Fast Picosecond Dynamics in Polynucleotides by Raman Spectroscopy

2009

Abstract. In this paper the Raman total half bandwidths of eight genomic DNAs from leaf tissues [potato (Solanum tuberosum L.), sword fern (Nephrolepis exaltata L.), scopolia (Scopolia carniolica Jacq.), redwood (Sequoia sempervirens D. Don. Endl.), orchids (Cymbidium × hybrida), chrysanthemum (Dendranthema grandiflora Ramat.) and common sundew (Drosera rotundifolia L.)] have been measured. The dependencies of the total half bandwidths and of the global relaxation times, on DNA molecular subgroup structure and on the type of genomic plant DNA, are reported. It is shown that changes in the (sub)picosecond dynamics of molecular subgroups in genomic DNAs from leaf tissues can be monitored with Raman spectroscopy.Particularly, the Raman band parameters for the vibrations at 879 cm1455 cm −1 (deoxyribose, dA, dC, dT) and 1482 cm −1 (dG, dA) of genomic leaf tissues DNAs are presented. In our study, the full widths at half-maximum (FWHM) of the bands in genomic DNAs from leaf tissues are typically in the wavenumber range from 7.8 to 23.1 cm −1 . It can be observed that the molecular relaxation processes studied in this work, have a global relaxation time smaller than 1.36 ps and larger than 0.46 ps.The fastest and the slowest relaxation processes of different DNA structural subgroups, for several types of genomic DNA extracted from leaf tissue, have been analyzed. Particularly, the slowest dynamics corresponding to the vibration near 1272 cm −1 takes place in the case of DNA extracted from common sundew (global relaxation time 1.36 ps).A comparison between different time scales of the vibrational energy transfer processes, characterizing several DNA complexes, has been given.We have found that the bands at 879 cm −1 (deoxyribose, phosphodiester, dA) and 1455 cm −1 (deoxyribose, dA, dC, dT) are suitable for the study of dynamical behavior of molecular subgroups in genomic DNA extracted from leaf tissues.Specific molecular relaxation processes, depending on the type of genomic DNA extracted from leaf tissues has been observed.

Section: Discussionmentioning

confidence: 99%

FT-Raman study of the (sub)picosecond dynamics in genomic DNA from plant tissues

2009

“…Macromolecular motion in fluids is generally too slow to be observed in the Raman time window that is accessible in the frequency domain (∼0.1 ps to ∼8 ps). In principle motion of molecular subgroups can be fast enough [3].…”

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

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.

“…Spontaneous Raman scattering can be used to study the fast (sub)picosecond dynamics of molecules [5]. This paper presents a Raman spectroscopic study into the vibrational total half bandwidths of molecular subgroups in calf-thymus DNA, upon changing the concentrations of Mn 2+ ions, in the presence of two different concentrations of Na + cations, respectively.…”

Section: Discussionmentioning

confidence: 99%

“…The macromolecular motion in fluids is generally too slow to be observed in the Raman time window that is accessible in the frequency domain. In principle motion of the molecular subgroups can be fast enough [5].…”

Section: Introductionmentioning

confidence: 99%

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

2008

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.