>
NIPAM is hydrophilic at room temperature, but switches to hydrophobic over 32 C. When it becomes hydrophobic, it shrinks to avoid water molecules. This structural change of NIPAM induces stress on the surface of liposomes, and consequently disrupts liposomes.<br>
+
<br>
 +
This structural change of NIPAM induces stress on the surface of the liposome, and consequently disrupts them.<br>
 
<div align="center">
 
<div align="center">
 
<Img Src="http://openwetware.org/images/9/95/NIPAM%E3%83%AA%E3%83%9D%E3%81%A1%E3%82%83%E3%82%933.png">
 
<Img Src="http://openwetware.org/images/9/95/NIPAM%E3%83%AA%E3%83%9D%E3%81%A1%E3%82%83%E3%82%933.png">
Line 85: Line 86:
 
<div align="center">Fig.1 Temperature-sensitive liposome</div>  
 
<div align="center">Fig.1 Temperature-sensitive liposome</div>  
 
<h3 id=sensing>2nd stage: Amplification system </h3>
 
<h3 id=sensing>2nd stage: Amplification system </h3>
We assume that 1st stage liposomes contain key molecules that initiate chain reactive burst of 2nd stage liposomes.<br>
+
The purpose of 2nd stage is to accept the key from the 1st stage and release a lot of payload molecules in a chain-reaction. <br>
 
There are two different approaches to realize the 2nd stage.<br>
 
There are two different approaches to realize the 2nd stage.<br>
 
   A) DNA Origami approach<br>
 
   A) DNA Origami approach<br>
Line 94: Line 95:
  
  
This approach is inspired by a paper about <a Href="http://www.ncbi.nlm.nih.gov/pubmed/19780639"> Membrane-bending proteins</a>
+
This approach is inspired by a paper about <a Href="http://www.ncbi.nlm.nih.gov/pubmed/19780639"> Membrane-bending proteins (Prinz WA, Hinshaw JE., Crit Rev Biochem Mol Biol., 2009)</a>.
 +
In this approach, we use “Origami-anchor DNA” which connects DNA Origami with liposome membrane.
  
In this approach, we name DNA stuck into liposome membrane, Origami-anchor DNA. A lot of DNA origamis are adsorbed on the surface of liposomes by using Origami-anchor DNA. DNA origami is supposed as a stiff, straight board like structure compared with liposome membrane, and as a result, liposome surface gets bending stress. At certain level of the absorbance, liposomes will burst. Also, DNA origamis on the surface of liposome repel each other because of negative charges on DNA backbone. This effect may add more stress on the membrane. We did analysis on this phenomenon (link).<br>
+
A lot of DNA origamis are adsorbed on the surface of liposomes by using Origami-anchor DNA. DNA origami is supposed to be a stiff, straight board compared with liposome membrane, and as a result, liposome surface gets bending stress. At certain level of the absorbance, liposomes will burst. Also, DNA origamis on the surface repel each other because of negative charges on DNA backbones. This effect may add more stress on the membrane.<br>
  
 
<div align="center">
 
<div align="center">
Line 103: Line 105:
 
<div align="center">Fig.2 Stress on liposome membrane</div><br>
 
<div align="center">Fig.2 Stress on liposome membrane</div><br>
  
From the reference, we learned that efficient structure design for destabilizing membranes should have the following properties: .<br>
+
From the reference, we learned that efficient structure design for destabilizing membranes should have the following properties: <br>
•  Having rigid scaffolds<br>
+
<ur><li>Having rigid scaffolds</li>
Having large surface areas to maximize the effect of the scaffold on the membrane<br>
+
<li>Having large surface areas to maximize the effect of the scaffold on the membrane</li></ur>
 
 
<ur>
 
 
<br>
 
<br>
  
 +
<Design of DNA origami><br>
 +
DNA origami is known as a designable rigid structure made of DNA. We use DNA origami to make the rigid scaffolds. In order to meet the requirements, we designed a 2D rectangular DNA origami.<br>
  
<Design of DNA origami> <br>
 
DNA origami is known as a designable rigid structure made of DNA. We use DNA origami to make rigid scaffolds. In order to meet the requirements, we designed 2D rectanglar DNA origami.
 
