Part:BBa_K1824561

RNA Thermometer FourU (Specially designed for T7)

This is a specially designed FourU RNA thermometer that with a unique spacer at the front, which would make it compatible with T7 promoter BBa_J64997.

FourU 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 T7 promoter BBa_J64997, transcription starts at CACTATAG (transcription start site indicated in bold). Based on this, BBa_K1824561 was specially designed with a spacer that had less probability to interact with the functional structure of RNA thermometer.

The possible secondary structure of FourU was simulated by RNAstructure (Fig.1). For testing results of T7-FourU, See BBa_K1824007.

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