Biomod/2011/Slovenia/BioNanoWizards/methemsa

From OpenWetWare
Revision as of 13:15, 1 November 2011 by Marko Verce (talk | contribs)
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to navigationJump to search
The printable version is no longer supported and may have rendering errors. Please update your browser bookmarks and please use the default browser print function instead.

<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;">EMSA</span></big></big></big></big><br>

<br><br> <span style="font-family: Arial;"> EMSA stands for Electrophoretic Mobility Shift Assay. It is a general term describing an assay where complex formation is observed with electrophoresis. A complex generally has different mobility in an electrophoresis gel than each of its components alone. This is noticed as a change or a shift in band position in an electrophoresis gel in comparison with its components. It is widely used in life sciences, most notably for analyzing DNA binding sites for transcription factors or other proteins, such as our chimeric zinc finger proteins. We used agarose gel and ethidium bromide staining to detect oligonucleotides and the complexes they form with zinc finger proteins. If such protein binds to DNA, the resulting complex is still negatively charged but of higher Mw than an oligonucleotide alone, therefore the oligonucleotide has an apparently higher Mw according to a ladder. <br> <br> </span> <span style="font-family: Arial;"> Samples for EMSA were prepared by adding different molar excesses of protein to 0.5 μl of 20 μM binding oligonucleotide solution and a buffer (20 mM Tris pH 7.6, 100 mM NaCl, 5 mM TCEP, 0.1 % BSA) up to a final volume of 27 μl. Protein was added 4-fold, 8-fold or 16-fold molar excess over binding oligonucleotide. One of the samples contained the same amount of oligonucleotide as the mixed samples, but no protein was added. Another contained the same amount of protein as the sample with the highest molar excess of protein, but without addition of oligonucleotide. After 1 h at room temperature 3 μl of 50 % glycerol were added and 25 μl of each sample were loaded onto a 2 % agarose gel with ethidium bromide and run for 50 minutes at 70 V in 1x TAE running buffer. DNA was visualized with UV illumination and photographed. </span>

</div> </div> </div> <!-- end #content --> <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; margin-bottom:30px;"
border="0" cellpadding="2" cellspacing="2">
 <tbody>
   <tr>
     <td style="text-align: right;"><a
href="http://openwetware.org/wiki/Biomod/2011/Slovenia/BioNanoWizards/methprotprodandisol"><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/methalphascreen"><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/methemsa&oldid=559119"