<br>
 
 
 
We expect the rectangle DNA origami to work as one scaffold in itself. Following is the design of our rectangular DNA origami.<br>
 
 
<div align="center">
 
<div align="center">
 
<Img Src="http://openwetware.org/images/4/45/Outsidefig8.png">
 
<Img Src="http://openwetware.org/images/4/45/Outsidefig8.png">
Line 125: Line 121:
 
  <Img Src="http://openwetware.org/images/a/a7/Lipo5.png" ><span>Fig.4 DNA origami designed by caDNAno</span>
 
  <Img Src="http://openwetware.org/images/a/a7/Lipo5.png" ><span>Fig.4 DNA origami designed by caDNAno</span>
 
</div>
 
</div>
We use <a href="http://cadnano.org/">caDNAno2</a> for our DNA origami design. The size of DNA origami is 67.6nm (26 helixes) in width and 127 nm (374 bases) in height. We cut out a smaller rectangle of 10 helixes (161 bases) at one of the corners, so that we could distinguish the two sides with AFM (Atomic Force Microscope) observation.  
+
We use <a href="http://cadnano.org/">caDNAno2</a> for our DNA origami design. <br>
Also, we put 141 staples sticking out from bottom face of the origami. Those staples hybridize with cholesterol-modified Origami-anchor DNA, which has high affinity with lipid membrane.
+
The size of DNA origami is 67.6nm (26 helixes) in width and 127 nm (374 bases) in height.<br>
 +
We cut out a smaller rectangle of 10 helixes (161 bases) at one of the corners,<br>
 +
so that we could distinguish the two sides with AFM (Atomic Force Microscope) observation. <br>
 +
Also, we put 141 staples sticking out from the bottom face of the origami.
 +
Those staples hybridize with cholesterol-modified Origami-anchor DNA, which has high affinity with lipid membrane.<br>
  
 
<div align="center">
 
<div align="center">
Line 134: Line 134:
 
<br>
 
<br>
 
<h4 id=6>Flower DNA approach</h4>
 
<h4 id=6>Flower DNA approach</h4>
 
+
This approach is inspired by a paper about <a href="http://pubs.acs.org/doi/ipdf/10.1021/jp104711q">Polymer Flower-micelle (Yukio Tominaga, Mari Mizuse, Akihito Hashidzume, Yotaro Morishima and Takahiro Sato, J. Phys. Chem. B, 2010)</a>.<br>
This approach is inspired by a paper about <a href="http://pubs.acs.org/doi/ipdf/10.1021/jp104711q">Polymer Flower-micelle</a>. <br>
+
To adapt the Polymer Flower-micelle to our project, the followings are required.<br>
 
+
<br>
To adapt Flower-micelle to our project, we should remark the followings.<br>
+
<ur><li>Embedding a lot of cholesterol-modified ss DNA on the liposome surface</li>
• Sticking a lot of cholesterol-modified DNA into liposome surface<br>
+
<li>Adding another ssDNA (complementary to the above DNA) which induces a structural change by DNA hybridization</li>
• Change of DNA’s property by hybridization with Key DNA<br>
+
<li>The induced structural change on the DNA results in disruption of the liposome</li>
In this approach, we call 50nt3’DNA partly hybridized with 10ntDNA, Flower-anchor DNA. 50nt3’DNA is cholesterol-modified and the part of it hybridizes with 10ntDNA. The rest of its 40nt complements Key DNA. <br>
+
<br>
 
+
At first, we designed “Flower-anchor DNA”, which is a couple of ss DNAs both having cholesterol modified groups (Fig.6): Flower-anchor1 is 10nt ss DNA and Flower-anchor2 is 50nt ss DNA. Both are cholesterol-modified at their 3’ ends. <br>
 +
In addition, the 5’ end of the Flower-anchor2 is complementary to Flower-anchor1. When they hybridize, the rest 40nt of Flower-anchor2 remains single-stranded.<br>
 
<div align="center">
 
<div align="center">
 
<Img Src="http://openwetware.org/images/4/45/Flower-new54.png" width="450px" height="350px" ></div><br>
 
<Img Src="http://openwetware.org/images/4/45/Flower-new54.png" width="450px" height="350px" ></div><br>
<div align="center">Fig6 Liposome with Flower-anchor DNA</div>
+
<div align="center">Fig.6 Liposome with Flower-anchor DNA</div>
The hybridization makes Flower-anchor DNA longer. It gives stretching stress to liposome membrane and ends up disrupting liposomes. <br>
 
 
 
