Difference between revisions of "Part:BBa K1824558"

Latest revision as of 12:13, 6 September 2015

RNA Thermometer A1 (Specially designed for T7)

This is a specially designed A1 RNA thermometer that with a unique spacer at the front, which would make it compatible with promoter T7 BBa_J64997.

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, truncation or alteration of the RNA sequence could be destructive. Hence, special designed RNA spacer between transcripted part of promoters and RNA thermometers are important for maintaining the secondary structure of RNA thermometer.

For BBa_J64997, transcription starts at CACTATAG (transcription start site indicated in bold). Based on this, BBa_K1824558 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 T7-A1, See BBa_K1824006.

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