Biomod/2011/Slovenia/BioNanoWizards/ideastateoftheart: Difference between revisions

From OpenWetWare
Jump to navigationJump to search
(New page: <html> <head> <style> #globalWrapper {width: 1000px; padding:0; border:0; margin:0 auto 0 auto;} @media screen { body { background: #E3E3E3 0 0 0 0 no-repeat; /* changed default backgrou...)
 
No edit summary
 
(12 intermediate revisions by 3 users not shown)
Line 484: Line 484:
<div class="entry"><big><big><big><big><span
<div class="entry"><big><big><big><big><span
  style="color: black; font-weight: bold;">State of the art</span></big></big></big></big><br>
  style="color: black; font-weight: bold;">State of the art</span></big></big></big></big><br>
<br>
<br><br>
<span style="font-family: Arial;">Natural biopolymers can
<span style="font-family: Arial;">Natural biopolymers can
form the most complex and variable
form the most complex and variable
Line 491: Line 491:
represents a formidable challenge, even today. The first successful
represents a formidable challenge, even today. The first successful
artificial nanostructures were built by Nadrian Seeman who used nucleic
artificial nanostructures were built by Nadrian Seeman who used nucleic
acids to form nanostructures based on nucleotide pairing (N. C. Seeman,
acids to form nanostructures based on nucleotide pairing (Seeman, 1982).
<span style="font-style: italic;">Journal of Theoretical
biology</span> 1982).
</span><br style="font-family: Arial;">
</span><br style="font-family: Arial;">
<br style="font-family: Arial;">
<br style="font-family: Arial;">
<span style="font-family: Arial;">
<span style="font-family: Arial;">
Debut of the DNA origami technique (Rothemund, <span
Debut of the DNA origami technique (Rothemund, 2006)
style="font-style: italic;">Nature</span> 2006)
spurred major advancement of this field. Desired DNA origami objects
spurred major advancement of this field. Desired DNA origami objects
are built by raster filling of a long single stranded DNA molecule into
are built by raster filling of a long single stranded DNA molecule into
Line 513: Line 510:
enhance DNA with advanced chemical and physical properties. DNA origami
enhance DNA with advanced chemical and physical properties. DNA origami
structures already served as a template for spatial positioning of
structures already served as a template for spatial positioning of
nanoparticles such as quantum dots (Bui et al, <span
nanoparticles such as quantum dots (Bui, 2010),
style="font-style: italic;">Nano Lett</span> 2010) ,
metal nanoparticles (Pal, 2010; Hung, 2010), carbon nanotubes (Maune, 2010) and proteins via biotin-streptavidin interactions (Sacca, 2010;
metal nanoparticles (Pal et al, <span style="font-style: italic;">Angewandte</span>
Shen, 2009; Numajiri, 2010) with nanometer precision.
2010; Hung et al, <span style="font-style: italic;">Nature
Nanotech</span> 2010), carbon nanotubes (Maune et al., <span
style="font-style: italic;">Nature Nanotech</span>
2010) and proteins via biotin-streptavidin interactions (Sacca et al., <span
style="font-style: italic;">Angewandte</span> 2010;
Shen et al., <span style="font-style: italic;">JACS</span>
2009; Numajiri et al, <span style="font-style: italic;">Chem
Commun</span> 2010) with nanometer precision.
</span><br style="font-family: Arial;">
</span><br style="font-family: Arial;">
<br style="font-family: Arial;">
<br style="font-family: Arial;">
<span style="font-family: Arial;">
<span style="font-family: Arial;">
The main advantage of DNA origami is a precise control over the
The main advantage of DNA origami is precise control over the
position of each staple strand used in the model. Since staple strands
position of each staple strand used in the model. Since staple strands
have unique nucleotide sequences, they can serve as specific attachment
have unique nucleotide sequences, they can serve as specific attachment
Line 534: Line 523:
with oligonucleotides that bind to extended parts of staple strands.
with oligonucleotides that bind to extended parts of staple strands.
These segments of staple strands do not anneal to long single stranded
These segments of staple strands do not anneal to long single stranded
DNA but protrude perpendicularly to the surface of DNA origami.
DNA but protrude perpendicularly from the surface of DNA origami.
</span>
</span>
<table style="margin-top: 20px; margin-bottom: 20px; width: 794px;"
<table style="margin-top: 30px; margin-bottom: 30px; width: 100%;"
  border="0" cellspacing="0">
  border="0" cellspacing="0">
   <tbody>
   <tbody>
     <tr>
     <tr>
       <td style="text-align: center;"><img
       <td style="text-align: left;"><img
  style="font-family: Arial; width: 794px; height: 574px;" alt=""
  style="font-family: Arial; width: 890px; height: 600px;" alt=""
  src="http://openwetware.org/images/b/b8/Slika15.png"></td>
  src="http://openwetware.org/images/3/30/Slika21nova.png"></td>
     </tr>
     </tr>
     <tr style="font-family: Arial;">
     <tr style="font-family: Arial;">
       <td style="text-align: justify;"><span
       <td style="text-align: justify;"><span
  style="font-weight: bold;">Current available DNA origami
  style="font-weight: bold;">Figure 1: DNA origami can be modified at selected positions using oligonucleotides, aptamers or chemical modification of staples. </span>Advantages and drawbacks are listed for each approach.
modifications for spatial positioning of various nanoparticles</span>
       </td>
       </td>
     </tr>
     </tr>
Line 554: Line 542:
<span style="font-family: Arial;">
<span style="font-family: Arial;">
Other popular techniques include protein-ligand interactions based on
Other popular techniques include protein-ligand interactions based on
modification of staple strands with biotin which strongly binds to
modification of staple strands with biotin, which strongly binds to
streptavidin. This approach requires individual synthesis of chemically
streptavidin. This approach requires individual synthesis of chemically
modified staple strands and selected nanoparticles. The bottleneck of
modified staple strands and selected nanoparticles. The bottleneck of
Line 561: Line 549:
the variability of molecules or particles that can be simultaneusly
the variability of molecules or particles that can be simultaneusly
bound to the DNA origami. Therefore, for the successful design of
bound to the DNA origami. Therefore, for the successful design of
complex systems involving many different chemical species a more
complex systems involving many different chemical species, a more
universal method of binding should be developed.
universal method of binding should be developed.
</span><br style="font-family: Arial;">
</span><br style="font-family: Arial;"><br>
<big style="font-family: Arial;"><big><big><big><span
<big style="font-family: Arial;"><big><big><big><span
  style="color: black; font-weight: bold;"></span></big></big></big></big><span
  style="color: black; font-weight: bold;"></span></big></big></big></big><span
Line 579: Line 567:
<br style="font-family: Arial;">
<br style="font-family: Arial;">
<span style="font-family: Arial;">
<span style="font-family: Arial;">
Therefore the use of protein domains as DNA add-ons seem to have very
Therefore the use of protein domains as DNA add-ons seems to have very
interesting prospects. In our project from june until november 2011 we
interesting prospects. In our project from June until November 2011 we
designed a novel and universal approach for protein immobilization on
designed a novel and universal approach for protein immobilization on
the surface of DNA origami, which could provide a straightforward and
the surface of DNA origami, which could provide a straightforward and
affordable way of targeted spatial positioning. Check next page to see
affordable way of targeted spatial positioning. Check next page to see
the solution proposed by the BioNanoWizards team.
the solution proposed by the BioNanoWizards team.
</span><br style="font-family: Arial;">
</span><br style="font-family: Arial;"><br>
<br style="font-family: Arial;">
 
