Biomod/2012/UTokyo/UT-Hongo/Function: Difference between revisions

From OpenWetWare
Jump to navigationJump to search
No edit summary
 
(21 intermediate revisions by 4 users not shown)
Line 2: Line 2:
{{Biomod/2012/UTokyo/UT-Hongo/Begin|pagetype=design|pagename=Function}}
{{Biomod/2012/UTokyo/UT-Hongo/Begin|pagetype=design|pagename=Function}}


=Structure=
=Main structure of DNA shell=
In this section we will describe the methods for designing our DNA Shell.
Our DNA Shell is designed as DNA Origami. In this section, we explain about DNA Origami, and then describe about our design of the typical structure and added functions of DNA Shell. Also, we simulated about stability of hybridization.
=Outline=
 
[[Image:Biomod-2012-UTokyo-UT-Hongo-outline-2.jpg|400px|thumb]]
==DNA origami==
We designed the structure shell-shaped so that it can efficiently capture target molecule with a dramatic change in the fluorescence for easy detection.
 
We actually created three shell-shaped structures.  
DNA Origami is a complex 2D or 3D structure which is fabricated using herical structure of DNA. Generally, DNA Origami is composed of one Scaffold DNA, long single strand DNA, and many Staple DNA, short single strand DNA. Staple sticks a part of scaffold to the other part and achives the designed structure. For designing DNA Origami, the phase of hydrogen bond of DNA herical structure should be concerned. We could easily design DNA Shell using CAD Nano, the software for designing DNA Origami.
*Plane shell
 
*Shell with florescent molecules and quenching molecules attached
 
*Shell with florescent molecules, quenching molecules, and biotin attached
==DNA Shell==
For our DNA shell, We used a typical DNA material called M13 as scaffold DNA. It has approximately 7250 base pairs and it is an ideal number for our shell. A part of this DNA self-hybridizes, so we had to cut that part off for further design. On the other hand, we standardized the number of base pairs to 32bp, because the characteristic of hybridization is greatly affected by the number of base pairs.
 
[[Image:Biomod-2012-UTokyo-UT-Hongo-Design-CadNanoImage2D.jpg|thumb|500px|Fig. 1 The image of DNA Shell on CAD Nano.]]
 
Fig. 1 is the picture of DNA Shell on CAD Nano. The blue line is scaffold and the others are staples. the shell has three large domains which are about 40nm × 30nm. the center and right domains are the body of the shell and able to be added various functions. the left domain is used for immobilizing in microchannel. When hybridizing scaffold and staple, the tempereture in which the reaction is stable is determined by the length of staple, so we designed almost staples as same length. Furthermore, if the staples of the bridges which connect the domains are not added when hybridizing, these part of scaffold can be freely deformed, and shell can open and close like real shell.
 
<br style="clear: both;">
<br style="clear: both;">


=='''Structure of the body'''==
=Adding functionality=
[[Image:Biomod-2012-UTokyo-UT-Hongo-outline-1.jpg|500px|thumb]]
 
DNA origami is comprised of two elements, the scaffold and the staples.
[[Image:Biomod-2012-UTokyo-UT-Hongo-Design-ExtendedStaple.jpg|400px|thumb|Fig.2 The image of extended staple. We designed all these staples to extend from the same side of shell surface taking care of the phase of the hydrogen bond.]]
Scaffold is like the main body of the whole origami, and we can shape the structure as we like by attaching staples. Following is the description of how scaffold and staples were designed.
 
[[Image:Biomod-2012-UTokyo-UT-Hongo-outline-2.jpg|400px|thumb|Fig. 3 The 3D image of the position of functional molecules. The yellow sequences in the image are the staples to attach fluorescent/quenching molecules, the red sequences are the staples to attach functional parts.]]
 
In order to add functionality to the body, we extended  some of the staples so they could bond with DNA fragments that are modified (Fig. 2). Therefore, we added 13 base pairs to the staples which originally had 32 base pairs. We designed all these staples to extend from the same side of shell surface taking care of the phase of the hydrogen bond.
 
We needed to attach 12 single-stranded DNAs with fluorescent molecules (named as fluorescent DNAs) and two functional single-stranded DNAs to one side, and 12 single-stranded DNAs with quenching molecules (named as quenching DNAs) and two functional single-stranded DNAs to the other side. We had to think up of 4 different sequences that would bind to either:
# fluorescent DNAs
# quenching DNAs
# functional DNAs to the fluorescent side
# functional DNAs to the quenching side
 
We designed the structure so that the functional part is surrounded by fluorescent/quenching molecules (Fig. 3). For working quenching molecules appropriately, we designed the fluorescent molecules and the quenching molecules to face each other.
 


