Biomod/2013/StJohns/results
<html>
<head>
<link href='http://fonts.googleapis.com/css?family=Open+Sans' rel='stylesheet' type='text/css'>
</head>
<style>
body {
font-family: 'Trebuchet MS', 'Open Sans', sans-serif; overflow-y: auto;
}
.container {
background-color: #ffffff; margin-top:0px
} .OWWNBcpCurrentDateFilled { display: none; }
h5 {
font-family: 'Trebuchet MS', 'Open Sans', sans-serif; font-size: 11px; font-style: normal; text-align: center; margin:0px; padding:0px;
}
- column-content
{
width: 0px; float: left; margin: 0 0 0 0; padding: 0;
} .firstHeading {
display:none; width:0px;
}
- column-one
{
display:none; width:0px; background-color: #ffffff;
}
- globalWrapper
{
width: 1024px; background-color: #ffffff; margin-left: auto; margin-right: auto
}
- content
{
margin: 0 0 0 0; align: center; padding: 12px 12px 12px 12px; width: 1000px; background-color: #ffffff; border: 0;
}
- bodyContent
{
width: 974px; align: justify; background-color: #fffffff;
}
- column-content
{
width: 1024px; background-color: #ffffff;
}
- footer
{
position: absolute; bottom: 0; width: 1024px;
}
- menu
{
position: fixed; float: left; width: 180px; padding: 10px; background-color: #FFFFFF;
}
- resolutionwarning
{
display: none; text-align: center;
}
- pagecontent
{
text-align: justify; float: right; width: 744px; margin-left: 300px; min-height: 400px
}
- toc { display: none; }
@media all {
body { background: #ffffff 0 0 no-repeat;}
}
/*Expanding list*/ ul { list-style: none; }
- exp li ul { display: none; }
- exp li:hover ul { display: block; }
- exp li a:active ul { display: block; }
a:link {color:#007788;} /*unvisited link*/ a:visited {color:#007788;} /* visited link */ a:hover {color:#00ccff;} /* mouse over link */ a:active {color:#00ccff;} /* selected link */
</style> </html>
<html><a href="http://lukemanlab.org"><img src="http://openwetware.org/images/thumb/f/f9/Lukemanlab-toehold-conga-nanny-header.jpg/180px-Lukemanlab-toehold-conga-nanny-header.jpg"></a></html>
Summary
- We have synthesized versions of the claw with (‘sticky’) and without (‘blunt’) single-stranded binding elements.
- We have synthesized versions of the claw with and without fluorescent tags for FRET analysis.
We have visualized the above versions of the claw on AFM to show that they take the predicted shape.
- We have shown that the above versions of the claw form tight bands on a gel, indicating a single primary product of the anneal.
- We have verified that FRET-tagged origami can be visualized in a gel, providing easy visual discrimination between differently-tagged versions of the claw.
- We have demonstrated a binding interaction between the functionalized claw and functionalized capsid as well as a lack of interaction between the nonfunctionalized claw and capsid.
- We have not been able to differentiate bound and unbound complexes via DLS.
- We have generated and isolated FAB fragments for use as binding elements in future claw designs.
- We have demonstrated the potential for selecting claws based on their avidity using a chromatography augmented with photocleavable elements.
Data
Claw Visualization
Below are AFM images of the claws alone, with and without binding elements. <html><center><table><tbody align="center"><tr><td><img src="http://openwetware.org/images/thumb/6/66/Lukemanlab-Bluntclaw_afm.png/200px-Lukemanlab-Bluntclaw_afm.png"></td><td><img src="http://openwetware.org/images/thumb/9/9f/Lukemanlab-Stickyclaw_afm.png/200px-Lukemanlab-Stickyclaw_afm.png"></td></tr><tr><td>"Blunt" claw</td><td>"Sticky" claw</td></tr></tbody></table></center></html>
Binding Interaction
We used gel electrophoresis to characterize the binding interaction between origami structures and capsids with and without binding elements.
‘sticky’ DO bind sticky capsids strongly;
however, blunt DO binds sticky capsids.
FRET
<html> <center> <table> <tbody align="center"> <tr> <td> <img src="http://openwetware.org/images/thumb/d/d5/1a_ch1_FRET.tif/345px-1a_ch1_FRET.tif.png"> </td> <td> <img src="http://openwetware.org/images/thumb/6/69/1a_ch2_DONOR.tif/345px-1a_ch2_DONOR.tif.png"> </td> <td> <img src="http://openwetware.org/images/thumb/c/ce/1a_ch3_ACCEPTOR.tif/345px-1a_ch3_ACCEPTOR.tif.png"> </td> </tr> <tr> <td>FRET</td><td>DONOR</td><td>ACCEPTOR</td> </tr> </tbody> </table> </center> </html>
To determine FRET, FRET intensity - DONOR intensity - ACCEPTOR intensity
DA(i,j) = DA(i,j) - beta_leak * DD(i,j) - beta_dir * AA (i,j)
