BBa_K1824560

BBa_K1824560 Version 1

Component

Source: http://parts.igem.org/Part:BBa_K1824560

Generated By: https://synbiohub.org/public/igem/igem2sbol/1

Created by: Wenbo Xu

Date created: 2015-09-04 11:00:00

Date modified: 2015-09-05 11:32:25

RNA Thermometer FourU (Specially designed for pBAD)

Details

• Types: DnaRegion
• Roles: RNA; mature_transcript_region
• Sequences: BBa_K1824560_sequence (Version 1)

Description

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.

Notes

To maintain the secondary structure of RNA thermometers, researchers need to be careful with of the use of any parts that couple with it. For instance, in some cases, part of operator region can be transcribed into RNAs and form tight secondary structure and thus interfere RNA thermometers.

Source

FourU was previously submitted by TuDelft 2008.

Other Properties

• igem#status: Planning
• synbiohub#ownedBy: user/james
• synbiohub#ownedBy: user/myers
• synbiohub#topLevel: BBa_K1824560/1

Member of these Collections

• iGEM Parts Registry