In this doctoral thesis, the impact of sodium and magnesium ions on the structure and dynamics of deoxyribonucleic acid (DNA) was investigated utilizing Fourier transform infrared spectroscopy on DNA thin films. DNA thin films were obtained from a series of genomic DNA solutions of constant DNA concentration: Na-DNA (DNA with intrinsic sodium counterions) in pure water, 10 mM sodium chloride and magnesium chloride of various ionic strengths, and Mg-DNA (DNA with intrinsic magnesium counterions) in pure water and magnesium chloride of various ionic strengths. Such a choice of samples allowed the research of the effect of the concentration of the added salt as well as of the competition of intrinsic and added counterions on DNA structure and conformation. By preparation of thin films from solutions the influence of vibrational bands of bulk water that would impede the proper detection of DNA vibrational bands in the base region was avoided. Spectra of thin films obtained from Na-DNA in solution of sodium chloride and Na-DNA in pure water have shown that DNA retains its double helical structure (ds) under drying protocol so the spectrum of Na-DNA in pure water was chosen as a reference. In order to address how the behaviour of DNA evolves upon progressive addition of Mg2+ cations, an extensive investigation of infrared vibrational properties of Na-DNA in a broad range of added magnesium chloride salt concentration with cation to phosphate ratio, [Mg]/[P], between 0.0067 and 30 was performed. The obtained results revealed that at low magnesium concentrations the magnesium cations interact with the phosphate groups of the DNA, while with the further increase of magnesium concentration they interact with the base sites as well, via long-range electrostatic interactions. At highest [Mg]/[P] ratios the possibility of structural transition into a more compact form is discussed based on both the experimental results and calculations of DNA charge neutralization by Manning’s two variable condensation theory. The vibrational properties of Mg-DNA in pure water and Mg-DNA in a broad range of added magnesium chloride salt concentrations with cation to phosphate ratio, r=[Mg]/[P], between 0.0067 and 10 were investigated and compared with the results of Na-DNA in the same concentration range. The spectra of thin films Mg-DNA in pure water showed slightly different vibrational properties then Na-DNA in pure water and a significantly higher portion of B form DNA was observed. At low concentrations of magnesium ions (r < 1) spectra of Na-DNA in MgCl2 and Mg-DNA in MgCl2 show substantial differences which were attributed to the influence of the intrinsic sodium and magnesium ions on DNA. On the other hand, Na-DNA in MgCl2 and Mg-DNA in MgCl2 at higher concentrations of magnesium ions show similar vibrational properties.