Difference between revisions of "Part:BBa K115002:Design"

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===Design Notes===
 
===Design Notes===
  
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The figure shows the secondary structure of the original RNA thermometer as well as the secondary structure of this part. Because of the scar that is introduced during the ligation process, some nucleotides had to be changed in order to get the same secondary structure as that of the original one. The blue nucleotides are the ones that are being changed. The working of the RNA thermometer is based on this secondary structure and that is why it is important that this part has the same secondary structure (after ligation to a protein coding part) as the original RNA thermometer.
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The secondary structure is important to the function of RNA thermometer, but part of the secondary structure is destroyed by the introduction of the scar. We've tried to alter the sequence so that the predicted secondary structure is conserved. More information on the design of this part can be found [http://2008.igem.org/Team:TUDelft/Temperature_design here].
  
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More information on the design of this part can be found [http://2008.igem.org/Team:TUDelft/Temperature_design here].
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The figure shows the secondary structure of the wild type RNA thermometer, as predicted by RNAfold, on the left. On the right the predicted secondary structure of this part, after ligation to a protein coding part, is shown. Notice that the 3' prime including the scar and the start codon do not belong to this part. The light blue nucleotides show the mutations that were needed to regain the original secondary structure after introduction of the scar.
  
 
[[Image:BBa_K115002.png | 600px]]
 
[[Image:BBa_K115002.png | 600px]]

Revision as of 12:42, 28 October 2008

RNA thermometer (FourU)


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

The secondary structure is important to the function of RNA thermometer, but part of the secondary structure is destroyed by the introduction of the scar. We've tried to alter the sequence so that the predicted secondary structure is conserved. More information on the design of this part can be found [http://2008.igem.org/Team:TUDelft/Temperature_design here].

The figure shows the secondary structure of the wild type RNA thermometer, as predicted by RNAfold, on the left. On the right the predicted secondary structure of this part, after ligation to a protein coding part, is shown. Notice that the 3' prime including the scar and the start codon do not belong to this part. The light blue nucleotides show the mutations that were needed to regain the original secondary structure after introduction of the scar.

BBa K115002.png

Source

This sequence is taken from Salmonella Enterica Tyhpy ([http://www.ncbi.nlm.nih.gov/sites/entrez?Db=genome&Cmd=ShowDetailView&TermToSearch=21688 NC_010102])).

References

  • Torsten Waldminghaus, Nadja Heidrich, Sabine Brantl, and Franz Narberhaus. FourU: a novel type of RNA thermometer in Salmonella. Molecular Microbiology, 65(2):413-424, 2007. [http://www.ncbi.nlm.nih.gov/pubmed/17630972 PMID:17630972]