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Title: Computational design of orthogonal microRNAs for synthetic biology
Authors: Trybilo, Maciej
Advisors: Gilbert, D
Harvey, A
Keywords: Circuit;Eukaryotic;Genetic
Issue Date: 2013
Publisher: Brunel University, School of Information Systems, Computing and Mathematics
Abstract: Upcoming applications of synthetic biology will require access to a wide array of robust genetic components (parts). The logic of a genetic system is encoded with regulatory elements such as pairs of transcription factors:promoters, miRNAs:target sites, or ribozymes:aptamers among others. Due to a relatively simple form and mode of operation of miRNAs, it is possible to design their synthetic variants. Out of all possible miRNA sequences the ones chosen should perform efficiently and should avoid cross-talk with both the host system circuits and within the imported synthetic ones. In this work, a computational method involving a series of heuristics is developed that can be used to design ensembles of such sequences depending on the host transcriptome. As an example, an ensemble of eight such miRNA sequences is produced using this method for use in a human host. Those have then been validated experimentally against the above-mentioned requirements by transfection into HEK 293 cells and flow cytometry measurements of fluorescent markers. The produced sequences are available for use from pENTR vectors of the Gateway cloning system. The required computations were facilitated by a modern cluster computing system—Kaichu—especially developed for this project, but fit for general purpose use and available under an open-source license.
Description: This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.
Appears in Collections:Computer Science
Dept of Computer Science Theses

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