Biomod/2011/TUM/TNT/LabbookA/Concentration measurement of labeled oligonucleotides

From OpenWetWare
Jump to navigationJump to search

<html> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> 

 <script type="text/javascript" src="http://ajax.googleapis.com/ajax/libs/jquery/1.4.2/jquery.min.js"></script>
 <script type="text/javascript">
  $(document).ready(function(){
   $('#lside1').mouseover(function() {
    $('#lside1').stop().animate({backgroundPosition: '0px 0px'}, 1000);
   });
   $('#lside1').mouseleave(function() {
    $('#lside1').stop().animate({backgroundPosition: '-250px 0px'}, 1000);
   });
   $('#lside2').mouseover(function() {
    $('#lside2').stop().animate({backgroundPosition: '0px 0px'}, 1000);
   });
   $('#lside2').mouseleave(function() {
    $('#lside2').stop().animate({backgroundPosition: '-250px 0px'}, 1000);
   });
   $('#lside3').mouseover(function() {
    $('#lside3').stop().animate({backgroundPosition: '0px 0px'}, 1000);
   });
   $('#lside3').mouseleave(function() {
    $('#lside3').stop().animate({backgroundPosition: '-250px 0px'}, 1000);
   });
     $('#lside4').mouseover(function() {
    $('#lside4').stop().animate({backgroundPosition: '0px 0px'}, 1000);
   });
   $('#lside4').mouseleave(function() {
    $('#lside4').stop().animate({backgroundPosition: '-250px 0px'}, 1000);
   });
    $('#lside5').mouseover(function() {
    $('#lside5').stop().animate({backgroundPosition: '0px 0px'}, 1000);
   });
   $('#lside5').mouseleave(function() {
    $('#lside5').stop().animate({backgroundPosition: '-250px 0px'}, 1000);
   });
  });
 </script>

<style type="text/css"> 

  #side1 {
   width: 250px;
   height: 100px;
   position: relative;
   top: 0px;
   left: 20px;}

  #lside1 {
   width: 250px;
   height: 100px;
   background: url(http://openwetware.org/images/e/ee/1project.png) -250px 0px no-repeat;
   position: absolute;
   top: 0px;
   left: 0px;}

  #side2 {
   width: 250px;
   height: 100px;
   position: relative;
   top: 0px;
   left: 20px;}

  #lside2 {
   width: 250px;
   height: 100px;
   background: url(http://openwetware.org/images/6/68/2results.png) -250px 0px no-repeat;
   position: absolute;
   top: 0px;
   left: 0px;}

  #side3 {
   width: 250px;
   height: 100px;
   position: relative;
   top: 0px;
   left: 20px;}

  #lside3 {
   width: 250px;
   height: 100px;
   background: url(http://openwetware.org/images/f/f5/3methods.png) -250px 0px no-repeat;
   position: absolute;
   top: 0px;
   left: 0px;}

  #side4 {
   width: 250px;
   height: 100px;
   position: relative;
   top: 0px;
   left: 20px;}

  #lside4 {
   width: 250px;
   height: 100px;
   background: url(http://openwetware.org/images/8/8f/4team.png) -250px 0px no-repeat;
   position: absolute;
   top: 0px;
   left: 0px;}

 #side5 {
   width: 250px;
   height: 100px;
   background: url(http://openwetware.org/images/f/f5/3methods.png) -250px 0px no-repeat;
   position: relative;
   top: 0px;
   left: 20px;}

  #lside5 {
   width: 250px;
   height: 100px;
   background: url(http://openwetware.org/images/1/11/5labbook.png) -250px 0px no-repeat;
   position: absolute;
   top: 0px;
   left: 0px;}

 </style>
  <style>
  1. column-one { display:none; width:0px;}

.container{background-color: #f5f5f5; margin-top:50px} .OWWNBcpCurrentDateFilled {display: none;}

  1. content { width: 0px; margin: 0 auto auto 0; padding: 1em 1em 1em 1em; align: center;}
  1. column-content {width: 0px; float: left; margin: 0 0 0 0;padding: 0;}

