Difference between revisions of "Part:BBa K115016:Design"

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===Source===
 
===Source===
  
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Based on ROSE RNA thermometer sequences from Rfam database.
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''Bradyrhizobium japonicum USDA 110'' ([http://www.ncbi.nlm.nih.gov/sites/entrez?Db=genome&Cmd=ShowDetailView&TermToSearch=272 <code>NC_004463</code>]), residing at location [http://www.ncbi.nlm.nih.gov/projects/sviewer/?id=NC_004463.1&v=5784144..5784239 <code>5784144-5784239</code>] within the genome, which is at the 5' side of the gene [http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=NC_004463%20hspb hspB].
  
 
===References===
 
===References===

Revision as of 07:30, 28 October 2008

RNA thermometer (ROSE 27C)


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 designed sequence is based on a ROSE RNA thermometer retrieved from Bradyrhizobium japonicum USDA 110 . The temperature sensitive hairpin of this RNA thermometer is destabilized in order to get a lower switching temperature. Incorporation of weak base pairs, bulge loops, and internal loops is used for the destabilization, while ensuring that the secondary structure remains unaltered, and the distribution of the free energy within the temperature sensitive hairpin remains similar to the characteristic distribution which seems to be similar to all RNA thermometers of this type as shown [http://2008.igem.org/Team:TUDelft/Temperature_analysis#Results here]. The dark blue line in the graph shows the found trend which is the characteristic distribution of free energy within 32 RNA thermometers which have their switching point around 37°C. The light blue shows the distribution of the free energy for this part at 27°C (as calculated with RNAeval). This line is fitted to the trend line, so that its temperature sensitive hairpin has the same stability, but at a lower temperature (27°C instead of 37°C). The assumption is that this will also cause the switching temperature to 27°C.

The secondary structure of the part after ligation to a protein coding part, as predicted by RNAfold, is given at the right of the figure. The light blue region is the Shine Dalgarno region, which is the ribosome binding site.

See our [http://2008.igem.org/Team:TUDelft/Temperature_design2 wiki] for an extended description of the design of this part.

BBa K115016.png

Source

Bradyrhizobium japonicum USDA 110 ([http://www.ncbi.nlm.nih.gov/sites/entrez?Db=genome&Cmd=ShowDetailView&TermToSearch=272 NC_004463]), residing at location [http://www.ncbi.nlm.nih.gov/projects/sviewer/?id=NC_004463.1&v=5784144..5784239 5784144-5784239] within the genome, which is at the 5' side of the gene [http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=NC_004463%20hspb hspB].

References