Molecular dynamics in calf-thymus DNA, at neutral and low pH, in the presence of Na⁺, Ca²⁺ and Mg²⁺ ions: A Raman microspectroscopic study

Abstract

In this paper the Raman total half bandwidths of calf-thymus DNA vibrations have been measured as a function of pH, monovalent and divalent cations' type and concentration. The dependence of different band parameters on DNA molecular subgroup structure, on pH and on Na⁺, Ca²⁺ and Mg²⁺ ions concentrations, respectively, are reported. It is shown that changes in (sub)picosecond dynamics of molecular subgroups in calf-thymus DNA can be monitored with confocal Raman microspectroscopy.The half bandwidths and the global relaxation times for the vibrations at 728 cm⁻¹ (dA), 785 cm⁻¹ (dC), 1094 cm⁻¹ (PO₂⁻), 1377 cm⁻¹ (dA, dG, dT, dC), 1488 cm⁻¹ (dG, dA) and 1580 cm⁻¹ (dG, dA) of calf-thymus DNA are presented. The full-widths at half-height (FWHH) of the bands in calf-thymus DNA are typically in the wavenumber range from 7.4 to 31 cm⁻¹. The bandwidths in the Raman spectra are sensitive to a dynamics active on a time scale from 0.34 to 1.44 ps.Low pH-induced melting of double helical structure in calf-thymus DNA results for some bands in shorter global relaxation times, as a consequence of the increased interaction of the base moieties with the solvent molecules.The molecular dynamics characterizing the 785, 1094, 1377 and 1580 cm⁻¹ vibrations, is faster in the case of high divalent cations DNA sample (pH 7), as compared to the respective low divalent cations DNA sample (pH 7), for both Ca²⁺ and Mg²⁺ ions. The vibrational energy transfer process of the guanine band at 1488 cm⁻¹ is slower for the high salt DNA sample, pH 7 as compared to the corresponding low salt DNA sample, pH 7, for both Ca²⁺ and Mg²⁺. Molecular dynamics characterizing the vibration at 1488 cm⁻¹ is faster for DNA sample at high Na⁺ ions (pH 7), as compared to the DNA sample at low Na⁺ ions (pH 7).As far as the CaDNA and MgDNA complexes are concerned (pH 7), the global relaxation times of some base vibrations decrease for the case of magnesium ions, as compared to the case of the same concentration of calcium ions. The different ionic radius of the two types of metal cations (0.72 Å for Mg and 0.99 Å for Ca) were considered in explaining these results.Molecular relaxation processes of DNA subgroups, upon lowering the pH, in the presence of Na⁺, Ca²⁺ and Mg²⁺ ions are presented. Particularly, at low Ca²⁺ concentration, upon lowering the pH, the molecular dynamics of DNA subgroups corresponding to vibrations at 728, 1376, 1488 and 1580 cm⁻¹ is much faster, probably due to the denaturation process of the double helical DNA.