Abstract

Small regulatory RNA is an active area of research with untapped possibilities for application in biotechnology. Such applications include convenient gene silencing and fine-tuning of gene expression, which are currently cumbersome processes restricted to well studied bacteria. We have investigated a novel type of RNA regulation, where the inhibition caused by a small regulatory RNA is relieved by another RNA called trap-RNA. We explore the possibility of using the system to uniquely target and repress any gene of interest providing unprecedented specificity and control of gene silencing.

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.

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Experiments 1

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.

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Experiments 2

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Modeling

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.

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Data

The data page provides a description of the constructed BioBricks and how they work.