Investigating stability of RNA i-motif

Campos Carrillo De Preciado, Zara (2018) Investigating stability of RNA i-motif. Masters thesis, University of East Anglia.

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Abstract

Cytosine-rich sequences can form 4-stranded structures called i-motifs. i-Motifs are formed by two duplexes intercalated in an antiparallel direction and held together through the hemi- protonated cytosine-cytosine base pairs, and they are stabilized by acidic conditions, which promote C-C base pairing via hemi-protonation of the N3. i-Motif structure can form in both molecules of DNA and RNA, but RNA i-motifs are less stable than their DNA counterparts. This dissertation describes the study of the stability of RNA i-motifs including characterizing 10 cytosine-rich sequences with variable tract length in [CnU3]3Un at two different pH: 5.5 and pH 7.4. A plant sequence AT5G08230.1 RNA identified in Arabidopsis thaliana was characterized at pH 5.8 by mimicking crowding with PEG 8,000, and drought conditions using KCl. From our knowledge, there are no examples of functional i-motif structures in plants, but they are of particular interest with respect to potential i-motif formation knowing that plants often thrive in acidic conditions where i-motifs are stable. By using some biophysical techniques like Ultraviolet (UV), Circular Dichroism (CD), and thermal difference spectra (TDS), we found all our cytosine-rich sequences were shown to be stable at pH 5.5, except C1U3 and sequences with 5 or more cytosines per tract length fold into stable i-motif structure. Also, we have found the stability of the folded structures increases as the number of cytosines per tract. UV spectroscopy has showed an increase in the melting and annealing temperature for all C-rich sequences when the number of cytosines per tract increase. On the other hand, at pH 7.4 RNA i-motif structure was not observed. We have observed that AT5G08230.1 RNA can form i-motif at pH 5.8 where plants normally thrive, and have confirmed the RNA i-motif can be stabilized at 4°C using PEG 8,000 (40%) and KCl (100 mM and 800 mM).

Item Type: Thesis (Masters)
Faculty \ School: Faculty of Science > School of Pharmacy
Depositing User: Gillian Aldus
Date Deposited: 07 Dec 2018 10:40
Last Modified: 07 Dec 2018 10:40
URI: https://ueaeprints.uea.ac.uk/id/eprint/69193
DOI:

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