Difference between revisions of "Biomod/2011/Slovenia/BioNanoWizards"

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<div class="entry"><span style="font-family: Arial;">Nucleic
 
<div class="entry"><span style="font-family: Arial;">Nucleic
 
acid nanostructural design is a powerful tool for constructing complex
 
acid nanostructural design is a powerful tool for constructing complex
assemblies of different shapes that can be addressed at nanometer
+
assemblies of different shapes that can be addressed with nanometer
 
resolution. For technological applications DNA origami has to be
 
resolution. For technological applications DNA origami has to be
 
functionalized in different ways and at selected positions. We
 
functionalized in different ways and at selected positions. We
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which increases the density of integration and represents a
 
which increases the density of integration and represents a
 
technological platform for nanoelectronic components.
 
technological platform for nanoelectronic components.
</span><br style="font-family: Arial;"><br><br>
+
</span><br style="font-family: Arial;"><br>
  
  
<iframe width="853" height="480" src="http://www.youtube.com/embed/zpa1YJXFAuk?rel=0" frameborder="0" align: middle; allowfullscreen></iframe><br><br>
+
<iframe width="853" height="480" src="http://www.youtube.com/embed/zpa1YJXFAuk?rel=0" frameborder="0"
 +
allowfullscreen></iframe><br><br><br>
  
  
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   <li>Explore the feasibility of preparing vertical DNA origami
 
   <li>Explore the feasibility of preparing vertical DNA origami
 
stacks using DNA or protein tethers for potential applications.<br>
 
stacks using DNA or protein tethers for potential applications.<br>
    <br>
 
 
     <br>
 
     <br>
 
   </li>
 
   </li>
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<span style="font-weight: bold;">a)</span> We
 
<span style="font-weight: bold;">a)</span> We
 
demonstrated proof of the principle for the use of DNA-binding
 
demonstrated proof of the principle for the use of DNA-binding
protein domains for adressing specific positions on DNA origami
+
protein domains for addressing specific positions on DNA origami
 
rectangles and introducting selected functional protein domains<br>
 
rectangles and introducting selected functional protein domains<br>
 
<span style="font-weight: bold;">b)</span> We
 
<span style="font-weight: bold;">b)</span> We
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   <li>Solve in vitro solubility problem of ZFPs, which is
 
   <li>Solve in vitro solubility problem of ZFPs, which is
 
essential for manufacturing protein-derivatized DNA origami. We
 
essential for manufacturing protein-derivatized DNA origami. We
achieved this by the addition of GST and MBP domains.We constructed,
+
achieved this by the addition of GST and MBP domains.We constructed,  
 
expressed and purified 11 different combinations of short and long ZFPs
 
expressed and purified 11 different combinations of short and long ZFPs
 
fused to other protein domains.</li>
 
fused to other protein domains.</li>
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protein (mCitrine) and Renilla luciferase (RLuc) that can sense the
 
protein (mCitrine) and Renilla luciferase (RLuc) that can sense the
 
proximity of their DNA-bound positions up to 10 nm distance and
 
proximity of their DNA-bound positions up to 10 nm distance and
generates optical signals without external illumination.</li>
+
generate optical signals without external illumination.</li>
 
   <li>Experimentaly determine the selectivity of long zinc finger
 
   <li>Experimentaly determine the selectivity of long zinc finger
 
domain chimeras for their DNA origami attachment staples using
 
domain chimeras for their DNA origami attachment staples using
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   <li>Design DNA biding staples for DNA-tethered vertical stacks.</li>
 
   <li>Design DNA biding staples for DNA-tethered vertical stacks.</li>
 
   <li>Prepare and purify twin ZFP protein chimeras as DNA origami
 
   <li>Prepare and purify twin ZFP protein chimeras as DNA origami
tethers.<br>
+
tethers.
 
     <br>
 
     <br>
 
   </li>
 
   </li>
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applications</span></big></big></big><br>
 
applications</span></big></big></big><br>
 
<span style="font-family: Arial;"><br>
 
<span style="font-family: Arial;"><br>
Our results <span style="font-weight: bold;">provides the
+
Our results <span style="font-weight: bold;">provide the
 
foundation for many real world potential applications</span>.The
 
foundation for many real world potential applications</span>.The
 
ability of DNA origami to fold into almost any desired shape combined
 
ability of DNA origami to fold into almost any desired shape combined

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<div id="page" class="container"> <div id="marketing"> <p class="text1">Our project in 5 minutes</p> <p class="text2"><a

href="http://openwetware.org/wiki/Biomod/2011/Slovenia/BioNanoWizards/tour">Take

Tour</a></p> </div> <div id="content"> <div class="post"> <div class="entry"><span style="font-family: Arial;">Nucleic acid nanostructural design is a powerful tool for constructing complex assemblies of different shapes that can be addressed with nanometer resolution. For technological applications DNA origami has to be functionalized in different ways and at selected positions. We significantly extend the repertoire of available modifiers by "DNA origami add-ons", introducing DNA-binding protein domains, which can be selected from hundreds of modular zinc finger proteins (ZFPs). We modified DNA origami by site-specific incorporation of binding staples that contain the recognition site for different ZFPs, thus replacing the need for chemical modifications with self-assembly. An additional advantage of using proteins for DNA origami functionalization is the ability to prepare genetic fusions with variable protein functional domains. Specific binding of ZFP-fusions to DNA origami was demonstrated by AFM. Further step towards applications was provided by the idea and experimental demonstration of vertical DNA origami stacks that can arrange functionalized DNA origami layers in a defined order, which increases the density of integration and represents a technological platform for nanoelectronic components. </span><br style="font-family: Arial;"><br>


