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Team:TUDelft/Temperature overview
From 2008.igem.org
Overview
We want to create an RNA-based system that is able to have differential gene expression when temperature changes take place (comparable to the [http://parts.mit.edu/wiki/index.php/Berkeley2006-RiboregulatorsMain Berkeley iGEM 2006] riboregulator lock/key part). There are several systems suggested in literature that are based on RNA secondary structure [1]. The idea in general is that if the temperature drops below a certain temperature, the RNA will form stable base-pairs on the Shine-Dalgarno sequence, disabling the ribosome to bind. The base-pairing of this RNA region will block the expression of the protein encoded behind it. In this way gene expression can be regulated on the RNA level by temperature.
. In the first phase it is tested if it is possible to turn an existing RNA thermometer into a biobrick and get it to work in e. coli. Some known RNA thermometers are taken from literature and turned into a standard biobrick. The parts are added to the partsregistry and the ordered to be tested. The aim of the second phase is to design an artificial RNA thermometer that has a different temperature threshold, i.e. initiate the translation process at a different temperature. A literature study is done as a basis for the design, which is used to design parts that should theoretically be switched on at 27 and 32 degrees Celcius.
At the beginning of the project, an analysis has been performed to get more insight into the functioning of an RNA thermometer. The design of the temperature sensitive switch is divided in two phases. In the first phase existing RNA thermometers are turned into BioBrick Standard Biological Parts. In the second phase, an RNA thermometer has been redesigned in order to shift the switching temperature using the knowledge gained during the analysis.
Also some Team:TUDelft/Temperature_software tools have been developed during the project. The first tool, the Stability Profile PlotterTeam:TUDelft/Temperature_software#Stability_Profile_Plotter, has been used for the analysis to produce plots that characterize the stability of an RNA hairpin structure. The second tool, the RNA Hairpin Designer, provides a (partial) implementation of the design approach as proposed in the second design phase. This tool can be used for the design of temperature sensitive RNA hairpins.
References
- ^ Narberhaus F. mRNA-mediated detection of environmental conditions. Archives of Microbiology, 178(6):404-410, 2002. [http://www.ncbi.nlm.nih.gov/pubmed/16680139 PMID:16680139]
