Biomod/2011/Slovenia/BioNanoWizards

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*Team name: BioNanoWizards
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<html>
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*Institution: National institute of chemistry, Ljubljana, Slovenia
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<head>
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*Faculty mentor: Roman Jerala
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  <style>
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*Postdoc mentor: Iva Hafner Bratkovič
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#globalWrapper {width: 1000px; padding:0; border:0; margin:0 auto 0 auto;}
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*Team members:
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@media screen { body { background: #E3E3E3 0 0 0 0 no-repeat; /* changed default background */ } }
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**Vid Kočar
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#column-one {display:none; width:0px;}
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**Jernej Turnšek
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**Marko Verce
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</head>
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<body>
 +
<div id="wrapper">
 +
<div id="headercss" class="container">
 +
<div id="logo">
 +
<div id="logolinknabiomod">
 +
<p><a href="http://openwetware.org/wiki/Biomod/2011">&lt;--
 +
Back to BioMod 2011</a></p>
 +
</div>
 +
<div id="jebenimeni">
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<!-- Start PureCSSMenu.com MENU -->
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<ul class="pureCssMenu pureCssMenum">
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href="http://openwetware.org/wiki/Biomod/2011/Slovenia/BioNanoWizards">Home</a></li>
 +
  <li class="pureCssMenui"><a class="pureCssMenui"
 +
href="#"><span>Idea</span></a><!--[if lte IE 6]><table><tr><td><![endif]-->
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 +
      <li class="pureCssMenui"><a class="pureCssMenui"
 +
href="http://openwetware.org/wiki/Biomod/2011/Slovenia/BioNanoWizards/ideastateoftheart">State
 +
of the art</a></li>
 +
      <li class="pureCssMenui"><a class="pureCssMenui"
 +
href="http://openwetware.org/wiki/Biomod/2011/Slovenia/BioNanoWizards/ideaproteinaddons">Protein
 +
add-ons</a></li>
 +
<!-- TUKI SEM IZBRISAL PROTEIN CHIMERAS -->
 +
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href="http://openwetware.org/wiki/Biomod/2011/Slovenia/BioNanoWizards/ideaverticalstacks">Vertical
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stacks</a></li>
 +
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 +
<!--[if lte IE 6]></td></tr></table></a><![endif]--></li>
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  <li class="pureCssMenui"><a class="pureCssMenui"
 +
href="#"><span>Results</span></a><!--[if lte IE 6]><table><tr><td><![endif]-->
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    <ul class="pureCssMenum">
 +
      <li class="pureCssMenui"><a class="pureCssMenui"
 +
href="http://openwetware.org/wiki/Biomod/2011/Slovenia/BioNanoWizards/resultssummary">Summary</a></li>
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 +
href="#"><span>Protein add-ons</span></a><!--[if lte IE 6]><table><tr><td><![endif]-->
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 +
          <li class="pureCssMenui"><a
 +
class="pureCssMenui"
 +
href="http://openwetware.org/wiki/Biomod/2011/Slovenia/BioNanoWizards/resultssolublezfp">Soluble
 +
ZFPs</a></li>
 +
          <li class="pureCssMenui"><a
 +
class="pureCssMenui"
 +
href="http://openwetware.org/wiki/Biomod/2011/Slovenia/BioNanoWizards/resultstightbindingzfp">Tight
 +
binding ZFPs</a></li>
 +
          <li class="pureCssMenui"><a
 +
class="pureCssMenui"
 +
href="http://openwetware.org/wiki/Biomod/2011/Slovenia/BioNanoWizards/resultsfunctionalizedzfp">Functionalized
 +
ZFPs</a></li>
 +
          <li class="pureCssMenui"><a
 +
class="pureCssMenui"
 +
href="http://openwetware.org/wiki/Biomod/2011/Slovenia/BioNanoWizards/protdnahybrid">Protein-DNA
 +
origami hybrid</a></li>
 +
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 +
<!--[if lte IE 6]></td></tr></table></a><![endif]--></li>
 +
      <li class="pureCssMenui"><a class="pureCssMenui"
 +
href="#"><span>Vertical stacks</span></a><!--[if lte IE 6]><table><tr><td><![endif]-->
 +
        <ul class="pureCssMenum">
 +
          <li class="pureCssMenui"><a
 +
class="pureCssMenui"
 +
href="http://openwetware.org/wiki/Biomod/2011/Slovenia/BioNanoWizards/resultsdnatethers">DNA
 +
tethers</a></li>
 +
          <li class="pureCssMenui"><a
 +
class="pureCssMenui"
 +
href="http://openwetware.org/wiki/Biomod/2011/Slovenia/BioNanoWizards/resultsproteintethers">Protein
 +
tethers</a></li>
 +
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 +
<!--[if lte IE 6]></td></tr></table></a><![endif]--></li>
 +
    </ul>
 +
<!--[if lte IE 6]></td></tr></table></a><![endif]--></li>
 +
  <li class="pureCssMenui"><a class="pureCssMenui"
 +
href="#"><span>Discussion</span></a><!--[if lte IE 6]><table><tr><td><![endif]-->
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 +
      <li class="pureCssMenui"><a class="pureCssMenui"
 +
href="http://openwetware.org/wiki/Biomod/2011/Slovenia/BioNanoWizards/discussion">Discussion</a></li>
 +
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 +
href="#"><span>Applications</span></a><!--[if lte IE 6]><table><tr><td><![endif]-->
 +
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 +
          <li class="pureCssMenui"><a
 +
class="pureCssMenui"
 +
href="http://openwetware.org/wiki/Biomod/2011/Slovenia/BioNanoWizards/applabonchip">Lab-on-a-nanochip</a></li>
 +
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 +
class="pureCssMenui"
 +
href="http://openwetware.org/wiki/Biomod/2011/Slovenia/BioNanoWizards/appbiosynthteticcompartments">Biosynthetic
 +
compartments</a></li>
 +
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 +
class="pureCssMenui"
 +
href="http://openwetware.org/wiki/Biomod/2011/Slovenia/BioNanoWizards/appbiosensors">Biosensors</a></li>
 +
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 +
class="pureCssMenui"
 +
href="http://openwetware.org/wiki/Biomod/2011/Slovenia/BioNanoWizards/appnanoelectronics">Nanoelectronics</a></li>
 +
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 +
      </li>
 +
    </ul>
 +
<!--[if lte IE 6]></td></tr></table></a><![endif]--></li>
 +
  <li class="pureCssMenui"><a class="pureCssMenui"
 +
href="#"><span>Methods</span></a><!--[if lte IE 6]><table><tr><td><![endif]-->
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 +
      <li class="pureCssMenui"><a class="pureCssMenui"
 +
href="#"><span>DNA origami design</span></a><!--[if lte IE 6]><table><tr><td><![endif]-->
 +
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 +
          <li class="pureCssMenui"><a
 +
class="pureCssMenui"
 +
href="http://openwetware.org/wiki/Biomod/2011/Slovenia/BioNanoWizards/methgeneraldesignstrategy">General
 +
design strategy</a></li>
 +
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 +
class="pureCssMenui"
 +
href="http://openwetware.org/wiki/Biomod/2011/Slovenia/BioNanoWizards/methmodifications%20">Modifications</a></li>
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 +
<!--[if lte IE 6]></td></tr></table></a><![endif]--></li>
 +
      <li class="pureCssMenui"><a class="pureCssMenui"
 +
href="http://openwetware.org/wiki/Biomod/2011/Slovenia/BioNanoWizards/methplasmidconst">Plasmid
 +
construction</a></li>
 +
      <li class="pureCssMenui"><a class="pureCssMenui"
 +
href="http://openwetware.org/wiki/Biomod/2011/Slovenia/BioNanoWizards/methprotprodandisol">Protein
 +
production and isolation</a></li>
 +
      <li class="pureCssMenui"><a class="pureCssMenui"
 +
href="#"><span>Protein characterization</span></a><!--[if lte IE 6]><table><tr><td><![endif]-->
 +
        <ul class="pureCssMenum">
 +
          <li class="pureCssMenui"><a
 +
class="pureCssMenui"
 +
href="http://openwetware.org/wiki/Biomod/2011/Slovenia/BioNanoWizards/methemsa">EMSA</a></li>
 +
          <li class="pureCssMenui"><a
 +
class="pureCssMenui"
 +
href="http://openwetware.org/wiki/Biomod/2011/Slovenia/BioNanoWizards/methalphascreen">AlphaScreen
 +
assay</a></li>
 +
          <li class="pureCssMenui"><a
 +
class="pureCssMenui"
 +
href="http://openwetware.org/wiki/Biomod/2011/Slovenia/BioNanoWizards/methbret">BRET
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assay</a></li>
 +
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 +
<!--[if lte IE 6]></td></tr></table></a><![endif]--></li>
 +
      <li class="pureCssMenui"><a class="pureCssMenui"
 +
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<div id="page" class="container">
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<div id="marketing">
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<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>
 +
 
