Difference between revisions of "Part:BBa K1824562"

Latest revision as of 17:01, 5 September 2015

RNA Thermometer U6 (Specially designed for J23119)

This is a specially designed U6 RNA thermometer that with a unique spacer at the front, which would make it compatible with promoter BBa_J23119. It is important to noted that this part is not compatible with RFC[10]. XJTLU-CHINA used Gibson method to assembly this part to others.

U6 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 BBa_J23119, transcription starts at TAATGCTAGCA (transcription start site indicated in bold). Based on this, BBa_K1824562 was specially designed with a spacer that had less probability to interact with the functional structure of RNA thermometer.

The possible secondary structure of U6 was simulated by RNAstructure (Fig.1). For testing results of J23119-U6, See BBa_K1824002.

Left picture: XJTLU-CHINA (2015) Figure 1: Possible secondary structure of RNAT U6.
Right picture: TuDelft (2008) Figure 2: Responsiveness of mRNA structures to environmental cues.

Sequence and Features