<span style="font-family: Arial;"></span><br>
<hr style="width: 100%; height: 2px;"><span
style="font-family: Arial; font-size: smaller;">
<ul>
<li>Bui H, Onodera C, Kidwell C, Tan Y, Graugnard E, Kuang W, Lee J, Knowlton WB, Yurke B, Hughes WL (2010) Programmable periodicity of quantum dot arrays with DNA origami nanotubes. <em>Nano Lett. </em>10:3367-72.</li>
<li>Hung AM, Micheel CM, Bozano LD, Osterbur LW, Wallraff GM, Cha JN (2010) Large-area spatially ordered arrays of gold nanoparticles directed by lithographically confined DNA origami. <em>Nat. Nanotechnol. </em>5:121-6.</li>
<li>Maune HT, Han SP, Barish RD, Bockrath M, Goddard III WA, Rothemund PW, Winfree E (2010) Self-assembly of carbon nanotubes into two-dimensional geometries using DNA origami templates. <em>Nat. Nanotechnol. </em>5:61-6.</li>
<li>Numajiri K, Kimura M, Kuzuya A, Komiyama M (2010)Stepwise and reversible nanopatterning of proteins on a DNA origami scaffold. <em>Chem Commun</em>46:5127-9.</li>
<li>Pal S, Deng Z, Ding B, Yan H, Liu Y (2010) DNA-origami-directed self-assembly of discrete silver-nanoparticle architectures. <em>Angew. Chem.</em> 49:2700-4.</li>
<li>Rothemund PWK (2006) Folding DNA to create nanoscale shapes and patterns. <em>Nature </em>440: 297-302.</li>
<li>Sacca B, Meyer R, Erkelenz M, Kiko K, Arndt A, Schroeder H, Rabe KS, Niemeyer CM (2010) Orthogonal protein decoration of DNA origami. <em>Angew. Chem. </em>49: 9378-83.</li>
<li>Seeman  NC (1982)  Nucleic acid junctions and lattices. <em>J Theor Biol </em>499: 237-47.</li>
<li>Shen W, Zhong H, Neff D, Norton ML (2009) NTA directed protein nanopatterning on DNA Origami nanoconstructs. <em>J. Am. Chem. Soc. </em>131:6660-1.</li>
</ul>
 