 +
 
 +
<iframe width="853" height="480" src="http://www.youtube.com/embed/zpa1YJXFAuk?rel=0" frameborder="0"
 +
allowfullscreen></iframe><br><br><br>
 +
 
 +
 
 +
<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>
 +
<table
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Current revision

Our project in 5 minutes

Take Tour

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.




Goals of the project
  • Explore the potential of DNA-binding proteins (zinc finger proteins - ZFPs) for the versatile and multiple position-specific addressing on DNA origami.
  • Explore the feasibility of preparing vertical DNA origami stacks using DNA or protein tethers for potential applications.

Achievements

a) 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
b) We designed and experimentally confirmed formation of verticaly stacked DNA origami layers
Those results would not have been possible without solving many smaller challenges:
  • 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.
  • 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.
  • Experimentaly determine the selectivity of long zinc finger domain chimeras for their DNA origami attachment staples using AlphaScreen and electrophoretic mobility shift assay (EMSA).
  • Design attachment staples for binding ZFP chimeras to DNA origami.
  • Design DNA biding staples for DNA-tethered vertical stacks.
  • Prepare and purify twin ZFP protein chimeras as DNA origami tethers.

Relevance and applications

Our results provide the foundation for many real world potential applications.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.

We expect that ZFP chimeras will push forward the development of high-tech applications such as lab-on-a-nanochip, novel types of artificial biosynthetic organelles, light emitting nanosensors 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 nanoelectronic components, such as nanocapacitors, nanobatteries, ID tags and other devices with dimensions at the nanoscale.

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