Spectroscopic studies of ligand binding to DNA are based on measuring the change in the spectroscopic properties of the sample solution resulting from the binding itself. Thus, with the help of UV-Vis spectroscopy, we can measure the absorption UV-Vis spectra during binding, and with the help of the Scatchard diagram, we can determine the strength and stoichiometry of the binding of the ligand to DNA.
In my diploma thesis, I studied the binding of ligands to a molecule of natural double-stranded DNA from bovine sputum. The selected ligands were DAPI, acridine orange and methylene blue. The analysis confirms that ligands bind to DNA in a similar way, namely in a narrower DNA channel, with electrostatic interactions between the ligand molecule and DNA playing an important role. All ligands also have in common that they intercalate between base pairs in DNA, which we were able to demonstrate only for the ligand methylene blue.
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