* Scaffold：We used a typical DNA material called M13. It has approximately 7250 base pairs and it is an ideal number for our shell. A part of this DNA self-hybridizes, so we had to cut that part off for further design.
* Staple：The characteristic of hybridization is greatly affected by the number of base pairs. In order to make it go efficiently, we standardized the number of base pairs to 32bp. We had difficulty in deciding the position of staples because it must be strongly attached to the body. Also, we wanted to control the flexibility of the shells in response to the purposed functions. To realize this demand, staples at the junctions of the shell was designed so as not to affect other parts. By doing so, the junctions of the shell became more flexible while the whole body became stronger at the same time.
<br style="clear: both;">
<br style="clear: both;">


=='''Adding functionality'''==
=Simulation Techniques=
In order to add functionality to the body, we extended  some of the staples so they could bond with DNA fragments that are modified. Therefore, we added 13 base pairs to the staples which originally had 32 base pairs.
We needed to attach 12 single-stranded DNAs with fluorescent molecules (named as fluorescent DNAs) and two functional single-stranded DNAs to one side, and 12 single-stranded DNAs with quenching molecules (named as quenching DNAs) and two functional single-stranded DNAs to the other side. We had to think up of 4 different sequences that would bind to either 1.fluorescent DNAs, 2.quenching DNAs, 3.functional DNAs to the fluorescent side, and 4.functional DNAs to the quenching side. 
We designed the structure so that the functional part is surrounded by fluorescent/quenching molecules. (The yellow sequences in the image are the staples to attach fluorescent/quenching molecules, the red sequences are the staples to attach functional parts. For quenching molecules to function, we had to design the positions so that the fluorescent molecules and the quenching molecules face each other.)


Generally, in designing moderate arrangement of staples it is required to make sure that the staples are hybridized only at the points we want hybridization to occur. That is, we have to keep the energy for hybridization high in inappropriate areas and keep it low in the correct areas. In order to achieve this requirement, we focused on these three points.  
Simulation techniques were applied in the design especially 1. to make sure that the staples are hybridized only at the points we want hybridization to occur. That is, we have to keep the energy for hybridization high in inappropriate areas and keep it low in the correct areas. In order to achieve this requirement, we focused on these three points.  


* To make sure that the complementary arrangements of the designed staples does not appear in inappropriate area  
* To make sure that the complementary arrangements of the designed staples does not appear in inappropriate area  
Line 42: Line 55:
:If we hybridized the arrangements extended from staples and functionalized parts simultaniously, there would be some steric hindrance. To weaken this effect, we set a realm where the staples will not be hybridized. Concretely, we embedded two T (thymine) bases in the staples.
:If we hybridized the arrangements extended from staples and functionalized parts simultaniously, there would be some steric hindrance. To weaken this effect, we set a realm where the staples will not be hybridized. Concretely, we embedded two T (thymine) bases in the staples.


=='''Simulation Techniques'''==
To simulate the energy of hybridization and melting temperature, we used the software named DINAMelt and NUPAC supported on online.
To simulate the energy of hybridization and melting temperature, we used the software named DINAMelt and NUPAC supported on online.
Since there is no absolute solutions for design, we needed to get over the difficulties by trial and error; It was serious and troublesome work.
Since there is no absolute solutions for design, we needed to get over the difficulties by trial and error; It was serious and troublesome work.
In designing the arrangement extended from staples, we need to attach the same arrangement to the staples attached with functional parts. This work of discovering moderate arrangement cost us immense labor, because it is required to make these staples added only ONE pattern of arrangement hybridized stably. The work of discovering a arrangement compatible to several staples was like finding one penny lost somewhere in campus.
In designing the arrangement extended from staples, we need to attach the same arrangement to the staples attached with functional parts. This work of discovering moderate arrangement cost us immense labor, because it is required to make these staples added only ONE pattern of arrangement hybridized stably. The work of discovering a arrangement compatible to several staples was like finding one penny lost somewhere in campus.