We designed the sequences of Flower-anchor DNA and Key DNA by <A Href="http://www.dna.caltech.edu/DNAdesign/">DNA design</A>, software for designing DNA sequences. <br>
 
 
<br>
 
<br>
 
+
The key DNA released from stage 1 liposome is complementary to this single-stranded part. When the key hybridizes on it, a double-stranded section is formed. The length of the section is shorter than its persistence length; therefore it works as a rigid strut. The strut is anchored on the liposome at both ends, thus it extends the membrane. As a consequence, this may lead to drastic conformational change of the liposome, namely, disruption. <br>
 
 
 
<img src="http://openwetware.org/images/6/65/Flower3new8.png"><br>
 
<img src="http://openwetware.org/images/6/65/Flower3new8.png"><br>
<div align="center">Fig.7 Process of flower micelle approach</div><br><br>
+
<div align="center">Fig.7 Process of flower DNA approach</div><br><br>
 
<Img Src="http://openwetware.org/images/d/dd/Flower4newa.png" Align="center" width="900px" hight="800" ><br>
 
<Img Src="http://openwetware.org/images/d/dd/Flower4newa.png" Align="center" width="900px" hight="800" ><br>
<div align="center">Fig.8 How to straighten loop</div>
+
<div align="center">Fig.8 How to disrupt a liposome</div>
 
 
このアプローチは「高分子フラワーミセル」の論文をDNAに応用したものである。
 
フラワーミセルをリポソームに応用するためには、<br>
 
・多くのコレ付きDNAを表面に埋め込むこと<br>
 
・鍵DNAのハイブリによってDNAの性質が変化すること<br>
 
といった要素が重要になってくる。<br><br>
 
 
 
このアプローチでは10ntとそれと一部が相補になっている50nt3’コレ付きDNAがハイブリしたものをFlower アンカーDNAと呼ぶ。Flower アンカーDNAの一本鎖になっている40ntの部分に鍵DNAが相補になっており、ハイブリダイゼーションによって持続長が長くなったフラワーDNAはリポソーム膜面に「引っ張り(引き裂き)」ストレスを与え、リポソームを壊すのである。
 
以下の図のように持続長の変化によって変形するDNAを設計した
 
 
 
 
 
We designed the sequences of Flower-anchor DNA and Key DNA by <A Href="http://www.dna.caltech.edu/DNAdesign/">DNA design</A>, software for designing DNA sequences. <br>
 
<br>
 
私たちはこのソフトでFlower DNAとKey DNA のDNAを設計しました。
 
 
 
 
       </article>
 
       </article>
 
</section>
 
</section>

Revision as of 02:17, 26 October 2013

<html> <head> <style>


/********************** Hide MediaWiki and init CSS, overwrite by bootstrap.css バルス**********************/

body{

background:none;

} html, body, div, span, applet, object, iframe, h1, h2, h3, h4, h5, h6, p, blockquote, pre, a, abbr, acronym, address, big, cite, code, del, dfn, em, img, ins, kbd, q, s, samp, small, strike, strong, sub, sup, tt, var, b, u, i, center, dl, dt, dd, ol, ul, li, fieldset, form, label, legend, table, caption, tbody, tfoot, thead, tr, th, td, article, aside, canvas, details, embed, figure, figcaption, footer, header, hgroup, menu, nav, output, ruby, section, summary, time, mark, audio, video{

margin:0;
padding:0;
/* font-size:100%; */
 border:0;
outline:0;

} a, a:link, a:visited, a:hover, a:active{

text-decoration:none

}

/*訪れたリンクを白くするよ*/ .whiteSendai:visited{

color:#FFFFFF!important;

}

/*左詰め、真ん中、右詰め*/ .leftSendai { text-align: left; } .centerSendai { text-align: center; } .rightSendai { text-align: right; }


.firstHeading {

display:none;

}

  1. content{
border-style:none;
margin:0;
padding:0;

}

  1. globalWrapper{
font-size:100%;

}

  1. contentSub{
display:none;

}

  1. column-one{
display:none;

}

  1. footer{
display:none;

}

  1. globalWrapper{
font-size:100%;

}

  1. bodyContent h1, #bodyContent h2{
 margin-top: 20px;
 margin-bottom: 10px;

}


  1. bodyContent h3{
 margin-top: 20px;
 margin-bottom: 10px;
 border-bottom-width: medium;
 border-bottom-style: solid;
 border-bottom-color: gray;

