The Impact of ions on RNA aptamer-aminoglycoside interactions

Download

index.pdf

Date

2019

Author

Fazlıoğlu, Rezzan

Metadata

Show full item record

This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Item Usage Stats

177
views

95
downloads

Aptamers are small nucleic acid or peptide molecules that can bind to specific targets with high affinity. They have been applied for diagnostic, therapeutic and imaging purposes. In order to have the best performance of aptamers, it is worth understanding their structural dynamics. Previous studies have demonstrated that aptamer structures and thus their performances are affected by the surrounding sodium, potassium and magnesium ion concentrations. Based on these findings, we hypothesized that these ions may differently affect the binding affinity of nucleic acid aptamers. In our study, we investigated the effects of varying concentrations of sodium, potassium and magnesium ions on RNA aptamers that bind aminoglycosides. Using Isothermal Titration Calorimetry (ITC) and UV spectrophotometry, four neomycin-B binding RNA aptamers were tested in buffer solutions with different ionic contents. Our findings showed that the presence of magnesium leads to a significant change in both binding mode and affinity; whereas, potassium and sodium only affect the binding affinity of the aptamers. Depending on these results, we performed fluorescence assays with fluorophore-modified aptamers and the same buffers as used before. The change in the fluorescence signal between bound and unbound aptamers verified specific ligand binding and indicated that the concentrations and composition of these ions alter the three-dimensional structure and consequently affect the binding characteristics of aptamers. The main reason for the observed variation in aptamer performance seems to be the result of aptamers adapting to a predominant structure under a specific buffer condition. Therefore, components of the buffer systems that the aptamers are selected and optimized need to be carefully considered by researchers, because in the light of our results, the binding may get affected once the buffer system is modified by end-users.

Subject Keywords

RNA., RNA Aptamers, Metal Ions, Aminoglycosides, Isothermal Titration Calorimetry, UV Spectroscopy.

URI

http://etd.lib.metu.edu.tr/upload/12624760/index.pdf
https://hdl.handle.net/11511/44750

Collections

Graduate School of Natural and Applied Sciences, Thesis

Suggestions

OpenMETU
Core

The effect of para-cyclophane structure on cyclacenes Türker, Burhan Lemi (2000-02-01) Semiempirical molecular orbital treatment at the level of AMI type has been performed on the Huckel type cyclacenes having the normal and the skew type para-cyclophane moiety embedded into their structures. The cyclophane effect is found to be operative on the lower members by veiling the cryptoannulenic effect which is influential on the heats of formation values and the frontier molecular orbital energies of the higher members as well as the parent cyclacenes.
Investigating the malleability of RNA aptamers İlgü, Müslüm; Lamm, Monica H.; Nilsen-Hamilton, Marit (Elsevier BV, 2013-09-15) Aptamers are short, single-stranded nucleic acids with structures that frequently change upon ligand binding and are sensitive to the ionic environment. To achieve facile application of aptamers in controlling cellular activities, a better understanding is needed of aptamer ligand binding parameters, structures, intramolecular mobilities and how these structures adapt to different ionic environments with consequent effects on their ligand binding characteristics. Here we discuss the integration of biochemic...
The effect of cysteine-43 mutation on thermostability and kinetic properties of citrate synthase from Thermoplasma acidophilum Kocabıyık, Semra; Russel, RJM; Danson, MJ; Hough, DW (Elsevier BV, 1996-07-05) In this study, we have substituted serine-43 by cysteine in the recombinant citrate synthase from a moderately thermophilic Archaeon Thermoplasma acidophilum, for site-specific attachment of labels and have investigated the effects of this mutation on the biochemical properties and thermal stability of the enzyme. Both wild-type and the mutant enzymes were purified to homogenity using affinity chromatography on Matrex Gel Red A. The mutant Thermoplasma citrate synthase is very similar to wild-type citrate s...
Analysis of motifs in microRNA-transcription factor gene regulatory networks Sürün, Bilge; Acar, Aybar Can; Purutçuoğlu Gazi, Vilda; Department of Bioinformatics (2014) MicroRNAs are small non-coding RNA molecules which contain 21-25 nucleotides, and function in post transcriptional regulation by inhibiting the translation of mRNA targets. miRNAs typically affect gene regulation by forming composite feed forward circuits (cFFCs) which also comprise a transcription factor (TF) and a target gene. By analyzing these cFFCs, the contribution of miRNAs in altering TF networks can be revealed. These contributions could either be the de-escalation of the target gene repertoire or ...
The influence of humic acids extracted from Chaouia soil on the behavior of transition metal ions and pesticides Bougarrani, S.; El Azzouzi, L.; Bouzıanı, Asmae; Akel, S.; Latrach, L.; Baicha, Z.; El Azzouzi, M. (2017-01-01) Humic acids (HAs) exist ubiquitously in environments and have a variety of functional groups, which allow them to complex with metal ions and pesticides. Furthermore, these interactions can not only alter the environmental behavior, but also influence the removal and transportation of those pollutants. The study of the interaction between Cu (II), VO (II) and Mn (II) with HAs provides environmental information on the oxidation states of paramagnetic metals and their mechanisms of binding to humic acids. Ele...

Citation Formats

R. Fazlıoğlu, “The Impact of ions on RNA aptamer-aminoglycoside interactions,” Thesis (M.S.) -- Graduate School of Natural and Applied Sciences. Biotechnology., Middle East Technical University, 2019.