Part:BBa_K1824557
RNA Thermometer A1 (Specially designed for pBAD)
This is a specially designed A1 RNA thermometer that with a unique spacer at the front, which would make it compatible with pBAD BBa_I13453.
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 37 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 transcribed RNA usually carry part of promoter sequence. However, for regulatory parts like RNA thermometer, truncation or alteration of the RNA sequence could be destructive. Hence, special designed RNA spacer between transcribed part of promoters and RNA thermometers are important for maintaining the secondary structure of RNA thermometer.
For pBAD BBa_I13453, transcription starts at TCTCCATA (transcription start site indicated in bold). Based on this, BBa_K1824557 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 pBAD-A1, See BBa_K1824003.
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.
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE WITH RFC[1000]
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