<span style="font-family: Arial;"></span>
</div>
</div>
</div>
</div>

Latest revision as of 18:16, 2 November 2011

<html> <head> 

 <style>
  1. globalWrapper {width: 1000px; padding:0; border:0; margin:0 auto 0 auto;}

@media screen { body { background: #E3E3E3 0 0 0 0 no-repeat; /* changed default background */ } }

  1. column-one {display:none; width:0px;}
  2. contentSub {display:none; width:0px;}
  3. column-content {border:0px; width: 1000px; padding:0; margin:0;}

.firstHeading {display:none;}

  1. footer {display:none;}
  2. content {background-color: #e3e3e3; border:0; padding:0; margin:0;}
  3. bodyContent {background: none; border:0x; padding0; margin:0;}
  4. header{display:none;}
 </style>
 <style type="text/css">

/* Design by Free CSS Templates http://www.freecsstemplates.org Released for free under a Creative Commons Attribution 2.5 License

  • /

body { margin: 0; padding:0; background: #E3E3E3; font-family: Arial, Helvetica, sans-serif; font-size: 12px; color: #616161; } p, ul, ol { margin-top: 0; line-height: 180%; } ul, ol { } a { text-decoration: none; color: #274775; } a:hover { }

  1. wrapper {

margin: 0 auto; padding: 0; } .container { width: 1000px; margin: 0px auto; } /* Header */

  1. headercss {

width: 900px; height: 150px; margin: 0 auto; padding: 0px 50px; background: url(http://openwetware.org/images/c/cc/Img01.PNG) no-repeat left top; position: relative; z-index:10; } /* Logo */

  1. logo {

width: 800px; margin: 0 0 0 0; padding: 30px 0 0 0; }

  1. logolinknabiomod {

width: 800px; margin: 0 0 0 0; padding: 0 0 0 0; }

  1. logolinknabiomod h1, #logo p {

}

  1. logolinknabiomod h1 {

padding: 60px 0px 0px 0px; letter-spacing: -2px; font-size: 3.8em; background: none; }

  1. logolinknabiomod p {

margin: 0 0 0 0; padding: 0 0 0 0; letter-spacing: -1px; font: normal 14px Georgia, "Times New Roman", Times, serif; font-style: normal; color: #8e8e8e; } #logolinknabiomod p a { color: #8E8E8E; }

  1. logolinknabiomod a {

border: none; background: none; text-decoration: none; } /* Splash */

  1. splash {

height: 300px; } /* Menu */ /* Page */

  1. page {

width: 890px; margin: 0 auto; padding: 30px 55px; background: url(http://openwetware.org/images/e/e6/Lepidimg03.jpg) repeat-y left top; } /* Content */

  1. content {

float: left; width: 890px; padding: 0px 0px 0px 0px; background: none; } .post .entry { text-align: justify; font: Arial; letter-spacing: 0px; z-index:5; } /* Three Column Footer Content */

  1. footer-content {

background: url(http://openwetware.org/images/e/e3/Img04brezcrne.JPG) repeat-y left top; color: #BFBFBF; }

  1. footer-bg {

overflow: hidden; width: 890px; padding: 10px 55px 80px 55px; background: url(http://openwetware.org/images/0/06/Footerbrezozadja.jpg) no-repeat left bottom; }

