Phylogenetic and synteny analysis supported gdi3 as a novel gene currently found only in Anura and Teleosti. This novel gene, designated as gdi3, was shown to belong to the gdi family of proteins known to function as Rab-GTPAse effectors. One of these promoters drove a previously unknown gene which was selected for further functional analysis.

Circular dichroism was used to validate the presence A-form elements within five identified promoters and EMSA confirmed these putative cis-acting elements were targets for specific DNA binding proteins. Here a novel bioinformatic tool was used to screen the Xenopus genome for combined promoter sequences consisting of an A-DNA secondary structure in combination with a known sequence motif. DNA sequences with A-form propensity have been proposed to be involved in gene regulation through an indirect readout promoter recognition mechanism.

There are several different DNA conformations, one of which is A-form. In general, less is known about DNA regions that may adopt non-canonical DNA structures than other sequences and specifically little is known about the non-conventional ways that transcription factors can interact with unusual DNA structures. Genes are preceded by non-coding promoter regions which contain the regulatory cis- elements, read by the trans-acting transcription factors, some of these promoters are known to adopt unusual DNA structures. Each cell type resulting in the process of development has a signature of specifically expressed genes and conversely a set of specifically silenced genes. Genetic information must be decoded by a single cell embryo to allow development into an adult organism. In particular, the importance of non-coding DNA sequences and the mechanisms by which these sequences can regulate gene expression is an area of growing research. iiiĤ Abstract Despite the incredible technological advancements of the last 100 years much is still to be learnt about the biological function of DNA. The results and conclusions embodied in this thesis are the work of the named candidate, except where specified, and have not been submitted for any other academic award. February 2016 Institute of Biomedical & Biomolecular Sciences School of Biological Sciences University of PortsmouthĢ This thesis is dedicated to the loving memory of my brother Teofil! iiģ Declaration While registered as a candidate for the above degree, I have not been registered for any other research award. 1 Identification and characterization of an A-form DNA promoter and its downstream novel Rab-Gdi gene in Xenopus Liliya Angelova Nazlamova The thesis is submitted in partial fulfilment of the requirements for the award of the degree of Doctor of Philosophy of the University of Portsmouth.

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