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−1vibrations, 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−1is 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−1is 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−1is much faster, probably due to the denaturation process of the double helical DNA.

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“…A confocal Raman microspectroscopic study into the vibrational half bandwidths of molecular subgroups in calf-thymus DNA at pH 7 and pH 3, in the presence of Na + , Ca 2+ and Mg 2+ ions, respectively, was previously reported by us [6]. The bandwidths in the Raman spectra were sensitive to a dynamics active on a time scale ranging from 0.34 to 1.44 ps [6,8,9].…”

“…Relating to molecular relaxation processes, Rakov developed one of the well-known procedures of obtaining the relaxation times and the activation energy [6][7][8][9][10]17].…”

“…In this approximation, the total half bandwidth of the depolarized Raman lines contains, two contributions [6][7][8][9]:…”

“…On contrary, the motion of molecular subgroups can be fast enough [9,16]. Different vibrational modes of a DNA molecule can behave quite different, upon changing the structure of nucleic acid by varying the pH or by the presence of proteins, metal ions and intercalators in the system [6,7,9,15].…”

“…The bandwidths in the Raman spectra were sensitive to a dynamics active on a time scale ranging from 0.34 to 1.44 ps [6,8,9].…”