Part:BBa_K4761040

RNAT U6-1

RNA thermometer U6-1. 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 U6-1

Fig.2 MFE structure, the thermodynamic ensemble of RNA structures, and the centroid structure，the positional entropy for each position of RNAT U6-1

Sequence and Features

Assembly Compatibility:

• 10
  INCOMPATIBLE WITH RFC[10]

  Illegal EcoRI site found at 1
  Illegal SpeI site found at 15
  
• 12
  INCOMPATIBLE WITH RFC[12]

  Illegal EcoRI site found at 1
  Illegal SpeI site found at 15
  
• 21
  INCOMPATIBLE WITH RFC[21]

  Illegal EcoRI site found at 1
  
• 23
  INCOMPATIBLE WITH RFC[23]

  Illegal EcoRI site found at 1
  Illegal SpeI site found at 15
  
• 25
  INCOMPATIBLE WITH RFC[25]

  Illegal EcoRI site found at 1
  Illegal SpeI site found at 15
  
• 1000
  COMPATIBLE WITH RFC[1000]

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