Raman spectroscopic study on the subpicosecond dynamics in calf-thymus DNA, upon lowering the pH and in the presence of Mn²⁺ions

Abstract

In this paper the Raman total half bandwidths of calf-thymus DNA vibrations have been measured as a function of pH (3.45–6.4), in the presence of Mn2+ions, respectively. The dependencies of the half bandwidths and of the global relaxation times, on DNA molecular subgroup structure and on pH, are reported. It is shown that changes in the subpicosecond dynamics of molecular subgroups in calf-thymus DNA can be monitored with Raman spectroscopy.Particularly, the Raman band parameters for the vibrations at 728 cm–1(dA), 787 cm–1(dC), 1093 cm–1(PO2–), 1376 cm–1(dA, dG, dT, dC), 1489 cm–1(dG, dA) and 1578 cm–1(dG, dA) of MnDNA complexes, at reduced and low pH values, are presented. In our study, the full widths at half-maximum (FWHM) of the bands in calf-thymus DNA are typically in the wavenumber range from 11 to 27 cm–1. It can be observed that the molecular relaxation processes studied in this work, have a global relaxation time smaller than 0.965 ps and larger than 0.393 ps. The limit values are characteristic for dA and dC residues, respectively (vibrations at 728 and 787 cm–1).Low pH-induced melting of double helical structure in calf-thymus DNA, in the presence of Mn2+ions, results for some bands in smaller global relaxation times, and larger bandwidths, respectively, as a consequence of the increased interaction of the base moieties with the solvent molecules. This behaviour is most evident for the bands at 787 cm–1up to pH 3.8, at 1578 cm–1up to pH 3.45 and is partially confirmed for the DNA backbone PO2–symmetric stretching vibration at 1093 cm–1.The fastest molecular dynamics was obtained for the adenine band at 728 cm–1in the pH interval 3.45–3.8 (global relaxation time 0.885 ps), for the cytosine ring breathing mode near 787 cm–1around the pH 3.8 (global relaxation time 0.393 ps), for the band at 1093 cm–1in the pH interval 3.8–4.4 (global relaxation time 0.518 ps) and for the vibration near 1578 cm–1at pH 3.45 (global relaxation time 0.544 ps).A comparison between different time scales of the vibrational energy transfer processes, characterizing the protonated MnDNA structural subgroups has been given.We have found that metal ion's type and concentration are modulators for the (sub)picosecond dynamics of protonated DNA molecular subgroups.

Subpicosecond dynamics in DNA from leaves ofin vitro-grown apple plants: A SERS study

“…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].…”

“…Among the techniques available for the study of molecular motions in liquids, Raman scattering has the distinct advantage, that it enables simultaneous analyses of both reorientational and vibrational processes ( [3,4,8,9] and references therein).…”

“…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].…”

“…Also, the dependencies of the full widths at half-maximum (FWHM) and of the global relaxation times on DNA molecular subgroup structure and on pH values, in the presence of Mn 2+ ions, have been studied [8].…”

“…A study of the dynamics of the PO 3 2− group in aqueous solution can give information on the mononucleotide mobility and interactions in its natural solvent [2,8].…”