The image shown below is one example of simulation　using　DINAMelt (http://mfold.rna.albany.edu). This is a simulation of the melting temperature and the possibility of correct hybridization.　
Fig. 4 is one example of simulation　using　DINAMelt (http://mfold.rna.albany.edu). This is a simulation of the melting temperature and the possibility of correct hybridization.　
[[Image:Biomod-2012-UTokyo-UT-Hongo-Exsample_of_simulation_about_hybrizidation_for_mid.jpg|thumb|450px]]
[[Image:Biomod-2012-UTokyo-UT-Hongo-Design-HybridizationSimulation.jpg|thumb|450px|Fig. 4 Simulation of the melting temperature and the possibility of correct hybridization. The horizontal axis is the melting temperature and the vertical axis is the possibility of hybridization. The appropriate hybridization is dominant at low temperature.]]
This is simulated under a situation of  
This is simulated under a situation of  
*From 0°C by 1°C to 100°C as DNA
*From 0°C by 1°C to 100°C as DNA

Latest revision as of 08:31, 26 October 2012

<html> <head> <style> <!-- HIDE WIKI STUFF -->

  1. column-one { display:none; width:0px;}

.container{background-color: #ffffff; margin-top:0px} .OWWNBcpCurrentDateFilled {display: none;}

  1. content { width: 0px; margin: 0 auto auto 0; padding: 0em 0em 0em 0em; align: center;}
  2. column-content {width: 0px; float: left; margin: 0 0 0 0;padding: 0;}

.firstHeading {display:none; width:0px;}

  1. globalWrapper{width:984px; background-color: #ffffff; margin-left: auto; margin-right: auto}
  2. column-one {display:none; width:0px;background-color: #ffffff;}
  3. content{ margin: 0 0 0 0; align: center; padding: 12px; width: 960px;background-color: #ffff; border: 0;}
  4. bodyContent{ width: 960px; align: center; background-color: #ffffff;}
  5. column-content{width: 984px;background-color: #ffff;}
  6. footer{display: none; position: center; width: 960px}

@media screen { 

   body { background: #ffffff url(http://openwetware.org/images/1/14/Biomod-2012-utokyo-uthongo-wrapper-bg.jpg) repeat; }

}

</style>

<style>

  • {

text-shadow: 0px 1px 2px #aaa; }

  1. bodyContent, #column-content, #content {

background: #ffffff url(http://openwetware.org/images/1/14/Biomod-2012-utokyo-uthongo-wrapper-bg.jpg) repeat; }

  1. column-content {
border-left: 1px solid #888;
border-right: 1px solid #888;

}

  1. header {
 width: 960px;
 height: 304px;
 background: url(http://openwetware.org/images/3/3b/Biomod-2012-UTokyo-UT-Hongo_header_test2.png) no-repeat;
 background-size: 100% auto;
 margin-bottom: 0px;
 padding: 0px 0px 0px 0px;

/* border-bottom: 1px solid #DEDEDE; */ }

  1. menu {
 display: block;
 width: 956px;
 padding: 0px;
 background-color: black;
 border: 2px solid #888;
 margin-bottom: 15px;

}

ul.menu li a { 

 display: block;

/* border: 1px solid #474655; */ 

 padding: 8px 10px;
 text-decoration: none;

/* color: #333; */ 

 color: #fff;

/* width: 121px; */ 

 margin: 0px;
 text-align: center;
 font-size: large;

}

ul.menu li a:hover{ 

 color: cyan;

}

ul.menu { /* display: none; 

 position: absolute; */
 height: 40px;
 margin:0;
 padding:0;
 list-style:none;
 float: center;

}

ul.menu li { /* display:inline;*/ 

 margin:0;
 padding:6px;
 float: left;
 position: relative;

}

ul.menu li:hover ul { 

 display: block;
 position: absolute;
 z-index: 100;

}

ul.submenu { 

 display: none;
 list-style: none;
 background-color: #f0f0f0;
 border: 1px solid #ccc;

}

ul.submenu li { 

 float: none;
 margin: 0px;

}

ul.submenu li a { 

 text-align: left;
 margin: 0px;
 width: 340px;
 padding: 0 0 0 12px;
 color: black;
 text-decoration: none;
 font-size: large

}

ul.submenu li a:hover { 

 color: black;
 text-decoration: underline;

}

.thumb { 

 border-image: url(http://openwetware.org/images/1/14/Biomod-2012-utokyo-uthongo-wrapper-bg.jpg) repeat;