}

  1. bodyContent h4{
 margin-top: 20px;
 margin-bottom: 10px;
 border-bottom-width: thin;
 border-bottom-style: solid;
 border-bottom-color: gray;

}

  1. bodyContent h5, #bodyContent h6{
 margin-top: 10px;
 margin-bottom: 10px;

/**** border-bottom-width: thin;

 border-bottom-style: solid;
 border-bottom-color: gray;
        • /

}

/********************************* Hide MediaWiki end *********************************/


/* Structure */ html{ background: #eee; } body {

 padding: 0px;
 background: #fff;
 color: #333;
 margin: 0 auto;
 max-width: 900px;
 font: 1em/1.5 "Helvetica Neue", Helvetica, Arial, sans-serif;
 }

a {

 color: #105672;

}

header {/****position: fixed; ****/

       /******width: 100%;****/
       height: 90px;
       z-index: 1;

background: #F17F25;

        padding:0.01em 0.5em 1.5em ;

color: #fff; line-height: 1;

}

header h1{ margin-bottom: 0; }

header h1 span{ display: inline; color: rgba(255,255,255,.4); }

header span{ display: block; color: rgba(255,255,255,.2); font-weight: 300; margin-bottom: 1.6em }

header nav{ float: right; text-align: right } header nav div{ font-size: .8em; } header nav div a { font-weight: 300; padding: .3em .5em } header nav a{ color: #fff; display: inline-block; padding: .3em .8em }

header nav a:hover, header nav a:focus{ color: rgba(255,255,255,.6) }


[role=main]{ padding:1.5em 3em; } article{ padding: 1em 0; text-align: justify; text-justify: inter-ideograph;

}


footer{ background: #333; color: #fff; padding: 1em 3em;

       clear: both;    /***2段組みの左右のfloatを解除***/

}

/* Typography */

p{ font: 1em/1.5 Palatino, "Palatino Linotype", Georgia, Times, "Times New Roman", serif; }

p.sukima{

       font-size: 150%;
       font-weight: normal;
       font-family: Helvetica;
       background: #bbb;
       padding-left: 1.2em;

}

img{ max-width: 100%; /***** height: auto; *****/ }


blockquote{ float: left; margin: 1em 3em; } blockquote p{ font-size: 1.4em; line-height: 1.2; font-weight: 700; font-style:italic; } a{ font: 700 1em/1.5 "Helvetica Neue", Helvetica, Arial, sans-serif; text-decoration: none } a:hover, a:focus{ color: #000; } a:active{ position: relative; top:1px; }

ol{margin: 1em 0 1em 0; padding-left: 2em; } li{ margin: 0; }

/* Tabs */

  1. tabs

{ /*****position:fixed;****/

      width: 900px; 

}

.js-on #tabs article { display:none }

  1. tabs, #tabs nav a.active{

background: #FFF; color: #111; }

  1. tabs nav

{ position: relative; overflow: hidden; display: table; background: #bbb; }


  1. tabs nav a

{ width:900px; display:table-cell; padding:1em; text-align:center; color: #333; }

  1. tabs nav a:hover,#tabs nav a:focus

{ background:#eee }

  1. tabs article

{ padding:2em; }


.js-on #tabs article.active { display:block; }

  1. tabs #mobiles{

display:none; border-radius: 0; }

  1. tabs #mobiles a, #tabs #mobiles a:first-child, #tabs #mobiles a:last-child{

width:300px; border-radius: 0; }


/* Media queries */ @media screen and (min-width:900px) { body{font-size: 1.1em;} }

@media screen and (max-width:600px) { #tabs nav{ display: none; position: relative; } #tabs #mobiles{ display:block; } #tabs article { display:block; } } @media screen and (max-width:480px) { blockquote{ float: none; }

header nav a{ padding:.7em .8em } header nav{ float: none; margin: -.5em -3em 0; background: #000; overflow: hidden; text-align: left } header nav a{ border-right: 1px solid #222 } [role=main]{ padding:1.5em 2em; } header nav div{ display: none; }

}

/*column content*/

  1. content-right {

width:48%; /***段落の横幅***/ float:right; /***右に寄せる(他の要素を左に回り込ませる)***/ margin: 10px; }

