Team:Penn State/Codon Optimization Results

From 2012.igem.org

(Difference between revisions)
 
(5 intermediate revisions not shown)
Line 159: Line 159:
}
}
-
#desc h2 {
+
#desc h3 {
color: #fff;
color: #fff;
padding: 15px 15px 0;
padding: 15px 15px 0;
Line 300: Line 300:
#maintabs {
#maintabs {
clear:both;
clear:both;
 +
        margin-top: 15px;
}
}
Line 400: Line 401:
   <div id="navitabs">
   <div id="navitabs">
     <h2 class="hide">Sample navigation menu:</h2>
     <h2 class="hide">Sample navigation menu:</h2>
-
     <a class="navitab"http://2012.igem.org/Team:Penn_State">Home</a>
+
     <a class="navitab" href="http://2012.igem.org/Team:Penn_State">Home</a>
     <span class="hide"> | </span> <a class="navitab" href="http://2012.igem.org/Team:Penn_State/Team">Team</a>
     <span class="hide"> | </span> <a class="navitab" href="http://2012.igem.org/Team:Penn_State/Team">Team</a>
     <span class="hide"> | </span> <a class="activenavitab" href="http://2012.igem.org/Team:Penn_State/Project">Projects</a>
     <span class="hide"> | </span> <a class="activenavitab" href="http://2012.igem.org/Team:Penn_State/Project">Projects</a>
     <span class="hide"> | </span> <a class="navitab" href="http://2012.igem.org/Team:Penn_State/Parts">Parts</a>
     <span class="hide"> | </span> <a class="navitab" href="http://2012.igem.org/Team:Penn_State/Parts">Parts</a>
-
     <span class="hide"> | </span> <a class="navitab" href="http://2012.igem.org/Team:Penn_State/Modeling">Modeling</a>
+
     <span class="hide"> | </span> <a class="navitab" href="http://2012.igem.org/Team:Penn_State/Modeling">Main Results</a>
     <span class="hide"> | </span> <a class="navitab" href="http://2012.igem.org/Team:Penn_State/Notebook">Notebook</a>
     <span class="hide"> | </span> <a class="navitab" href="http://2012.igem.org/Team:Penn_State/Notebook">Notebook</a>
     <span class="hide"> | </span> <a class="navitab" href="http://2012.igem.org/Team:Penn_State/Other">Other</a>
     <span class="hide"> | </span> <a class="navitab" href="http://2012.igem.org/Team:Penn_State/Other">Other</a>
Line 410: Line 411:
      
      
   <div id="desc">
   <div id="desc">
-
     <h2>Codon Optimization</h2>
+
     <h3>Codon Optimization</h3></br>
     <p>The genetic code is a degenerate one; there are more 3-part combinations of nucleotides than there are amino acids. The topic of codon optimization-that is, the cell's preference for one codon sequence over another in translation-has been heavily researched in an effort to determine the optimal genetic sequences for an organism. This project looks at the effects of repeated amino acid sequences of varying lengths and codons and their effect on the cell. </p>  
     <p>The genetic code is a degenerate one; there are more 3-part combinations of nucleotides than there are amino acids. The topic of codon optimization-that is, the cell's preference for one codon sequence over another in translation-has been heavily researched in an effort to determine the optimal genetic sequences for an organism. This project looks at the effects of repeated amino acid sequences of varying lengths and codons and their effect on the cell. </p>  
   </div>
   </div>
Line 427: Line 428:
<h3>Data Collection</h3>
<h3>Data Collection</h3>
     <p>A 6-repeated sequence of a single threonine codon was successfully ligated into the initial construct. The resulting fluorescence was measured using a TECAN machine. The results are displayed graphically below.</p>
     <p>A 6-repeated sequence of a single threonine codon was successfully ligated into the initial construct. The resulting fluorescence was measured using a TECAN machine. The results are displayed graphically below.</p>
-
<br/>
+
<P><img src="http://2012.igem.org/wiki/images/c/cc/Threonine6_results.png"></p>
-
<P><a href="http://2012.igem.org/wiki/images/1/1e/PennState_MSC_Data_1.jpg"><img src="http://2012.igem.org/wiki/images/1/1e/PennState_MSC_Data_1.jpg" width="400"></a></p><p>Figure 1. Fluorescence of E.coli with threonine 6-repeat sequence</p><br/>
+
<P>The figure above demonstrates the fluorescence of both mCherry and GFP when the ribosome translates four 6-repeat sequences of a single codon of threonine. mCherry levels fluctuate while GFP fluorescence remains the same. Further characterization with repeating sequences will provide more quantitative data, but preliminary testing suggests that with constant levels of GFP, the cell is able to send tRNA strands complementary to each threonine codon without disturbing GFP production. Thus, the codon sequence with the highest mCherry expression indicates the most preferred threonine codon.</p>     
<P>The figure above demonstrates the fluorescence of both mCherry and GFP when the ribosome translates four 6-repeat sequences of a single codon of threonine. mCherry levels fluctuate while GFP fluorescence remains the same. Further characterization with repeating sequences will provide more quantitative data, but preliminary testing suggests that with constant levels of GFP, the cell is able to send tRNA strands complementary to each threonine codon without disturbing GFP production. Thus, the codon sequence with the highest mCherry expression indicates the most preferred threonine codon.</p>     
Line 449: Line 449:
     <h3>Projects</h3>
     <h3>Projects</h3>
     <ul>
     <ul>
-
       <li><a href="http://2012.igem.org/Team:Penn_State/MSC_Overview">Multiple Start Codons</a></li>
+
       <li><a href="http://2012.igem.org/Team:Penn_State/Multiple_Start_Codons">Multiple Start Codons</a></li>
-
       <li><a href="http://2012.igem.org/Team:Penn_State/Bidirectional_Promoters_Overview">Bidirectional Promoters</a></li>
+
       <li><a href="http://2012.igem.org/Team:Penn_State/Bidirectional_Promoters">Bidirectional Promoters</a></li>
-
       <li><a href="http://2012.igem.org/Team:Penn_State/Codon_Optimization_Overview">Codon Optimization</a></li>
+
       <li><a href="http://2012.igem.org/Team:Penn_State/Codon_Optimization">Codon Optimization</a></li>
     </ul>
     </ul>
   </div>
   </div>

Latest revision as of 03:23, 27 October 2012

Bidirectional Promoters Overview

Codon Optimization


The genetic code is a degenerate one; there are more 3-part combinations of nucleotides than there are amino acids. The topic of codon optimization-that is, the cell's preference for one codon sequence over another in translation-has been heavily researched in an effort to determine the optimal genetic sequences for an organism. This project looks at the effects of repeated amino acid sequences of varying lengths and codons and their effect on the cell.

Codon Optimization

Sample navigation menu:

Overview | Design | Results

Data Collection

A 6-repeated sequence of a single threonine codon was successfully ligated into the initial construct. The resulting fluorescence was measured using a TECAN machine. The results are displayed graphically below.

The figure above demonstrates the fluorescence of both mCherry and GFP when the ribosome translates four 6-repeat sequences of a single codon of threonine. mCherry levels fluctuate while GFP fluorescence remains the same. Further characterization with repeating sequences will provide more quantitative data, but preliminary testing suggests that with constant levels of GFP, the cell is able to send tRNA strands complementary to each threonine codon without disturbing GFP production. Thus, the codon sequence with the highest mCherry expression indicates the most preferred threonine codon.

Additional Testing

Several more repeated sequences of identical and non-identical single amino acid codons are intended for testing in this construct. To view the completed and prospective sequences, please visit our Parts page