}

.mytable { 

 border-image: url(http://openwetware.org/images/1/14/Biomod-2012-utokyo-uthongo-wrapper-bg.jpg) repeat;

}

</style> </head> <body> 

 <!--<div style="text-align: right">
   <p><a href="http://openwetware.org/index.php?title=Template:Biomod/2012/UTokyo/UT-Hongo&action=edit">edit this header</a></p>
 </div>-->

 <div style="height: 60px; margin-bottom: 18px;">
   <div style="float: left; width: 250px; padding: 3px; background-color: white;">
     <a href="http://biomod.net/"><img src="http://openwetware.org/images/8/82/Biomod2012-logo.png" width="250px" height="50px"></img></a>
   </div>
   <div style="float: right; width: 240px; padding: 3px; background-color: white;">
     <a href="http://www.u-tokyo.ac.jp/en/" target="_blank"><img src="http://www.u-tokyo.ac.jp/en/images/banner/UT-logo.gif" width="234" height="60" border="0" alt="The University of Tokyo"></img></a>
   </div>
 </div>

   <div id="header">
   </div>

   <div id="menu">
     <ul class="menu">

<li class="toppage"><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo">Top</a></li> <li class="motives"><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Intro">Motives</a></li> <!-- <li class="design"><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Function">Design</a></li> --> <li class="result"><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Assembly">Design & Results</a> <ul class="submenu"> <li><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Assembly#Assembly_of_the_DNA_Shell">Assembly of the DNA Shell</a></li> <li><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Assembly#Capturing_ability">Capturing Ability</a></li> <li><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Assembly#Immobilizing_on_microfluidic_device">Immobilizing on microfluidic device</a></li> <li><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Assembly#Supporting_Enzyme">Supporting Enzyme</a></li> </ul> </li> <li class="method"><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Method">Method</a></li> <li class="futurework"><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/FutureWork">Progress & Beyond</a></li> <li class="team"><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Team">Team</a></li> <li class="acknowledgement"><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Acknowledgement">Acknowledgement</a></li> 

     </ul>
   </div>

</body> </html>

<html> 

 <style>

ul.menu li.</html>design<html> a { 

 color: cyan;

}

  1. toc {
 display: none;

}

  1. mytoc {
 background: #dedede;
 width: 200px;

}

  1. toc ul ul, .toc ul ul {
 margin: 0 0 0 1em;

}

  1. mytoc a, #mytoc a:visited {
 font-size: normal;
 color: black;

}

  1. mytoc a:hover {
 font-weight: bold;
 text-decoration: none;

}

  1. wiki-toc {
 width: 200px;
 margin-top: 6px;
 float: left;

}

  1. wiki-body {
 margin-left: 200px;
 padding-left: 12px;

}

  1. toctitle span {
 display: none;

}

  1. wiki-body p,
  2. wiki-body li,
  3. wiki-body dd,

div.thumbcaption { 

 font-size: medium;

} 

 </style>

 <script type="text/javascript">

window.onload = function () { 

 document.getElementById('mytoc').appendChild(document.getElementById('toc').firstChild);

}; 

 </script>

<html>

<html><div id="wiki-contents"> <div id="wiki-toc"> 

 <table id="mytoc" class="toc" summary="Contents">
 </table>
 <div style="text-align: right">
   <p><a href="http://openwetware.org/index.php?title=Biomod/2012/UTokyo/UT-Hongo/</html>Function<html>&action=edit">edit this page</a></p>
 </div>

</div> <div id="wiki-body"></html>

Main structure of DNA shell

Our DNA Shell is designed as DNA Origami. In this section, we explain about DNA Origami, and then describe about our design of the typical structure and added functions of DNA Shell. Also, we simulated about stability of hybridization.

DNA origami

DNA Origami is a complex 2D or 3D structure which is fabricated using herical structure of DNA. Generally, DNA Origami is composed of one Scaffold DNA, long single strand DNA, and many Staple DNA, short single strand DNA. Staple sticks a part of scaffold to the other part and achives the designed structure. For designing DNA Origami, the phase of hydrogen bond of DNA herical structure should be concerned. We could easily design DNA Shell using CAD Nano, the software for designing DNA Origami.


DNA Shell

For our DNA shell, We used a typical DNA material called M13 as scaffold DNA. It has approximately 7250 base pairs and it is an ideal number for our shell. A part of this DNA self-hybridizes, so we had to cut that part off for further design. On the other hand, we standardized the number of base pairs to 32bp, because the characteristic of hybridization is greatly affected by the number of base pairs.