  1. content-left {

width:47%; /***サイドの横幅***/ float:left; /***左に寄せる***/ margin: 10px; }

/*****キャプションレフト*****/

div.caption-left{ float: left; padding: 0 5px 5px 5px; }

.caption-left span{ display: block; text-align: center;

       font-size: smaller;
       font-weight: bold;

}

div.clear{ clear: both; margin: 0 0 10px 0; }

/*****キャプションライト*****/

div.caption-right{ float: right; padding: 0 5px 5px 5px; }

.caption-right span{ display: block; text-align: center;

       font-size: smaller;
       font-weight: bold;

}

div.clear{ clear: both; margin: 0 0 10px 0; }

/***floatの影響を絶つ。<div class="c-both"></div> のように使う***/

.c-both { clear: both; }

div.title{

        font-style: normal;
        font-weight: bold;
        font-size: 70px;
        line-height: 70px;
        font-family: Helvetica;

}

div.caption{

       text-align: center;
       font-size: smaller;
       font-weight: bold;

}

div.captiontable{

       font-size: smaller;
       font-weight: bold;

}

/*topに戻る*/

  1. ttop {position:fixed;
      bottom:140px;
      left:auto;margin:0 0 0 905px; /* マージン:上 右 下 左 */
      width:100px;
      height:390px;
      background:url(http://openwetware.org/images/f/f2/%E5%90%8D%E7%A7%B0%E6%9C%AA%E8%A8%AD%E5%AE%9A-1.png) no-repeat left bottom;}

/* IE6以下用、アスタリスクハックでググれ */

  • 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;}
  1. ttop:hover {background:url(http://openwetware.org/images/b/b9/Top2.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:100px;height:390px;}


</style> </head> </html> <html xmlns="http://www.w3.org/1999/xhtml"> <head>

   <title>Biomod2013 Sendai ver2.0</title>
   <meta name="viewport" content="width=device-width,initial-scale=1">
   
   <style type="text/css">
   h1{color: white;}
   </style>

</head>

<body> <!-- <div style="max-width:900px; position:fixed;">****/ -->

   <header>
        <nav>      
          <div>

<!--

               <a href="#"  class="whiteSendai">Blog</a> 
               <a href="#"  class="whiteSendai">Twitter</a>
               <a href="#"  class="whiteSendai">Facebook</a>

--> <br><br>

           </div>
          <a href="http://openwetware.org/wiki/Biomod/2013/Sendai" class="whiteSendai">Top</a> 
           <a href="http://openwetware.org/wiki/Biomod/2013/Sendai/project" class="whiteSendai">Project</a>
           <a href="http://openwetware.org/wiki/Biomod/2013/Sendai/design" class="whiteSendai">Design</a> 
           <a href="http://openwetware.org/wiki/Biomod/2013/Sendai/calcuation" class="whiteSendai">Calculation</a>
           <a href="http://openwetware.org/wiki/Biomod/2013/Sendai/experiment" class="whiteSendai">Experiment</a>

<a href="http://openwetware.org/wiki/Biomod/2013" class="whiteSendai" style="float:right;"><img src="http://openwetware.org/images/6/6e/Biomod-logo.jpg"

                                              width="75" height="75" alt="Biomod2013" border="0"></a><br>
           <a href="http://openwetware.org/wiki/Biomod/2013/Sendai/protocol" class="whiteSendai">Protocol</a>   
           <a href="http://openwetware.org/wiki/Biomod/2013/Sendai/future" class="whiteSendai">Future</a> 
           <a href="http://openwetware.org/wiki/Biomod/2013/Sendai/member" class="whiteSendai">Member</a>
           <a href="http://openwetware.org/wiki/Biomod/2013/Sendai/sponsor" class="whiteSendai">Sponsor</a>
           </nav>
            <a href="http://openwetware.org/wiki/Biomod/2013/Sendai"><h1 style="color:white;" ><b>Biomod<span>2013<br>&emsp; Team</span>Sendai</b></h1></a> 

</header>


<section role="main">
       <article>
        <h2>Design</h2>

<table id="toc" class="toc" summary="Contents"><tr><td><div id="toctitle"><h2>Contents</h2></div> <ul> <li class="toclevel-1"><a href="#chain"> <span class="tocnumber"></span> <span class="toctext">Project goal</span></a></li> <ul> <li class="toclevel-2"><a href="#Flower"> <span class="tocnumber"></span> <span class="toctext">1st stage:Sensing system</span></a></li> <li class="toclevel-2"><a href="#sensing"> <span class="tocnumber"></span> <span class="toctext">2nd stage:Amplification system</span></a></li> <ul> <li class="toclevel-3"><a href="#5"> <span class="tocnumber"></span> <span class="toctext">DNA origami approach</span></a></li> <li class="toclevel-3"><a href="#6"> <span class="tocnumber"></span> <span class="toctext">FlowerDNA approach</span></a></li> </li>


