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Team:UPO-Sevilla/Project/Improving Flip Flop/Bioinformatics/RybB Structure
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<p>Obtain the secondary structure of the asRNA described in the flip-flop system designed by our V sublab.</p> | <p>Obtain the secondary structure of the asRNA described in the flip-flop system designed by our V sublab.</p> | ||
<h2>Background</h2> | <h2>Background</h2> | ||
| - | <p>In order to improve the robustness of genetic silencing, one of the possible mechanisms is to implement an asRNA inhibition system. Our V sublab implemented the <a href="http://www.cell.com/molecular-cell/retrieve/pii/S1097276508008071"> | + | <p>In order to improve the robustness of genetic silencing, one of the possible mechanisms is to implement an asRNA inhibition system. Our V sublab implemented the RybB-ompN inhibition system described by Bouvier <a href="http://www.cell.com/molecular-cell/retrieve/pii/S1097276508008071">(Bouvier et al. 2008)</a>.<p> |
<h2>Strategy:</h2> | <h2>Strategy:</h2> | ||
<p>Use <a href="http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi">the RNAfold Web Server</a> to obtain a possible secondary structure for the asRNA mentioned above.</p> | <p>Use <a href="http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi">the RNAfold Web Server</a> to obtain a possible secondary structure for the asRNA mentioned above.</p> | ||
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<p>The output of the RNAfold Web Server for our asRNA is shown in Figure 5. The free energy of the optimal secondary structure is quite high which would be expected as the RNA under study is an asRNA whose objective is the silencing of the ompN sequence by physical binding to this sequence. So, this asRNA may not have a quite stable secondary structure. The predicted structures are shown in Figure 6.</p> | <p>The output of the RNAfold Web Server for our asRNA is shown in Figure 5. The free energy of the optimal secondary structure is quite high which would be expected as the RNA under study is an asRNA whose objective is the silencing of the ompN sequence by physical binding to this sequence. So, this asRNA may not have a quite stable secondary structure. The predicted structures are shown in Figure 6.</p> | ||
<div class="center"><img src="https://static.igem.org/mediawiki/2011/c/cd/UPOSevilla_RNAfold_figure5.png" width="700px"></div> | <div class="center"><img src="https://static.igem.org/mediawiki/2011/c/cd/UPOSevilla_RNAfold_figure5.png" width="700px"></div> | ||
| - | <p><strong> | + | <p><strong>Figure 5.</strong> Main RNAfold resulted figures for the introduced asRNA sequence.</p><br/> |
<div class="center"><img src="https://static.igem.org/mediawiki/2011/c/c8/UPOSevilla_RNAfold_figure6.png" width="700px"></div> | <div class="center"><img src="https://static.igem.org/mediawiki/2011/c/c8/UPOSevilla_RNAfold_figure6.png" width="700px"></div> | ||
| - | <p><strong> | + | <p><strong>Figure 6.</strong> Possible predicted secondary structures for the RybB asRNA. The structures are displayed in both cases by plain sequence and base-pair probabilities.<p><br/> |
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Latest revision as of 22:22, 27 October 2011
RybB Structure
Goal:
Obtain the secondary structure of the asRNA described in the flip-flop system designed by our V sublab.
Background
In order to improve the robustness of genetic silencing, one of the possible mechanisms is to implement an asRNA inhibition system. Our V sublab implemented the RybB-ompN inhibition system described by Bouvier (Bouvier et al. 2008).
Strategy:
Use the RNAfold Web Server to obtain a possible secondary structure for the asRNA mentioned above.
Procedure:
Find the sequence of> the asRNA which is going to be introduced in our genetic flip-flop system (in this case the sequence of the RybB RNA).
Introduce the sequence in the RNAfold Web Server.
Results and Discussion:
The output of the RNAfold Web Server for our asRNA is shown in Figure 5. The free energy of the optimal secondary structure is quite high which would be expected as the RNA under study is an asRNA whose objective is the silencing of the ompN sequence by physical binding to this sequence. So, this asRNA may not have a quite stable secondary structure. The predicted structures are shown in Figure 6.
Figure 5. Main RNAfold resulted figures for the introduced asRNA sequence.
Figure 6. Possible predicted secondary structures for the RybB asRNA. The structures are displayed in both cases by plain sequence and base-pair probabilities.
Sponsors