Fig. 1 The image of DNA Shell on CAD Nano.

Fig. 1 is the picture of DNA Shell on CAD Nano. The blue line is scaffold and the others are staples. the shell has three large domains which are about 40nm × 30nm. the center and right domains are the body of the shell and able to be added various functions. the left domain is used for immobilizing in microchannel. When hybridizing scaffold and staple, the tempereture in which the reaction is stable is determined by the length of staple, so we designed almost staples as same length. Furthermore, if the staples of the bridges which connect the domains are not added when hybridizing, these part of scaffold can be freely deformed, and shell can open and close like real shell.


Adding functionality

Fig.2 The image of extended staple. We designed all these staples to extend from the same side of shell surface taking care of the phase of the hydrogen bond.
Fig. 3 The 3D image of the position of functional molecules. The yellow sequences in the image are the staples to attach fluorescent/quenching molecules, the red sequences are the staples to attach functional parts.

In order to add functionality to the body, we extended some of the staples so they could bond with DNA fragments that are modified (Fig. 2). Therefore, we added 13 base pairs to the staples which originally had 32 base pairs. We designed all these staples to extend from the same side of shell surface taking care of the phase of the hydrogen bond.

We needed to attach 12 single-stranded DNAs with fluorescent molecules (named as fluorescent DNAs) and two functional single-stranded DNAs to one side, and 12 single-stranded DNAs with quenching molecules (named as quenching DNAs) and two functional single-stranded DNAs to the other side. We had to think up of 4 different sequences that would bind to either:

  1. fluorescent DNAs
  2. quenching DNAs
  3. functional DNAs to the fluorescent side
  4. functional DNAs to the quenching side

We designed the structure so that the functional part is surrounded by fluorescent/quenching molecules (Fig. 3). For working quenching molecules appropriately, we designed the fluorescent molecules and the quenching molecules to face each other.



Simulation Techniques

Simulation techniques were applied in the design especially 1. to make sure that the staples are hybridized only at the points we want hybridization to occur. That is, we have to keep the energy for hybridization high in inappropriate areas and keep it low in the correct areas. In order to achieve this requirement, we focused on these three points.

  • To make sure that the complementary arrangements of the designed staples does not appear in inappropriate area
The　combination of Watson-Crick base pair is stable, therefore if there are no other possibilities of hybridization of the staple and the scaffold in inappropriate areas,

the energy of hybridization would become the lowest in the appropriate area, which means that the possibility of achieving the correct hybridization will increase.

  • To keep the melting temperature of correct hybridization low, and to keep the melting temperature of incorrect hybridization high
We achieved this requirement through trial and error.
  • To avoid steric hindrance
If we hybridized the arrangements extended from staples and functionalized parts simultaniously, there would be some steric hindrance. To weaken this effect, we set a realm where the staples will not be hybridized. Concretely, we embedded two T (thymine) bases in the staples.

To simulate the energy of hybridization and melting temperature, we used the software named DINAMelt and NUPAC supported on online. Since there is no absolute solutions for design, we needed to get over the difficulties by trial and error; It was serious and troublesome work. In designing the arrangement extended from staples, we need to attach the same arrangement to the staples attached with functional parts. This work of discovering moderate arrangement cost us immense labor, because it is required to make these staples added only ONE pattern of arrangement hybridized stably. The work of discovering a arrangement compatible to several staples was like finding one penny lost somewhere in campus.

Fig. 4 is one example of simulation　using　DINAMelt (http://mfold.rna.albany.edu). This is a simulation of the melting temperature and the possibility of correct hybridization.　

Fig. 4 Simulation of the melting temperature and the possibility of correct hybridization. The horizontal axis is the melting temperature and the vertical axis is the possibility of hybridization. The appropriate hybridization is dominant at low temperature.

This is simulated under a situation of

  • From 0°C by 1°C to 100°C as DNA
  • [A0] = 1.6e-07 M, [B0] = 1.6e-07 M  ;[A0] is concentration of extended staple and [B0] is concentration of modified functional part
  • [Na+] = 0.2 M, [Mg++] = 0.0125 M

As seen below, a hybridization of A and B (appropriate hybridization) is dominant at low temperature(from 0°C to 30°C).

