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Identifier

000414789

Title

A QCM-D study of the interactions of intercalating molecules with DNA

Alternative Title

Μελέτη των αλληλεπιδράσεων μεταξύ των μορίων του DNA και μορίων που παρεμβάλλονται στην δομή του με τον ακουστικό βιοαισθητήρα QCM-D

Author

Γιαρματζιάδη, Σοφία Α.

Thesis advisor

Γκιζελή, Ηλέκτρα

Abstract

Small molecules that interact with DNA have been used in the form of dyes, therapeutic agents for different diseases and in diagnostic applications throughout the years. All these drugs interact with DNA either covalently or non-covalently. Intercalation, a non-covalent type of binding, generally causes stabilization, local unwinding and lengthening in the DNA, but also interrupt some other biological functions. Ethidium bromide (EtBr), a typical example of mono-intercalator, is a widely-known trypanocidal drug which has been found to inhibit nucleic acid synthesis in a variety of organisms. GelRed, in the contrary, is a bis-intercalator designed with the purpose of replacing the highly toxic ethidium bromide (EtBr) in gel electrophoresis. To find the mechanism of binding of those small molecules to nucleic acids, several experimental studies have been performed. In this study, we wanted to monitor the structural changes in DNA molecules, after the binding of both ethidium bromide and GelRed with the use of a label-free acoustic technique, the quartz crystal microbalance (QCM-D). Measurements of the acoustic ratio ΔD/ΔF of the dsDNA molecules of various lengths, in combination with the “discrete molecule binding” approach are used to confirm the elongation of the DNA in the case of ethidium bromide. A further study of the mechanism of binding of GelRed with the DNA double helix is necessary. Spectrophotometric experiments were also carried out to study the binding kinetics of the two different agents and finally atomic force microscopy (AFM) experiments have confirmed the above mentioned elongation. To conclude, our results suggest that DNA elongation can be detected with a much easier and non-invasive method and this will further help in better and more efficient drug design and in the fields of acoustic biophysics and Nano biotechnology.

Language

English

Subject

AFM

Acoustic biosensors

EtBr

GelRed

Interclators

Βρωμιούχο αιθίδιο

Νουκλεϊκό οξύ

Issue date

2018-03-23