Biomod/2013/StJohns/results
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We have successfully synthesized and characterized this structure with (‘sticky’) and without (‘blunt’) single-stranded binding sites. Below are AFM images of the 100nm armed claws. <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>
Additionally, we have used gel electrophoresis to characterize the binding of Sticky/Blunt DO to Sticky/WT capsids.
![](https://s3-us-west-2.amazonaws.com/oww-files-thumb/3/3a/Lukemanlab-2013-0001.png/400px-Lukemanlab-2013-0001.png)
‘sticky’ DO bind sticky capsids strongly;
however, blunt DO binds sticky capsids.
We use FRET as a molecular ruler to measure the distance between the claw and capsid during binding.
The following gel images demonstrate FRET fluoresnce.
<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)