  1. footer-content h2 {

margin: 0px; padding: 0px 0px 20px 0px; letter-spacing: -1px; text-transform: lowercase; font-size: 26px; color: #202020; }

  1. footer-content ul {

margin: 0px; padding: 0px 0px 0px 0px; }

  1. footer-content a {

color: #447ECF; }

  1. column1 {

float: left; width: 423px; margin: 0px 0px 0px 0px; text-align: justify; }

  1. column2 {

float: right; width: 423px; margin: 0px 0px 0px 0px; text-align: justify; } /* Footer */

  1. footerCSS {

height: 20px; width: 600px; padding: 0px 200px 0px 200px; font-family: Arial, Helvetica, sans-serif; }

  1. footerCSS p {

margin: 0; padding-top: 0px; line-height: normal; font-size: 9px; text-align: center; color: #202020; }

  1. footerCSS a {

color: #202020; }

  1. marketing {

overflow: hidden; margin-bottom: 30px; padding: 20px 0px 10px 0px; border-top: 1px solid #E3E3E3; border-bottom: 1px solid #E3E3E3; }

  1. marketing .text1 {

float: left; margin: 0px; padding: 0 0 0 100px; font-size: 34px; color: #345E9B; }

  1. marketing .text2 {

float: right; }

  1. marketing .text2 a {

display: block; width: 252px; height: 38px; padding: 15px 100px 0px 0px; background: url(http://openwetware.org/images/f/f4/Lepidimg07.jpg) no-repeat left top; letter-spacing: -2px; text-align: center; font-size: 30px; color: #ffffff; }

  1. jebenimeni {

width: 800px; height: 30px; padding: 45px 0 0 0;} <!-- Start PureCSSMenu.com STYLE -->

  1. pcm{display:none;}

ul.pureCssMenu ul{display:none} ul.pureCssMenu li:hover>ul{display:block} ul.pureCssMenu ul{position: absolute;left:-1px;top:98%;} ul.pureCssMenu ul ul{position: absolute;left:98%;top:-2px;} ul.pureCssMenu,ul.pureCssMenu ul { margin:0px; list-style:none; padding:0px 2px 2px 0px; background-color:#2A4B7D; background-repeat:repeat; border-color:#cccccc #111111 #111111 #cccccc; border-width:1px; border-style:solid; } ul.pureCssMenu table {border-collapse:collapse}ul.pureCssMenu { display:block; zoom:1; float: left; } ul.pureCssMenu ul{ width:260.40000000000003px; } ul.pureCssMenu li{ display:block; margin:2px 0px 0px 2px; font-size:0px; } ul.pureCssMenu a:active, ul.pureCssMenu a:focus { outline-style:none; } ul.pureCssMenu a, ul.pureCssMenu li.dis a:hover, ul.pureCssMenu li.sep a:hover { display:block; vertical-align:middle; background-color:#2A4B7D; border-width:1px; border-color:#2A4B7D; border-style:solid; text-align:left; text-decoration:none; padding:2px 5px 2px 10px; _padding-left:0; font:16px Trebuchet MS; color: #ffffff; text-decoration:none; cursor:default; } ul.pureCssMenu span{ overflow:hidden; } ul.pureCssMenu li { float:left; } ul.pureCssMenu ul li { float:none; } ul.pureCssMenu ul a { text-align:left; white-space:nowrap; } ul.pureCssMenu li.sep{ text-align:left; padding:0px; line-height:0; height:100%; } ul.pureCssMenu li.sep span{ float:none; padding-right:0; width:3px; height:100%; display:inline-block; background-color:#cccccc #111111 #111111 #cccccc; background-image:none;} ul.pureCssMenu ul li.sep span{ width:100%; height:3px; } ul.pureCssMenu li:hover{ position:relative; } ul.pureCssMenu li:hover>a{ background-color:#377D9F; border-color:#377D9F; border-style:solid; font:16px Trebuchet MS; color: #FFFFFF; text-decoration:none; } ul.pureCssMenu li a:hover{ position:relative; background-color:#377D9F; border-color:#377D9F; border-style:solid; font:16px Trebuchet MS; color: #FFFFFF; text-decoration:none; } ul.pureCssMenu li.dis a { color: #666 !important; } ul.pureCssMenu img {border: none;float:left;_float:none;margin-right:2px;width:16px; height:16px; } ul.pureCssMenu ul img {width:16px; height:16px; } ul.pureCssMenu img.over{display:none} ul.pureCssMenu li.dis a:hover img.over{display:none !important} ul.pureCssMenu li.dis a:hover img.def {display:inline !important} ul.pureCssMenu li:hover > a img.def {display:none} ul.pureCssMenu li:hover > a img.over {display:inline} ul.pureCssMenu a:hover img.over,ul.pureCssMenu a:hover ul img.def,ul.pureCssMenu a:hover a:hover ul img.def,ul.pureCssMenu a:hover a:hover img.over,ul.pureCssMenu a:hover a:hover a:hover img.over{display:inline} ul.pureCssMenu a:hover img.def,ul.pureCssMenu a:hover ul img.over,ul.pureCssMenu a:hover a:hover ul img.over,ul.pureCssMenu a:hover a:hover img.def,ul.pureCssMenu a:hover a:hover a:hover img.def{display:none} ul.pureCssMenu a:hover ul,ul.pureCssMenu a:hover a:hover ul{display:block} ul.pureCssMenu a:hover ul ul{display:none} ul.pureCssMenu span{ display:block; background-image:url(http://openwetware.org/images/5/50/Arr_white.gif); background-position:right center; background-repeat: no-repeat; padding-right:12px;} ul.pureCssMenu li:hover>a>span{ background-image:url(http://openwetware.org/images/6/6f/Arrv_white.gif); } ul.pureCssMenu a:hover span{ _background-image:url(http://openwetware.org/images/6/6f/Arrv_white.gif)} ul.pureCssMenu ul span,ul.pureCssMenu a:hover table span{background-image:url(http://openwetware.org/images/5/50/Arr_white.gif)} <!-- End PureCSSMenu.com STYLE --> 

