Team:Uppsala University/Modelling
From 2012.igem.org
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The modelling of our constructed sRNA is a vital part for evaluating hypotheses of how sRNA molecules interact with their target. One canonical approach for sRNA stability is to evaluate secondary structures by minimum free energy (MFE) approaches. This gives a pointer for approximating the probability of different kind of interactions. | The modelling of our constructed sRNA is a vital part for evaluating hypotheses of how sRNA molecules interact with their target. One canonical approach for sRNA stability is to evaluate secondary structures by minimum free energy (MFE) approaches. This gives a pointer for approximating the probability of different kind of interactions. | ||
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+ | <b>Stabile structures prevents translation</b> | ||
+ | A thermodynamic scheme of RNA interactions at different stages were made to show how an interaction between mRNA and sRNA could possibly work. So called toeholds are belived to play an important role in the interaction between sRNA and mRNA. (G. Rodrigo, T.E.Landrain,A.Jaramillo, 2012) | ||
+ | Understanding the interaction between rna with different structures is a key to learn how to design a sRNA. Often the hybridization reaction between the sRNA and the mRNA starts with the unpaired sequences, the so called toeholds. To start a basepairing reaction, the sRNA needs a few basepairs to start hybridize to. The sRNA and the mRNA can then create a more stable secondary complex, hindering translation. </p> | ||
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+ | <b>Reaction diagram sRNA</b> | ||
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+ | <a href="https://static.igem.org/mediawiki/2012/7/78/Reaction_diagrame_sRNA_low.png"><img src="https://static.igem.org/mediawiki/2012/7/78/Reaction_diagrame_sRNA_low.png" width="580"></a> | ||
+ | </td> | ||
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+ | <tr style="border-top:thin solid;border-color:black"> | ||
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+ | <p>The sRNA 17 and mRNA for the AAC(6)-UTR were first calculated in CLC main workbench separately, after that we calculated the interaction structure between them . | ||
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+ | This is an idea of how a secondary complex can be created between the sRNA and mRNA. </p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | </table> | ||
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<p style="margin-right:10px;font-size:10px;padding:0 0 0 0;float:left"><a href="https://static.igem.org/mediawiki/2012/b/b5/Natural_spot42_structure_medium.png"><img src="https://static.igem.org/mediawiki/2012/b/b5/Natural_spot42_structure_medium.png" width=300></a><br> | <p style="margin-right:10px;font-size:10px;padding:0 0 0 0;float:left"><a href="https://static.igem.org/mediawiki/2012/b/b5/Natural_spot42_structure_medium.png"><img src="https://static.igem.org/mediawiki/2012/b/b5/Natural_spot42_structure_medium.png" width=300></a><br> | ||
- | + | The native spot42 with the scaffold marked in blue. | |
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To gain better understanding of the mechanisms of smallRNA translation inhibition we have made 2D models of all our found smallRNAs. The 2D models were calculated in CLC main workbench.<br> | To gain better understanding of the mechanisms of smallRNA translation inhibition we have made 2D models of all our found smallRNAs. The 2D models were calculated in CLC main workbench.<br> | ||
IntaRNA, an RNA-interaction prediction software adapted for sRNA and ncRNA interactions (Smith et. al., 2010) was used to predict the sRNA-mRNA interactions of the candidate sRNAs. | IntaRNA, an RNA-interaction prediction software adapted for sRNA and ncRNA interactions (Smith et. al., 2010) was used to predict the sRNA-mRNA interactions of the candidate sRNAs. | ||
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<b>AAC(6')-SYFP2 + sRNA UU17 interaction </b> | <b>AAC(6')-SYFP2 + sRNA UU17 interaction </b> | ||
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- | <a href="https://static.igem.org/mediawiki/2012/3/3d/AAC%286%29%27UTR_Structure_medium2.png"><img src="https://static.igem.org/mediawiki/2012/3/3d/AAC%286%29%27UTR_Structure_medium2.png" | + | <a href="https://static.igem.org/mediawiki/2012/3/3d/AAC%286%29%27UTR_Structure_medium2.png"><img src="https://static.igem.org/mediawiki/2012/3/3d/AAC%286%29%27UTR_Structure_medium2.png" width="300" ></a> |
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∆G = -23,4 kcal/mol<br> | ∆G = -23,4 kcal/mol<br> | ||
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Revision as of 00:22, 27 September 2012
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sRNA UU46
sRNA UU55
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AAC(6')-SYFP2 + sRNA UU17 interaction
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