Team:DTU-Denmark/Project

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A bioinformatic study was performed to investigate the possibilities of engineering the trap-RNA system to target any gene. The study elucidates interesting features of sequence and secondary structure conservation guiding future application. For full analysis go to [[Team:DTU-Denmark/Bioinformatic|bioinformatic]].
A bioinformatic study was performed to investigate the possibilities of engineering the trap-RNA system to target any gene. The study elucidates interesting features of sequence and secondary structure conservation guiding future application. For full analysis go to [[Team:DTU-Denmark/Bioinformatic|bioinformatic]].
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==References==
 
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[1] Datsenko, K.A. & Wanner, B.L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proceedings of the National Academy of Sciences 97, 6640-6645(2000).
 
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[2] Figueroa-Bossi, Nara, Martina Valentini, Laurette Malleret, and Lionello Bossi. “Caught at its own game: regulatory small RNA inactivated by an inducible transcript mimicking its target.” Genes & Development 23, no. 17 (2009): 2004 -2015.
 
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[3] Hayashi, K. et al. Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110. Molecular Systems Biology 2, 2006.0007(2006).
 
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[4] Lambert, J.M., Bongers, R.S. & Kleerebezem, M. Cre-lox-based system for multiple gene deletions and selectable-marker removal in Lactobacillus plantarum. Applied and environmental microbiology 73, 1126-35(2007).
 
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[5] Overgaard, Martin, Jesper Johansen, Jakob Møller‐Jensen, and Poul Valentin‐Hansen. “Switching off small RNA regulation with trap‐mRNA.” Molecular Microbiology 73, no. 5 (September 2009): 790-800.
 
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Revision as of 17:55, 20 September 2011

Project

Contents

The abstract

Small regulatory RNA is an active area of research with untapped possibilities for application in biotechnology. A novel type of small RNA regulation displaying favorable properties was investigated ...

Schematic representation of RNA interactions in trap-RNA system. Blue is any target mRNA. Red is sRNA. Green is trap-RNA.

Experiments

Verifying that the envisioned small RNA based gene silencing is possible. Plasmids containing and strains deleted for the components were constructed providing a biological model. The dynamic range of the araBAD promoter was expanded. For full description see experiments

Modeling

Kinetic models of the system are the basis for modeling. Blue is target mRNA, red is small RNA and green is trap-RNA

A framework for characterization was developed to guide rational design and test hypotheses. Steady state analysis revealed that each trap-RNA system has a characteristic fold repression. For more information got to modeling.

Bioinformatic

A bioinformatic study was performed to investigate the possibilities of engineering the trap-RNA system to target any gene. The study elucidates interesting features of sequence and secondary structure conservation guiding future application. For full analysis go to bioinformatic.

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