Temperature dependence of Raman vibrational bandwidths in poly(rA) and rAMP

Journal of Spectroscopy

2007

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.

Section: Introductionmentioning

confidence: 99%

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

Journal of Spectroscopy

2007

“…A study into the vibrational bandwidths of adenine in the polynucleotide poly(rA) has been done [8]. The bandwidths obtained for poly(rA) were compared with those of the mononucleotide rAMP, in the temperature range where poly(rA) gradually changes from a base stacked structure to an unstacked structure [8].…”

Section: Introductionmentioning

confidence: 99%

“…The bandwidths obtained for poly(rA) were compared with those of the mononucleotide rAMP, in the temperature range where poly(rA) gradually changes from a base stacked structure to an unstacked structure [8]. The influence of macromolecular dynamics and solvent dynamics on the bandwidths of base vibrations in the single stranded polynucleotide poly(rA) have been elucidated [8].…”

Section: Introductionmentioning

confidence: 99%

Molecular relaxation processes in calf-thymus DNA, in the presence of Mn²⁺and Na⁺ions: A Raman spectroscopic study

2008

Spectroscopy

Abstract. In this paper the Raman total half bandwidths of calf-thymus DNA vibrations have been measured as a function of Mn 2+ ion concentration (0-600 mM), in the presence of two concentrations of Na + cations, respectively. The dependencies of the half bandwidths and of the global relaxation times on DNA molecular subgroup structure, on Mn 2+ and Na + ions concentrations, respectively, are reported. It is shown that changes in the (sub)picosecond dynamics of molecular subgroups in calf-thymus DNA can be monitored with Raman spectroscopy.In this study the Raman band parameters for the vibrations at 729 cm1376 cm −1 (dA, dG, dT, dC), 1489 cm −1 (dG, dA) and 1578 cm −1 (dG, dA) of calf thymus DNA are presented. The fullwidths at half-height (FWHH) of the bands in calf-thymus DNA are typically in the wavenumber range from 9 to 33.5 cm −1 . It can be observed that the molecular relaxation processes studied in this work, have a global relaxation time smaller than 1.179 ps and larger than 0.317 ps.Mn 2+ -induced DNA structural changes result for the vibrations at 729 cm −1 and 787 cm −1 in smaller global relaxation times, and larger half bandwidths, respectively, as compared to the starting value of 0 mM Mn 2+ . The vibrational energy transfer processes of these two subgroups (dA, dC), respectively, are slower in the case of DNA samples at 10 mM NaCl, as compared to the corresponding DNA samples at 150 mM NaCl. However, the behaviour of the global relaxation times characteristic to the bands at 729 and 787 cm −1 is similar with respect to manganese(II) ions concentration, in the case of the two values of Na + ions content, respectively.On the contrary, the molecular dynamics is slower for the base vibrations at 1376, 1489 and 1578 cm −1 , in the case of DNA samples at 150 mM NaCl, as compared to the corresponding samples at lower Na + concentration, in almost all Mn 2+ ions concentration range. The molecular relaxation processes in these three cases, respectively, are quite different for the corresponding samples with different Na + ions content, upon increasing divalent manganese ions concentration.The molecular dynamics characterizing the band near 1094 cm −1 of the DNA backbone PO 2 − symmetric stretching vibration is faster upon increasing the Mn 2+ ions concentration between 0-600 mM and seems not to be influenced by the Na + ions content, specific to our experimental conditions.

“…Isotropic and anisotropic spontaneous Raman spectra were obtained from solutions of poly(rA) and rAMP in buffer [9]. The temperature dependence of these spectra was measured to elucidate the influence of macromolecular dynamics and solvent dynamics on the bandwidths of base vibrations in the single stranded polynucleotide poly(rA) [9]. It has been found that the full widths at half-maximum (FWHM) of the bands in poly(rA) are typically [9] of the order of 12-20 cm −1 .…”

Section: Introductionmentioning

confidence: 99%

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

2008

Spectroscopy

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.