Part:BBa_K4761049

RNAT U9(new)

RNA thermometer U9 for new plasmid pET28a. Activates around 37℃.

RNA thermometers (RNA thermosensors) are RNA-only translational control elements that sense temperature changes. They rely on a simple principle: the temperature-dependent melting of an RNA secondary structure in the 5′ untranslated region (5′ UTR). At low temperatures, the 5′ UTR adopts a conformation that masks the ribosome-binding site (Shine-Dalgarno (SD) sequence) by complementary base pairing and, in this way, makes it inaccessible to the 30S subunit of the bacterial ribosome. A shift to higher temperatures switches on translation by melting the secondary structure that harbors the SD sequence, thus allowing for ribosome binding and translation. Conversely, a shift from high to low growth temperatures switches off translation by allowing formation of the secondary structure that masks the SD sequence[1].

Online software (http://rna.tbi.univie.ac.at/) to simulate the secondary structure figure shown in Figure 1 . MFE structure, the thermodynamic ensemble of RNA structures, and the centroid structure，the positional entropy for each position，as shown in Figure 2[2].

Fig.1 MFE secondary structure of RNAT U9(new)

Fig.2 MFE structure, the thermodynamic ensemble of RNA structures, and the centroid structure，the positional entropy for each position of RNAT U9(new)

Sequence and Features

Assembly Compatibility:

• 10
  INCOMPATIBLE WITH RFC[10]

  Illegal XbaI site found at 4
  Illegal SpeI site found at 23
  Illegal PstI site found at 29
  
• 12
  INCOMPATIBLE WITH RFC[12]

  Illegal SpeI site found at 23
  Illegal PstI site found at 29
  
• 21
  INCOMPATIBLE WITH RFC[21]

  Illegal BamHI site found at 43
  
• 23
  INCOMPATIBLE WITH RFC[23]

  Illegal XbaI site found at 4
  Illegal SpeI site found at 23
  Illegal PstI site found at 29
  
• 25
  INCOMPATIBLE WITH RFC[25]

  Illegal XbaI site found at 4
  Illegal SpeI site found at 23
  Illegal PstI site found at 29
  
• 1000
  INCOMPATIBLE WITH RFC[1000]

  Illegal BsaI site found at 15
  

References

[1]Neupert, J., Bock, R. Designing and using synthetic RNA thermometers for temperature-controlled gene expression in bacteria. Nat Protoc 4, 1262–1273 (2009). [2]Juliane Neupert, Daniel Karcher, Ralph Bock, Design of simple synthetic RNA thermometers for temperature-controlled gene expression in Escherichia coli, Nucleic Acids Research, Volume 36, Issue 19, 1 November 2008, Page e124, https://doi.org/10.1093/nar/gkn545