From OpenWetWare
Revision as of 09:43, 27 October 2012 by Kazuki Hirahara (talk | contribs)
Jump to: navigation, search

<html> <head>

   <title>Team Sendai Top</title>
   <script type="text/javascript" src=""></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(); })



body{ background-image:url(; /*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(; 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;


border-left: 10px solid #000066;

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

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

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

       color:# 333333;



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




p img{

        	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*/ }



border: solid 1px #111111;


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



border: solid 1px #111111;


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

  1. red{

border: solid 1px #111111;


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

  1. blue{

border: solid 1px #111111;


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; }


  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( 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( 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=" ">Home</a></li> <li><a href=" ">Project</a></li> <li><a href="">Design</a> </li> <li><a href="">Simulation</a> </li> <li> <a href=" ">Experiment</a> </li> <li> <a href=" Application">Future Application</a> </li> <li> <a href="">Diary</a> </li> <li> <a href=" ">Team</a> </li> <li> <a href=" Sendai/header"></a> </li>


<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>

Aim of Simulation

Molecular robots works in meso-scale (from nm to sub-micro meter). In the meso-scale, characters of each molecule and cooperative movement of molecules could not be ignored. Without calculation of potentials or molecular dynamics simulations, it is difficult to predict the behaviors of the molecules in this scale. Thus, we calculated potentials to confirm the GATE effect, and simulated molecular dynamics of DNAs to strength reliability of our design.

Potential Calculation

Electric potential of the GATE was calculated inside and outside the GATE. The phosphate groups in the backbone of DNA are negatively-charged. Because the GATE is made by DNA origami, the GATE has the Coulomb force.

Model of DNA

A point-charge model is applied to DNA model. Each phosphate of a nucleotide was converted into one electric beads, which has elementary electoric charge (1.602176565 x 10^−19 [C]). In DNA helix, negative charges appear along the axis of the double helix every 10.4 base pairs. Debye–Hückel equation was used to calculate electric potential. Electric potential of each point around the GATE was deduced from summation of all the Electric Potential for every phosphate presented on DNA.

Debye–Hückel equation:

Potential fomula.png

reference: Debye length


Following figure shows the scheme of a point-charge model and potential calculations.

Condition: Temperature 298[K], Na+ 50mM


Electric potential was calculated by using C language. Under our conditions, the target DNA has 25 electric beads.

The following figure shows electric potentials between the target DNA and the GATE from the top of view of the GATE. The electric potentials were standardized by thermal energy, KBT (KB; Boltzmann constant). Potential energy was shown by a heat map.

Electric potential from the top of view of the GATE

Potential energy along axis indicated by the arrows were shown as the following figure.

Electric potential from the top of view of the GATE

Electric potential from the top of view of the GATE

Electric potential from the top of view of the GATE

Electric potential from the top of view of the GATE

MD Simulation

We carried out molecular dynamics simulation to examine the capturing mechanism and the effectiveness of our structure “CELL GATE".

DNA Model

Format DNA rasen.jpg

For simplicity, a course-grained DNA model was used in our simulation. One DNA nucleotide was represented by one bead in the model and each bead can be hybridized with a complementary bead.

The potential energy of the system includes 5 distinct contributions.

Format suusiki1.jpg

The first three terms are intramolecular interactions, bonds, bond angles, and dihedral angles. In order to express the “tether like structure”, only bond interactions are considered in our DNA model.

And the latter two terms are non-bonded interactions. Coulomb interactions are taken into account using the Debye-Huckel approximation which enables to internalize counterions contribution.

Parameters of these potentials were fit to the reference literature ; Thomas A. Knotts et al. A coarse grain model of DNA .

The force on bead i is given by a Langevin equation

Format suusiki2.jpg

The first term donates a conservative force derived from the potential Vtot and the second is a viscosity dependent friction.

The third term is a white Gaussian noise and effects of collision with solvent molecules which causes brownian motion are internalized in this term.

Langevin equation is integrated using a Velocity-Verlet method.

Toehold displacement of dsDNA

Format toea toeb.jpg

In order to test the model, here we carried out a simulation of Toehold displacement between two strands.

Length of strands and simulation condition were as follows:

Target strand / Toehold A / Toehold B : 16nt / 9nt / 13nt
Temperature : 300K
Time-step / simulation length : 0.01ps / 100ns
Ion concentration : 50mM Na+

<html><div style="clear:both;"></div></html>


<youtube width="450" align="left">FGpemnMLUMk&border=1&color1=0x6699&color2=0x54abd6</youtube> <html><div style="clear:both;"></div></html>

Movie1 : MD simulation of toehold strand displacement

<html><div style="clear:both;"></div></html>

Movie 1 shows the trajectory of each strand from the simulation. The target strand moves from Toehold A strand to Toehold B strand which are fixed on the field. This result agrees with the energy gradient.

Comparison of capture ability

One of constructional features of our structure ”Cell-Gate” is the use of a novel strand displacement method.

By comparing our selector strand to toehold strand, the most popular method for strand displacement, we looked at the effectiveness of our structure in terms of it's strand capturing ability.

Model and Method

According to the design of the experiment section, we modeled the selector strand and the toehold strand as shown below.

Format selector.jpg

<html><div style="clear:both;"></div></html>

Hex-cylinder is represented as the assembly of fixed electrically-charged mass points.

Format Hexagon.jpg

<html><div style="clear:both;"></div></html>

Simulation was carried out at the following condition:

Temperature : 300K
Ion concentration : Na+ 50mM
Box size : 20nm×20nm×20nm (periodic boundary condition)
Time-step / simulation length : 0.01ps / 10ns

Results and Conclusion

<youtube width="450" align="left">NXo4cYKkrF0&border=1&color1=0x6699&color2=0x54abd6</youtube> <html><div style="clear:both;"></div></html>

<youtube width="450" align="left">qidZS1pI0lc&border=1&color1=0x6699&color2=0x54abd6</youtube> <html><div style="clear:both;"></div></html>

Movie2 : MD simulation of porter strand

Movie3 : MD simulation of toehold strand

<html><div style="clear:both;"></div></html>

Movie2 and 3 shows the result of each simulation, selector-target and toehold-target.

We note that this simulation was carried out under a periodic boundary condition, where the size of the simulation box is 20nm×20nm×20nm. Then, the distance between the target strand and the Hex-cylinder is maintained virtually constant.

One of the advantages of the selector strand is shrinking ability. The selector strand hybridizes to the target making a loop which makes it possible to extend the strand length without changing the final structure's length.

Results obtained from this simulation show that the selector strand can catch the target strand exists outside of the Hex-cylinder and hybridize completely while the toehold strand never hybridize to the target strand in simulation time.

We run 5 simulations for each capturing mechanism under the same conditions and results were almost the same as we first obtained.

By considering results of electrostatic potential calculation around the hex-cylinder and MD simulation, it is clear that the electrostatic field prevents the entrance of DNA strands into the Hex-cylinder and the selector strand helps it to get into the cylinder.

Therefore, we concluded that our novel selector strand provides a high capture ability to our system “Cell-Gate”.


1. Thomas A. Knotts et al. A coarse grain model of DNA , J.Chem.Phys 126,084901(2007)

2. Carsten Svaneborg et al. DNA Self-Assembly and Computation Studied with a Coarse-Grained Dynamic Bonded Model, DNA 18,LNCS 7433, pp.123-134, (2012)

3. Xhuysn Guo & D.Thirumalai, Kinetics of Protein Folding: Nucleation Mechanism, Time Scales, and Pathways, Biopolymars, Vol.36, 83-102 (1995)

4. GROMACS manual ( )

5. Cafemol manual ( )