.firstHeading {display:none; width:0px;}

  1. globalWrapper{ width:1280px;}
  1. column-one {display:none; width:0px;background-color: #ffffff;}
  1. content{ margin: 0 0 0 0; padding: 1em 1em 1em 1em; position: center; width: 800px;background-color: #f5f5f5; }

.container{ width: 800px; margin: auto; background-color: #ffffff; text-align:justify; font-family: helvetica, arial, sans-serif; color:#555555; margin-top:25px; }

  1. bodyContent{ width: 1267px; align: center; background-color: #ffffff;}
  1. column-content{width: 1280px;background-color: #f5f5f5;}

.firstHeading { display:none;width:0px;background-color: #ffffff;}

  1. header{position: center; width: 800px;background-color: #ffffff;}
  1. footer{position: center;}

div.tright { border-bottom-width: 0em; border-left-width: 0px; border-right-width: 0px; border-top-width: 0em; clear: right; float: right; 

}

<style type="text/css"> body { 

   font-family: helvetica, arial, sans-serif;
   color: black;

background:#f5f5f5; 

 }

ul#topnav {

margin: 0 0 0 0px ; padding: 0 0 0 0px; float: left; width: 800px; list-style: none; position: relative; 

       font-family: helvetica, arial, sans-serif;

font-size: 12px; background: #f5f5f5; 

       height: 5px;

} ul#topnav li { float: left; margin: 0; padding: 0; border-right: 1px solid #ffffff; /*--Divider for each parent level links--*/ } ul#topnav li a { padding: 11px 15px; display: block; color: #333333; text-decoration: none; } ul#topnav li:hover { background: #f5f5f5;} /*--Notice the hover color is on the list item itself, not on the link. This is so it can stay highlighted even when hovering over the subnav--*/

ul#topnav li span { float: left; padding: 15px 0; position: absolute; left: 0; top:30px; display: none; /*--Hide by default--*/ width: 800px; background: #cccccc; color: #333333; /*--Bottom right rounded corner--*/ -moz-border-radius-bottomright: 5px; -khtml-border-radius-bottomright: 5px; -webkit-border-bottom-right-radius: 5px; /*--Bottom left rounded corner--*/ -moz-border-radius-bottomleft: 5px; -khtml-border-radius-bottomleft: 5px; -webkit-border-bottom-left-radius: 5px; }


  1. abstractandlinks{

display:block; width:800px; background-color:#f5f5f5; text-align:justify;font-family: helvetica, arial, sans-serif; color:#555555; margin-top:0px; }

  1. innerBox

{ display: block; padding: 5px; }

  1. abstract{

font-family: helvetica, arial, sans-serif; width: 490px; margin-top: 20px; padding:0px 5px; float: left;background-color:#f5f5f5; ; }

  1. links{

font-family: helvetica, arial, sans-serif; width: 290px; margin-top: 20px; padding:0px 5px; float: left; background-color:#f5f5f5;; } .clear { clear:both; }

  1. struktur{

font-family: helvetica, arial, sans-serif; width: 790px; padding:0px 5px; float: left;background:#f5f5f5; }

  1. toctitle {align: left; text-align: left; }
  2. table.toc {background-color:"#5f5f5f";align: left; text-align: left;}
  3. toc #toctitle, .toc #toctitle, #toc .toctitle, .toc .toctitle {

text-align: left; 

}
  1. toc, .toc, .mw-warning {

background-color: #f5f5f5; border-bottom-color: rgb(170, 170, 170); border-bottom-style: solid; border-bottom-width: 0px; border-left-color: rgb(170, 170, 170); border-left-style: solid; border-left-width: 0px; border-right-color: rgb(170, 170, 170); border-right-style: solid; border-right-width: 0px; border-top-color: rgb(170, 170, 170); border-top-style: solid; border-top-width: 0px; font-size: 105%; padding-bottom: 5px; padding-left: 5px; padding-right: 5px; padding-top: 5px; align: left; text-align: left; display: left 