<html></div></div></html> <html> <head> 

 <style>
  1. myfooter {
 border-top: 1px solid #a9a9a9;
 padding-top: 60px;
 margin-top: 18px;

}

  1. sitemap {
 width: 934px;
 height: 250px;
 background: #f0f0f0;
 padding: 12px;
 border: 1px solid #808080;

}

  1. sitemap a {
 color: #666;

}

  1. sitemap h3 a {
 text-decoration: underline;

}

  1. sitemap a:hover {

}

  1. footer-contents {
 padding: 12px;
 height: 140px;

}

  1. sitemap h2 {
 color: #888;

}

.footer-section { width: 96px; float: left; margin-right: 30px; }

  1. section1 {

width: 64px; }

  1. section3 {
 width: 124px;

}

  1. section4 {
 width: 108px;

}

  1. section5 {
 width: 135px;

}

  1. section6 {
 width: 72px;

}

  1. section7 {
 float: right;

}

.footer-section h3 { 

 font-size: small;

}

.footer-section ul li a { 

 font-size: small;

}

  1. copyright {
 text-align: center;
 color: #aaa;

} 

 </style>

</head> <body> 

 <div style="text-align: right">
   <p><a href="http://openwetware.org/index.php?title=Template:Biomod/2012/UTokyo/UT-Hongo/Footer&action=edit">edit this footer</a></p>
 </div>

<div id="myfooter"> 

 <div id="sitemap">
   <h2 style="border-bottom: none;">BIOMOD 2012 Team UT-Hongo</h2>
   <hr>
   <div id="footer-contents">
     <div class="footer-section" id="section1">

<h3><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo">Top</a></h3> <ul> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo#description">Abstract</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo#youtube">YouTube</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo#navi">Links</a></li> </ul> 

     </div>
     <div class="footer-section" id="section2">

<h3><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Intro">Motives</a></h3> <ul> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Intro#Focus">Focus</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Intro#Idea_of_DNA_Shell">Idea</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Intro#Functionalities_Exhibited">Funcitonalities</a></li> 

         <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Intro#Conceptual_Blueprint_of_the_Structure">Blueprint</a></li>

</ul> 

     </div>
     <div class="footer-section" id="section3">

<h3><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Assembly">Design & Results</a></h3> <ul> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Assembly#Design">Design</a></li> 

         <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Assembly#Adding_functionality">Function</a></li>
         <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Assembly#Result">Result</a></li>
         <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Assembly#Assembly_of_the_DNA_Shell">Experiments</a></li>

</ul> 

     </div>
     <div class="footer-section" id="section4">

<h3><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Method">Method</a></h3> <ul> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Method#AFM">AFM</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Method#Photometer">Photometer</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Method#Electrophoresis">Electrophoresis</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Method#Ultraviolet_Irradiation">Others</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Method#Reagent">Reagent</a></li> </ul> 

     </div>
     <div class="footer-section" id="section5">

<h3><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/FutureWork">Progress & Beyond</a></h3> <ul> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/FutureWork#Variety_of_Target_Substances">Target Variety</a></li> 

         <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/FutureWork#DNA_Shell_with_Functionality">Functionalization</a></li>
         <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/FutureWork#Shell_with_the_DNA_Hybridization_Circuits">Circuits</a></li>
         <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/FutureWork#A_Device_more_than_Shell_and_Enzyme">Conclusion</a></li>

</ul> 

     </div>
     <div class="footer-section" id="section6">

<h3><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Team">Team</a></h3> <ul> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Team#Info">Info</a></li> 

         <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Team#Team_members">Members</a></li>
         <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Team#Graduate_and_Post-Doctoral_Mentors">Mentors</a></li>
         <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Team#Team_Photos">Photos</a></li>

</ul> 

     </div>
     <div class="footer-section" id="section7">

<h3><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Acknowledgement">Acknowledgement</a></h3> <ul> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Acknowledgement#Mentor">Mentor</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Acknowledgement#Professors">Professors</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Acknowledgement#Sponsors">Sponsors</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2012/UTokyo/UT-Hongo/Acknowledgement#Special_Thanks">Special Thanks</a></li> </ul> 

     </div>
   </div>
   <p id="copyright">
     Copyright (C) 2012 | Design by Yuichi Nishwiaki | BIOMOD Team UT-Hongo
   </p>
   <br style="clear: both;">
 </div>

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

Retrieved from "https://openwetware.org/mediawiki/index.php?title=Biomod/2012/UTokyo/UT-Hongo/Function&oldid=643116"