Biomod/2012/Harvard/BioDesign/design: Difference between revisions

From OpenWetWare
Jump to navigationJump to search
No edit summary
No edit summary
Line 1: Line 1:
{{Template:Biomod/2012/Harvard/BioDesign}}
{{Template:Biomod/2012/Harvard/BioDesign}}


=Approaches=
Project Specifications<br><br><br>
 
??? --> Project Specifications<br><br><br>


Our final result was a 10 helix x 14 turn L-DNA sheet connected to the center of a 24 helix by 29 turn D-DNA template.  In principle, we could detach this L-DNA layer by addition of a nuclease to digest the template layer and isolate the L-DNA layer as L-DNA is resistant to nucleases.  However, due to time constraints as well as the ability to show the templating, we have imaged our results with the template attached.
Our final result was a 10 helix x 14 turn L-DNA sheet connected to the center of a 24 helix by 29 turn D-DNA template.  In principle, we could detach this L-DNA layer by addition of a nuclease to digest the template layer and isolate the L-DNA layer as L-DNA is resistant to nucleases.  However, due to time constraints as well as the ability to show the templating, we have imaged our results with the template attached.


The L-DNA layer is formed by formed by 2 unique, tessellating strands which are connected to the template by handles that stick out of the template.  These handles are designed into the strands of the template as an extra piece.
The L-DNA layer is formed by formed by 2 unique, tessellating strands which are connected to the template by handles that stick out of the template.  These handles are designed into the strands of the template as an extra piece.
(link L-DNA layer area)
(Biomod/2012/Harvard/BioDesign/LDNA_layer | Approach to the L-DNA Layer)


The template was generated from a series of strands for a 24x29 SST canvas (using Motif 1 - LINK THIS)  
The template was generated from a series of strands for a 24x29 SST canvas (using Motif 1 - LINK THIS)  
Line 20: Line 18:
We decided to template the L-DNA on the interior of the template.  This decision was made for a couple reasons: to be able to see the height differences with the AFM within every structure and so that the modified structure's rigidity would be enforced by a border of unmodified canvas.  
We decided to template the L-DNA on the interior of the template.  This decision was made for a couple reasons: to be able to see the height differences with the AFM within every structure and so that the modified structure's rigidity would be enforced by a border of unmodified canvas.  


(See Approach of Large)
[[Biomod/2012/Harvard/BioDesign/methods|Details of Large Canvas Approach]]


Given below, we see the 375 SST strands (each of 42 base pairs - see -Introduction link) which form our large template.
Given below, we see the 375 SST strands (each of 42 base pairs - see -Introduction link) which form our large template.
Line 26: Line 24:
[[Image: LgTemplate.png|300px]]
[[Image: LgTemplate.png|300px]]


Our L-DNA was designed to form a central structure, patterened to form this structure (represented in green) on top of the blue template.
Our L-DNA was designed to form a central structure, patterned to form this structure (represented in green) on top of the blue template.
   
   


Revision as of 19:59, 26 October 2012

<html>

<head>

<link href='http://fonts.googleapis.com/css?family=Open+Sans' rel='stylesheet' type='text/css'>

</head>



<style>

/*BUT ACTUALLY*/ body { 

 font-family: 'Open Sans', sans-serif;
 overflow-y: scroll;

}

.container { 

 background-color: #ffffff;
 margin-top:0px

} .OWWNBcpCurrentDateFilled { display: none; }

h5 { 

 font-family: 'Open Sans', sans-serif;
 font-size: 11px;
 font-style: normal;
 text-align: center;
 margin:0px;
 padding:0px;

}

  1. column-content

{ 

 width: 0px; 
 float: left; 
 margin: 0 0 0 0;
 padding: 0;

} .firstHeading { 

 display:none;
 width:0px;

}

  1. column-one

{ 

 display:none; 
 width:0px;
 background-color: #ffffff;

}

  1. globalWrapper

{ 

 width: 900px;
 background-color: #ffffff;
 margin-left: auto;
 margin-right: auto

}

  1. content

{ 

 margin: 0 0 0 0;
 align: center;
 padding: 12px 12px 12px 12px;
 width: 876px;
 background-color: #ffffff; border: 0;

}

  1. bodyContent

{ 

 width: 850px;
 align: center;
 background-color: #fffffff;

}

  1. column-content

{ 

 width: 900px;
 background-color: #ffffff;

}

  1. footer

{ 

 position: center;
 width: 900px;

} @media screen { 

   body { background: #000000 0 0 no-repeat;  /* changed default background */ }

}

  1. menu

{ 

 position: fixed;
 float: left;
 width: 180px;
 padding: 10px;
 background-color: #FFFFFF;

}

  1. pagecontent

{ 

 float: right;
 width: 620px;
 margin-left: 300px;
 min-height: 400px

}

  1. toc { display: none; }

/*Expanding list*/ ul { list-style: none; }

  1. exp li ul { display: none; }
  2. exp li:hover ul { display: block; }
  3. exp li a:active ul { display: block; }

a:link {color:#FF6060;} a:visited {color:#FF6060;} /* visited link */ a:hover {color:#B24343;} /* mouse over link */ a:active {color:#B24343; } /* selected link */

</style> </html>

Project Specifications


Our final result was a 10 helix x 14 turn L-DNA sheet connected to the center of a 24 helix by 29 turn D-DNA template. In principle, we could detach this L-DNA layer by addition of a nuclease to digest the template layer and isolate the L-DNA layer as L-DNA is resistant to nucleases. However, due to time constraints as well as the ability to show the templating, we have imaged our results with the template attached.

The L-DNA layer is formed by formed by 2 unique, tessellating strands which are connected to the template by handles that stick out of the template. These handles are designed into the strands of the template as an extra piece. (Biomod/2012/Harvard/BioDesign/LDNA_layer | Approach to the L-DNA Layer)

The template was generated from a series of strands for a 24x29 SST canvas (using Motif 1 - LINK THIS)

designed by Bryan Wei et. al in an ongoing project (results not published). This canvas is about 105nm x 55 nm, a size that is easy to view by AFM.

[[AFM Image Here

Caption: the original 24x29 unmodified large template: well defined, easy to image

We decided to template the L-DNA on the interior of the template. This decision was made for a couple reasons: to be able to see the height differences with the AFM within every structure and so that the modified structure's rigidity would be enforced by a border of unmodified canvas.

Details of Large Canvas Approach

Given below, we see the 375 SST strands (each of 42 base pairs - see -Introduction link) which form our large template.

Our L-DNA was designed to form a central structure, patterned to form this structure (represented in green) on top of the blue template.



To bind to the L-DNA template, we had designed handles coming off of the template at these locations, to grab the complementary handle of one set of L-DNA.



The first anneal was with for the template in the same pot as the first L-DNA set of strands (heated at 90C down). We also tried forming the structure first and then adding in the first set of ribbons. For other procedural,(See protocols)


After the first anneal, the second strand is added and then re-annealed but at a lower temperature (40C)- one that won't melt the strand. We designed the L-DNA layer sequences to have a lower anneal temperature than the template below it(See LDNA template design)

And our final product:

Link Product

Retrieved from "https://openwetware.org/mediawiki/index.php?title=Biomod/2012/Harvard/BioDesign/design&oldid=644317"