 </style>

</head> <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"> <!-- Start PureCSSMenu.com MENU --> <ul class="pureCssMenu pureCssMenum"> 

 <li class="pureCssMenui"><a class="pureCssMenui"
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]-->
   <ul class="pureCssMenum">
     <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 --> 

     <li class="pureCssMenui"><a class="pureCssMenui"
href="http://openwetware.org/wiki/Biomod/2011/Slovenia/BioNanoWizards/ideaverticalstacks">Vertical

stacks</a></li> 

   </ul>

<!--[if lte IE 6]></td></tr></table></a><![endif]--></li> 

 <li class="pureCssMenui"><a class="pureCssMenui"
href="#"><span>Results</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/resultssummary">Summary</a></li>
     <li class="pureCssMenui"><a class="pureCssMenui"
href="#"><span>Protein add-ons</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/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> 

       </ul>

<!--[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> 

       </ul>

<!--[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]-->
   <ul class="pureCssMenum">
     <li class="pureCssMenui"><a class="pureCssMenui"
href="http://openwetware.org/wiki/Biomod/2011/Slovenia/BioNanoWizards/discussion">Discussion</a></li>
     <li class="pureCssMenui"><a class="pureCssMenui"
href="#"><span>Applications</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/applabonchip">Lab-on-a-nanochip</a></li>
         <li class="pureCssMenui"><a
class="pureCssMenui"
href="http://openwetware.org/wiki/Biomod/2011/Slovenia/BioNanoWizards/appbiosynthteticcompartments">Biosynthetic

compartments</a></li> 

         <li class="pureCssMenui"><a
class="pureCssMenui"
href="http://openwetware.org/wiki/Biomod/2011/Slovenia/BioNanoWizards/appbiosensors">Biosensors</a></li>
         <li class="pureCssMenui"><a
class="pureCssMenui"
href="http://openwetware.org/wiki/Biomod/2011/Slovenia/BioNanoWizards/appnanoelectronics">Nanoelectronics</a></li>
       </ul>
     </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]-->
   <ul class="pureCssMenum">
     <li class="pureCssMenui"><a class="pureCssMenui"
href="#"><span>DNA origami design</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/methgeneraldesignstrategy">General

design strategy</a></li> 

         <li class="pureCssMenui"><a
class="pureCssMenui"
href="http://openwetware.org/wiki/Biomod/2011/Slovenia/BioNanoWizards/methmodifications%20">Modifications</a></li>
       </ul>

