Part:BBa_K1824556

RNA Thermometer A1 (Specially designed for J23119)

This is a special designed A1 RNA thermometer that with a unique spacer at the front, which would make it compatible with J23119.

A1 RNA thermometer have the hairpin structure that harbors the Shine-Dalgarno sequence (SD sequence) and, in this way, make it inaccessible to the 30S unit of the bacterial ribosome, resulting in translational inactivation (Figure 2). The melting temperature of this RNA thermometer is 42 Celsius degree. Once reaching the melting temperature, hairpin structure would vanish and as a result, exposing the SD sequence to trigger the translation process.

Different promoters have their own transcription start sites and, in most cases, + 1 sites are embedded in promoter sequence. Hence, it is normal that transcripted RNA usually carry part of promoter sequence. However, for regulatory parts like RNA thermometer, it is important to avoid truncation or alteration of the RNA sequence. Hence, special designed RNA spacer between transcripted part of promoters and RNA thermometers are important for maintaining the secondary structure of RNA thermometer.

For J23119, transcription starts at TAATGCTAGCA (transcription start site indicated in bold). Based on this, BBa_K1824556 was specially designed with a spacer that had less probability to interact with the functional structure of RNA thermometer.

The possible secondary structure of A1 was simulated by RNAstructure (Fig.1). For testing results of J23119-A1, See BBa_K1824000.

Left picture: XJTLU-CHINA (2015) Figure 1: Possible secondary structure of RNAT A1.
Right picture: TuDelft (2008) Figure 2: Responsiveness of mRNA structures to environmental cues.

Source

A1 RNA thermometer was derived from the ROSE family (ROSE stands for Repression Of heat Shock gene Expression).

References

1. Nocker, A. et al. mRNA-based thermosensor controls expression of rhizobial heat shock genes. Nucleic Acids Res. 29, 4800–4807 (2001).

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]