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<big style="font-family: Arial;"><big><big><span

style="color: black; font-weight: bold;">Goals of the project</span></big></big></big><br>

<span style="font-family: Arial;"><br> </span> <ul>

 <li>Explore the potential of DNA-binding proteins (zinc finger

proteins - ZFPs) for the versatile and multiple position-specific addressing on DNA origami.</li>

 <li>Explore the feasibility of preparing vertical DNA origami

stacks using DNA or protein tethers for potential applications.<br>

   <br>
 </li>

</ul> <big style="font-family: Arial;"><big><big><span

style="color: black; font-weight: bold;">Achievements</span></big></big></big><br>

<span style="font-family: Arial;"><br> <span style="font-weight: bold;">a)</span> We demonstrated proof of the principle for the use of DNA-binding protein domains for addressing specific positions on DNA origami rectangles and introducting selected functional protein domains<br> <span style="font-weight: bold;">b)</span> We designed and experimentally confirmed formation of verticaly stacked DNA origami layers<br> <br> <img style="width: 890px; height: 229px; margin-bottom: 10px;"

alt="" src="http://openwetware.org/images/2/2b/Uvodna.png"><br>

<br> </span> <div style="text-align: left;"><big

style="font-family: Arial;"><span
style="color: black; font-weight: bold;">Those results would

not have been possible without solving many smaller challenges:</span></big><br> </div> <span style="font-family: Arial;"><br> </span> <ul>

 <li>Solve in vitro solubility problem of ZFPs, which is

essential for manufacturing protein-derivatized DNA origami. We achieved this by the addition of GST and MBP domains.We constructed, expressed and purified 11 different combinations of short and long ZFPs fused to other protein domains.</li>

 <li>Prepare functional fusions of ZFPs with yellow fluorescent

protein (mCitrine) and Renilla luciferase (RLuc) that can sense the proximity of their DNA-bound positions up to 10 nm distance and generate optical signals without external illumination.</li>

 <li>Experimentaly determine the selectivity of long zinc finger

domain chimeras for their DNA origami attachment staples using AlphaScreen and electrophoretic mobility shift assay (EMSA).</li>

 <li>Design attachment staples for binding ZFP chimeras to DNA

origami.</li>

 <li>Design DNA biding staples for DNA-tethered vertical stacks.</li>
 <li>Prepare and purify twin ZFP protein chimeras as DNA origami

tethers.

   <br>
 </li>

</ul> <span style="font-family: Arial;"><br> </span><big style="font-family: Arial;"><big><big><span

style="color: black; font-weight: bold;">Relevance and

applications</span></big></big></big><br> <span style="font-family: Arial;"><br> Our results <span style="font-weight: bold;">provide the foundation for many real world potential applications</span>.The ability of DNA origami to fold into almost any desired shape combined with protein functionality at specific positions represents the perfect marriage for countless applications. Large number of available DNA binding protein domains show promise for simultaneous and specific position-specific addressing of DNA origami.</span><br

style="font-family: Arial;">

<br style="font-family: Arial;"> <span style="font-family: Arial;">We expect that ZFP chimeras will push forward the development of high-tech applications such as <a

href="http://openwetware.org/wiki/Biomod/2011/Slovenia/BioNanoWizards/applabonchip">lab-on-a-nanochip</a>,

novel types of <a

href="http://openwetware.org/wiki/Biomod/2011/Slovenia/BioNanoWizards/appbiosynthteticcompartments">artificial

biosynthetic organelles</a>, light emitting <a

href="http://openwetware.org/wiki/Biomod/2011/Slovenia/BioNanoWizards/appbiosensors">nanosensors</a>

and many others. We extended DNA origami assemblies into the third dimension by formation of vertical stacks where the vertical arrangement is formed based either on DNA or protein tethers. Vertical stacking of DNA origami allows combinations of differently derivatized (e.g. metalized, carbon nanotube derivatized) DNA layers for the formation of various <a

href="http://openwetware.org/wiki/Biomod/2011/Slovenia/BioNanoWizards/appnanoelectronics">nanoelectronic

components</a>, such as nanocapacitors, nanobatteries, ID tags and other devices with dimensions at the nanoscale.<br> </span><span style="font-family: Arial;"></span><span

style="font-family: Arial;"></span><br>

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