<!--[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

assay</a></li> 

       </ul>

<!--[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/methafm">AFM</a></li>
     <li class="pureCssMenui"><a class="pureCssMenui"
href="http://openwetware.org/wiki/Biomod/2011/Slovenia/BioNanoWizards/methtimeline">Timeline</a></li>
   </ul>

<!--[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/team">Team</a></li>
 <li class="pureCssMenui"><a class="pureCssMenui"
href="http://openwetware.org/wiki/Biomod/2011/Slovenia/BioNanoWizards/acknowledgments">Acknowledgments</a></li>

</ul> <!-- End PureCSSMenu.com MENU --> </div> </div> </div> <!-- end #header --> <div id="page" class="container"> <div id="content"> <div class="post"> <div class="entry"><big><big><big><big><span 

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

<br><br> <span style="font-family: Arial;">Natural biopolymers can form the most complex and variable nanostructures, which have not been surpassed by synthetic nanomaterials. Design of biopolymers to form defined nanostructures represents a formidable challenge, even today. The first successful artificial nanostructures were built by Nadrian Seeman who used nucleic acids to form nanostructures based on nucleotide pairing (Seeman, 1982). </span><br style="font-family: Arial;"> <br style="font-family: Arial;"> <span style="font-family: Arial;"> Debut of the DNA origami technique (Rothemund, 2006) spurred major advancement of this field. Desired DNA origami objects are built by raster filling of a long single stranded DNA molecule into the selected model with the help of synthetic short DNA oligonucleotides - so called staple strands. Since staple strands are used in excess, one can achieve high yields of various 2D or 3D DNA nanostructures. </span><br style="font-family: Arial;"> <br style="font-family: Arial;"> <span style="font-family: Arial;"> However, DNA origami by itself is of relatively limited use. Evolving supramolecular DNA nanotechnology combines DNA's remarkable feasibility of programmable self-assembly with other chemical species, which enhance DNA with advanced chemical and physical properties. DNA origami structures already served as a template for spatial positioning of nanoparticles such as quantum dots (Bui, 2010), metal nanoparticles (Pal, 2010; Hung, 2010), carbon nanotubes (Maune, 2010) and proteins via biotin-streptavidin interactions (Sacca, 2010; Shen, 2009; Numajiri, 2010) with nanometer precision. </span><br style="font-family: Arial;"> <br style="font-family: Arial;"> <span style="font-family: Arial;"> The main advantage of DNA origami is precise control over the position of each staple strand used in the model. Since staple strands have unique nucleotide sequences, they can serve as specific attachment sites with a resolution around 6 nm. Attachment has been usually achieved through direct chemical functionalization of nanoparticles with oligonucleotides that bind to extended parts of staple strands. These segments of staple strands do not anneal to long single stranded DNA but protrude perpendicularly from the surface of DNA origami. </span> <table style="margin-top: 30px; margin-bottom: 30px; width: 100%;" 

border="0" cellspacing="0">
 <tbody>
   <tr>
     <td style="text-align: left;"><img
style="font-family: Arial; width: 890px; height: 600px;" alt=""
src="http://openwetware.org/images/3/30/Slika21nova.png"></td>
   </tr>
   <tr style="font-family: Arial;">
     <td style="text-align: justify;"><span
style="font-weight: bold;">Figure 1: DNA origami can be modified at selected positions using oligonucleotides, aptamers or chemical modification of staples. </span>Advantages and drawbacks are listed for each approach.
     </td>
   </tr>
 </tbody>

</table> <span style="font-family: Arial;"> Other popular techniques include protein-ligand interactions based on modification of staple strands with biotin, which strongly binds to streptavidin. This approach requires individual synthesis of chemically modified staple strands and selected nanoparticles. The bottleneck of this approach for accelerated advancement of the field is the limited number of available orthogonal functionalization groups, which limits the variability of molecules or particles that can be simultaneusly bound to the DNA origami. Therefore, for the successful design of complex systems involving many different chemical species, a more universal method of binding should be developed. </span><br style="font-family: Arial;"><br> <big style="font-family: Arial;"><big><big><big><span 

style="color: black; font-weight: bold;"></span></big></big></big></big><span
style="font-family: Arial;">Proteins, although similar in

