Difference between revisions of "Part:BBa K115001"
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[[Image:rnat2.png]]
 
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===Characterization===
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<img src="https://2019.igem.org/wiki/images/1/16/T--Rice--BBa115001.png" width = 60%>
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<p><b>Figure 1.</b> Fluorescence intensity at 25 °C, 30 °C, and 37 °C.</p>
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<partinfo>BBa_K3247000 SequenceAndFeatures</partinfo>
  
  

Revision as of 23:47, 21 October 2019

RNA thermometer (ROSE)

An [http://2008.igem.org/Team:TUDelft/Temperature_analysis#RNA_thermometer RNA thermometer] that can be used for temperature sensitive post-transcriptional regulation which is based on a RNA thermometer from Bradyrhizobium japonicum that initiates translation at 42°C.

The image shows the secondary structure of the part after ligation to a protein coding part, as predicted by [http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi RNAfold]. Notice that the 3' end, including the scar and the start codon, does not belong to the part. The blue region is the Shine Dalgarno sequence which is the ribosome binding site. The blue nucleotides are the ones that had to be changed in order to get the desired secondary structure after introduction of the scar.

BBa K115001 ss.png

Sequence and Features


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]



3D Structure

(The following information is the contribution of SVCE_Chennai 2016)



3D Model when not ligated to any protein

RNAtfinal6.gif



Another representation of the 3D structure.

RNAt2.png



Secondary Structure when RNA thermometer is not ligated to any protein

Rnat.png

Rnat2.png

Characterization

Figure 1. Fluorescence intensity at 25 °C, 30 °C, and 37 °C.


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal XbaI site found at 7
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal XbaI site found at 7
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal XbaI site found at 7
  • 1000
    COMPATIBLE WITH RFC[1000]



References


SimRNAweb: a web server for RNA 3D structure modeling with optional restraints.