</ul> </li> </ul> </td></tr></table>

<h2 id=chain>Project goal</h2> In Lipo-HANABI project, we need to develop the following two subsystems.<br><br>

i) Sensing system (1st stage): liposome disruption by temperature control. <br><br>

ii) Amplification system (2nd stage): a chain-reactive disruption of the liposomes activated by the 1st stage. <br><br>

<h3 id=Flower>1st stage: Sensing system </h3> The purpose of 1st stage is to detect temperature change and release key molecules for the 2nd stage. This is achieved by temperature-sensitive liposomes containing the keys. To make the liposome, we used lipids conjugated with NIPAM polymer.<br> <br> This structural change of NIPAM induces stress on the surface of the liposome, and consequently disrupts them.<br> <div align="center"> <Img Src="http://openwetware.org/images/9/95/NIPAM%E3%83%AA%E3%83%9D%E3%81%A1%E3%82%83%E3%82%933.png"> </div> <div align="center">Fig.1 Temperature-sensitive liposome</div> <h3 id=sensing>2nd stage: Amplification system </h3> The purpose of 2nd stage is to accept the key from the 1st stage and release a lot of payload molecules in a chain-reaction. <br> There are two different approaches to realize the 2nd stage.<br>

  A) DNA Origami approach<br>
  B) Flower DNA approach<br>

<h4 id=5>DNA origami approach </h4>


This approach is inspired by a paper about <a Href="http://www.ncbi.nlm.nih.gov/pubmed/19780639"> Membrane-bending proteins (Prinz WA, Hinshaw JE., Crit Rev Biochem Mol Biol., 2009)</a>. In this approach, we use “Origami-anchor DNA” which connects DNA Origami with liposome membrane.

A lot of DNA origamis are adsorbed on the surface of liposomes by using Origami-anchor DNA. DNA origami is supposed to be a stiff, straight board compared with liposome membrane, and as a result, liposome surface gets bending stress. At certain level of the absorbance, liposomes will burst. Also, DNA origamis on the surface repel each other because of negative charges on DNA backbones. This effect may add more stress on the membrane.<br>

<div align="center"> <Img Src="http://openwetware.org/images/1/12/%E8%86%9C%E3%80%80%E5%8F%8D%E7%99%BAnew.png"> </div> <div align="center">Fig.2 Stress on liposome membrane</div><br>

From the reference, we learned that efficient structure design for destabilizing membranes should have the following properties: <br> <ur><li>Having rigid scaffolds</li> <li>Having large surface areas to maximize the effect of the scaffold on the membrane</li></ur> <br>

<Design of DNA origami><br> DNA origami is known as a designable rigid structure made of DNA. We use DNA origami to make the rigid scaffolds. In order to meet the requirements, we designed a 2D rectangular DNA origami.<br>

<div align="center"> <Img Src="http://openwetware.org/images/4/45/Outsidefig8.png"> </div> <div align="center">Fig.3 Rectangular origami</div> <br> <div class="caption-right">

<Img Src="http://openwetware.org/images/a/a7/Lipo5.png" ><span>Fig.4 DNA origami designed by caDNAno</span>

</div> We use <a href="http://cadnano.org/">caDNAno2</a> for our DNA origami design. <br> The size of DNA origami is 67.6nm (26 helixes) in width and 127 nm (374 bases) in height.<br> We cut out a smaller rectangle of 10 helixes (161 bases) at one of the corners,<br> so that we could distinguish the two sides with AFM (Atomic Force Microscope) observation. <br> Also, we put 141 staples sticking out from the bottom face of the origami. Those staples hybridize with cholesterol-modified Origami-anchor DNA, which has high affinity with lipid membrane.<br>

