Difference between revisions of "Part:BBa K1586000:Experience"

 
 
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This experience page is provided so that any user may enter their experience using this part.<BR>Please enter
 
This experience page is provided so that any user may enter their experience using this part.<BR>Please enter
 
how you used this part and how it worked out.
 
how you used this part and how it worked out.
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===Characterisation===
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<b>Experimental:</b>
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<br />
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In order to characterise that this part works as expected, fluorescence intensity was measured for the expression of K1586000 in a cell free system in the presence of different amounts of trigger RNA, where the plasmid encoding for the toehold was kept constant at 0.5 pmols. Below is a graph showing a positive correlation between amount of trigger RNA (in log10(nanograms) with 0ng normalised to 0) and GFP fluorescence intensity.
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https://static.igem.org/mediawiki/2015/5/5a/Exeter_GreenJ_trigger_conc_graph.png
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<html>
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<b><em>In silico</em>:</b>
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<br />
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As well as generating experimental data in the lab, <em>in silico</em> data was also generated through the software package <a href="http://www.nupack.org/">NUPACK</a> using free energies. For a full explanation of how this works, please visit http://2015.igem.org/Team:Exeter/Modeling.</br>
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</br>
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The equilibrium concentrations of the different components in our system were determined, along with free energy data for the different structures; the unbound trigger, the unbound toehold and the complex of the two.
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<img src="https://static.igem.org/mediawiki/2015/9/93/FreeEnergiesNupackGraph.png" width="700px">
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</br>
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</br>
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After obtaining this, the data was converted to an approximate normal distribution and after normalising these within the range of values, we could use the distribution as a probability distribution. Shown below are these obtained probability distributions based on the free energy data.
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<img src="https://static.igem.org/mediawiki/2015/d/df/NormalisedBindingProbabilityGraph.png" width="700px"
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<img src="https://static.igem.org/mediawiki/2015/a/a0/NormalisedSplittingProbability.png" width="700px">
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</html>
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===Applications of BBa_K1586000===
 
===Applications of BBa_K1586000===

Latest revision as of 15:20, 19 September 2015

This experience page is provided so that any user may enter their experience using this part.
Please enter how you used this part and how it worked out.


Characterisation

Experimental:
In order to characterise that this part works as expected, fluorescence intensity was measured for the expression of K1586000 in a cell free system in the presence of different amounts of trigger RNA, where the plasmid encoding for the toehold was kept constant at 0.5 pmols. Below is a graph showing a positive correlation between amount of trigger RNA (in log10(nanograms) with 0ng normalised to 0) and GFP fluorescence intensity.

Exeter_GreenJ_trigger_conc_graph.png


In silico:
As well as generating experimental data in the lab, in silico data was also generated through the software package NUPACK using free energies. For a full explanation of how this works, please visit http://2015.igem.org/Team:Exeter/Modeling.

The equilibrium concentrations of the different components in our system were determined, along with free energy data for the different structures; the unbound trigger, the unbound toehold and the complex of the two.




After obtaining this, the data was converted to an approximate normal distribution and after normalising these within the range of values, we could use the distribution as a probability distribution. Shown below are these obtained probability distributions based on the free energy data.




Applications of BBa_K1586000

User Reviews

UNIQ3c3b427b6d800cfb-partinfo-00000001-QINU UNIQ3c3b427b6d800cfb-partinfo-00000002-QINU