}


</style>

<head>

<script type="text/javascript"> var fullDates = new Array('08/11/2011','08/12/2011','08/16/2011','08/17/2011','08/23/2011','08/24/2011','08/25/2011','08/29/2011','08/30/2011','08/31/2011','09/01/2011','09/02/2011','09/06/2011','09/12/2011','09/13/2011','09/14/2011','09/15/2011','09/16/2011','09/19/2011','09/20/2011','09/21/2011','09/27/2011','09/28/2011','09/29/2011','09/30/2011','10/05/2011','10/06/2011','10/07/2011','10/10/2011','10/12/2011','10/13/2011','10/14/2011','10/17/2011','10/18/2011','10/19/2011','10/20/2011','10/21/2011','10/26/2011','10/27/2011','10/28/2011','10/30/2011');

$(document).ready(function() {

$("ul#topnav li").hover(function() { //Hover over event on list item $(this).css({ 'background' : '#cccccc'}); //Add background color and image on hovered list item $(this).find("span").show(); //Show the subnav

} ,

$("ul#topnav li").oneclick(function() { //Hover over event on list item $(this).css({ 'background' : '#cccccc'; 'display' : 'inline'}); //Add background color and image on hovered list item $(this).find("span").show(); //Show the subnav

} ,

function() { //on hover out...


$(this).css({ 'background' : 'none'}); //Ditch the background

//$(this).find("span").hide(); //Hide the subnav });

}); </script>


<script type="text/javascript" src="http://ajax.googleapis.com/ajax/libs/jquery/1.3/jquery.min.js"></script>




<title> 

       TUM NanU - Home

</title> </head>

<body background-color="#F0F0F0"> <!-- Header--> <div class="container"> 

   <div id="header"> <img src="http://openwetware.org/images/5/5c/Header2.png" /> </div>

<!--Menue--> <ul id="topnav"> 

   <li><a href="http://openwetware.org/wiki/Biomod/2011/TUM/TNT/Home">Home</a></li>
   <li><a href="http://openwetware.org/wiki/Biomod/2011/TUM/TNT/Project">Project</a>        
     <li><a href="http://openwetware.org/wiki/Biomod/2011/TUM/TNT/Results">Results & Discussion</a>
       
   </li>         
   </li>
   <li><a href="http://openwetware.org/wiki/Biomod/2011/TUM/TNT/Methods">Methods</a>    </li>

<li><a href="http://openwetware.org/wiki/Biomod/2011/TUM/TNT/Team">Team</a></li> 

      <li><a href="http://openwetware.org/wiki/Biomod/2011/TUM/TNT/LabbookA">Labbook</a>


</li> 

   <li><a href="http://openwetware.org/wiki/Biomod/2011/TUM/TNT/Extras">Extras</a>
       
  </li>
  <!--Subnav Starts Here-->
       
   </li>

</ul> <p> <br> </p> <p> <br> </p> <p> <br> </p>

</body> </html>

Concentration Measurement Of Labeled Oligonucleotides

We need to determine the concentrations of oligonucleotides for the composition of the folding batches. The first step ist to measure the absorption coefficient of the unlabeled oligonucleotide, then with this coefficient and the known parameters of the fluorophores the concentrations of the labeled oligonucleotides are determined.

Measuring Absorption Coefficients Of Unlabeled Oligonucleotides

All measurements are performed at a nanodrop photometer. Absorptions of three known concentrations are measured, the absorption coefficient is obtained by a fit using the Beer-Lambert law. The pathlength is 1mm, the concentrations of oligonucleotides are 10, 25 and 50µM.

concentration [µM] oligonucleotide 100µM [µl] 10x TBE [µl] 100mM MgCl2 [µl] ddH2O [µl]
50 5 0.5 1.1 3.4
25 2.5 0.5 1.1 5.9
10 1 0.5 1.1 7.4

Concentration Measurement Of Labeled Oligonucleotides

To A260 of the unlabeled oligonucleotide, A260 of the fluorophore labeled nucleotide is added to get the final absorption coefficient of the labeled oligonucleotide. Now with the average of three absorption measurements, we determined the concentration of the labeled oligonucleotide.

Retrieved from "https://openwetware.org/mediawiki/index.php?title=Biomod/2011/TUM/TNT/LabbookA/Concentration_measurement_of_labeled_oligonucleotides&oldid=563705"