<div align="center"> <Img Src="http://openwetware.org/images/2/2a/Outsidefig5o8o.png" width="450px" height="350px"> </div> <div align="center">Fig.5 Unstable liposome</div> <br> <h4 id=6>Flower DNA approach</h4> This approach is inspired by a paper about <a href="http://pubs.acs.org/doi/ipdf/10.1021/jp104711q">Polymer Flower-micelle (Yukio Tominaga, Mari Mizuse, Akihito Hashidzume, Yotaro Morishima and Takahiro Sato, J. Phys. Chem. B, 2010)</a>.<br> To adapt the Polymer Flower-micelle to our project, the followings are required.<br> <br> <ur><li>Embedding a lot of cholesterol-modified ss DNA on the liposome surface</li> <li>Adding another ssDNA (complementary to the above DNA) which induces a structural change by DNA hybridization</li> <li>The induced structural change on the DNA results in disruption of the liposome</li> <br> At first, we designed “Flower-anchor DNA”, which is a couple of ss DNAs both having cholesterol modified groups (Fig.6): Flower-anchor1 is 10nt ss DNA and Flower-anchor2 is 50nt ss DNA. Both are cholesterol-modified at their 3’ ends. <br> In addition, the 5’ end of the Flower-anchor2 is complementary to Flower-anchor1. When they hybridize, the rest 40nt of Flower-anchor2 remains single-stranded.<br> <div align="center"> <Img Src="http://openwetware.org/images/4/45/Flower-new54.png" width="450px" height="350px" ></div><br> <div align="center">Fig.6 Liposome with Flower-anchor DNA</div> <br> The key DNA released from stage 1 liposome is complementary to this single-stranded part. When the key hybridizes on it, a double-stranded section is formed. The length of the section is shorter than its persistence length; therefore it works as a rigid strut. The strut is anchored on the liposome at both ends, thus it extends the membrane. As a consequence, this may lead to drastic conformational change of the liposome, namely, disruption. <br> <img src="http://openwetware.org/images/6/65/Flower3new8.png"><br> <div align="center">Fig.7 Process of flower DNA approach</div><br><br> <Img Src="http://openwetware.org/images/d/dd/Flower4newa.png" Align="center" width="900px" hight="800" ><br> <div align="center">Fig.8 How to disrupt a liposome</div>

      </article>

</section> <!-- /***** </div> ****/ -->


   <footer>
       <p>&copy; Copyright Biomod 2013 Team Sendai
               <a href="http://www.molbot.mech.tohoku.ac.jp/index.html">

                  <img src="http://openwetware.org/images/3/36/Murata-nomura-logo.png"

                                     width="180" height="50" alt="Molcular Robotics Lab" border="0" align="right">

         </a>      </p>

       <p>E-MAIL:
           <a href="mailto:biomod.teamsendai.2012@gmail.com">biomod.teamsendai.2012@gmail.com
           </a>
       </p>
       <br>
       <a href="?action=edit" align="center"><p>edit</p></a>
   </footer>
   

</body> </html>


<html> <head>

       <script type="text/javascript">
     function tabs(a,g,j){document.body.className="js-on";var g=a.getElementsByTagName(g),d=[],c;this.active;this.total=g.length;this.container=a;e=a.insertBefore(document.createElement("nav"),g[0]),change=function(f){if(typeof this.active!=="undefined"){d[this.active].className=g[this.active].className=""}d[f].className=g[f].className="active";this.active=f},clickEvent=function(h,f){h.onclick=function(){change(f);return false}};for(var b=0;b<g.length;b++){d[b]=e.appendChild(document.createElement("a"));d[b].href="#";c=[g[b].getAttribute("data-title"),g[b].getElementsByTagName(j)[0]];d[b].innerHTML=c[0]!==null?c[0]:c[1]?c[1]["innerText"||"textContent"]:b+1;new clickEvent(d[b],b)}change(0)}tabs.prototype.change=function(b){change(b-1)};tabs.prototype.next=function(b){active===this.total-1?change(0):change(active+1)};tabs.prototype.prev=function(b){active===0?change(this.total-1):change(active-1)};tabs.prototype.responsive=function(d,c){nav=document.createElement("nav");nav.id="mobiles";nav.innerHTML='<a href="#" onclick="'+d+'.prev(); return false">'+c.prev+'</a><a href="#" onclick="'+d+'.next(); return false">'+c.next+"</a>";this.container.insertBefore(nav,this.container.firstChild);return this};
       </script>
       <script type="text/javascript">

var myTabs = new tabs(document.getElementById("tabs"), "article", "h2").responsive("myTabs", { prev: "Previous", next: "Next" }); </script> </head> </html>