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Undergraduate Thesis

This repository contains my Undergraduate Thesis entitled Computational Design and Experimental Testing of Biological Logic Gates with Synthetic Ribozymes

It was written for the completion of the B.Sc. Honours in Cell and Molecular Biology program in May 2014 at Concordia University in Montreal, Canada.

The Abstract

Computation and the generation of logic gates in biological systems has become a focus of research in the twenty-first century due to its significant potential in synthetic biology and bioengineering. The rational bioinformatic design process for the implementation of NOR, OR, XNOR and XOR logic gates using a novel pair of ribozyme-based RNAs is proposed and assessed. The use of RNA in the generation of logic gates is advocated as a modular, expedient and flexible alternative to traditional protein or DNA enzymes. The experimental testing of the XNOR gate is realized in vivo and proposed in vitro with the targeting of the RFP mRNA as the gate output. The generation of ribozyme expression vectors is accomplished through restriction enzyme digestion and ligation experiments, and a spectrophotometric assay for the RNA regulation via transcript degradation of RFP in DH5α culture is carried out. The obtained results for the success of the XNOR gate are inconclusive and require further study regarding the efficiency of ribozyme cleavage and sequestering and spectrofluorometric assays of the RFP output signal.


The formatted PDF file of the thesis is in the repository and can be downloaded directly from GitHub. The PDF is also available to view online here at

The License

This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. (CC BY-NC-ND 4.0). You are free to share this work, but if you do so, you must give me appropriate credit and provide a link to the license. This work cannot be used for commercial purposes, and you cannot distribute any new materials derived from this work. Here is the full legal code of the license in all its detail.


Undergraduate thesis for the completion of the B.Sc Honours in Cell and Molecular Biology at Concordia University (May 2014).






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