their chemical composition, are by the very nature of their design endowed with capabilities of performing a broad spectrum of roles such as enzymatic, defensive (e.g. antibodies), kinetic (i.e. proteins converting energy of chemical bond into movement), structural, optical etc. Since molecules of such variety can operate under the similar chemical conditions <span style="font-style: italic;">in vivo</span>, proteins seem a logical choice for further development of complex multicomponent nanoscale devices capable of executing complex tasks. </span><br style="font-family: Arial;"> <br style="font-family: Arial;"> <span style="font-family: Arial;"> Therefore the use of protein domains as DNA add-ons seems to have very interesting prospects. In our project from June until November 2011 we designed a novel and universal approach for protein immobilization on the surface of DNA origami, which could provide a straightforward and affordable way of targeted spatial positioning. Check next page to see the solution proposed by the BioNanoWizards team. </span><br style="font-family: Arial;"><br>

<hr style="width: 100%; height: 2px;"><span 

style="font-family: Arial; font-size: smaller;">

<ul> <li>Bui H, Onodera C, Kidwell C, Tan Y, Graugnard E, Kuang W, Lee J, Knowlton WB, Yurke B, Hughes WL (2010) Programmable periodicity of quantum dot arrays with DNA origami nanotubes. <em>Nano Lett. </em>10:3367-72.</li> <li>Hung AM, Micheel CM, Bozano LD, Osterbur LW, Wallraff GM, Cha JN (2010) Large-area spatially ordered arrays of gold nanoparticles directed by lithographically confined DNA origami. <em>Nat. Nanotechnol. </em>5:121-6.</li> <li>Maune HT, Han SP, Barish RD, Bockrath M, Goddard III WA, Rothemund PW, Winfree E (2010) Self-assembly of carbon nanotubes into two-dimensional geometries using DNA origami templates. <em>Nat. Nanotechnol. </em>5:61-6.</li> <li>Numajiri K, Kimura M, Kuzuya A, Komiyama M (2010)Stepwise and reversible nanopatterning of proteins on a DNA origami scaffold. <em>Chem Commun</em>46:5127-9.</li> <li>Pal S, Deng Z, Ding B, Yan H, Liu Y (2010) DNA-origami-directed self-assembly of discrete silver-nanoparticle architectures. <em>Angew. Chem.</em> 49:2700-4.</li> <li>Rothemund PWK (2006) Folding DNA to create nanoscale shapes and patterns. <em>Nature </em>440: 297-302.</li> <li>Sacca B, Meyer R, Erkelenz M, Kiko K, Arndt A, Schroeder H, Rabe KS, Niemeyer CM (2010) Orthogonal protein decoration of DNA origami. <em>Angew. Chem. </em>49: 9378-83.</li> <li>Seeman NC (1982) Nucleic acid junctions and lattices. <em>J Theor Biol </em>499: 237-47.</li> <li>Shen W, Zhong H, Neff D, Norton ML (2009) NTA directed protein nanopatterning on DNA Origami nanoconstructs. <em>J. Am. Chem. Soc. </em>131:6660-1.</li> </ul>

<span style="font-family: Arial;"></span> </div> </div> </div> <div style="clear: both;">&nbsp;</div> </div> <!-- end #page --></div> <div id="footer-content" class="container"> <div id="footer-bg"> <table 

style="width: 100%; text-align: left; margin-left: auto; margin-right: auto;"
border="0" cellpadding="2" cellspacing="2">
 <tbody>
   <tr>
     <td style="text-align: right;"><a
href="http://openwetware.org/wiki/Biomod/2011/Slovenia/BioNanoWizards"><img
alt="" style="border: 0px solid ; width: 132px; height: 39px;"
src="http://openwetware.org/images/d/d3/Previousblue.JPG"></a></td>
     <td style="text-align: left;"><a
href="http://openwetware.org/wiki/Biomod/2011/Slovenia/BioNanoWizards/ideaproteinaddons"><img
alt="" style="border: 0px solid ; width: 132px; height: 39px;"
src="http://openwetware.org/images/6/69/Nextblue.JPG"></a></td>
   </tr>
 </tbody>

</table> </div> </div> <div id="footerCSS"> <p>BioNanoWizards - BioMod 2011 team Slovenia. Design by <a href="http://www.freecsstemplates.org/">Free CSS Templates</a>.</p> </div> <!-- end #footer --> </body> </html>

Retrieved from "https://openwetware.org/mediawiki/index.php?title=Biomod/2011/Slovenia/BioNanoWizards/ideastateoftheart&oldid=562724"