IR Study on the Relaxation of the Phosphate Group of 5‘-dCMP in2H2O and H2O Solutions

Hernanz, A.; Bratu, and Ioan; Navarro, R.

doi:10.1021/jp030853o

Cited by 14 publications

(23 citation statements)

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“…photochemistry, electron transfer, reaction dynamics, thermal chemistry, photobiological processes such as vision and photosynthesis and excimer formation ( [1,8] and references therein).…”

Section: Introductionmentioning

confidence: 99%

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

Muntean

Bratu

2009

Spectroscopy

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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.

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“…photochemistry, electron transfer, reaction dynamics, thermal chemistry, photobiological processes such as vision and photosynthesis and excimer formation ( [1,8] and references therein).…”

Section: Introductionmentioning

confidence: 99%

“…In relation to the relaxation processes of the IR ν s (PO 3 2− ) band of disodium deoxycytidine 5 -monophosphate, 5 -dCMP, in 2 H 2 O and H 2 O, a band-shape analysis of this vibrational mode has been performed [1]. The second derivative spectra reveal the presence of 5 -dCMP aggregates when concentration reaches ∼0.28 mol dm −3 .…”

Section: Introductionmentioning

confidence: 99%

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

Muntean

Bratu

2009

Spectroscopy

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“…Self-association of this mononucleotide is detected at concentrations higher than ∼0.28 mol dm −3 [1].…”

Section: Introductionmentioning

confidence: 90%

“…The dynamics and vibrational relaxation processes of biomolecules in aqueous solutions have motivated several researches [1]. Studies of molecular relaxations in liquids are valuable in providing information about the intermolecular interaction processes in condenced matter [2].…”

Section: Introductionmentioning

confidence: 99%

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

Muntean

Bratu

2008

Spectroscopy

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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.

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“…Particularly, vibrational relaxation plays a crucial role in many aspects of chemistry, physics and biology ( [1,10] and references therein). A number of dynamical processes which have been considered to broaden the vibrational bands of nucleic acids in the frequency domain, are: vibrational resonance coupling, vibrational energy exchange, vibrational dephasing and rotational broadening ( [7,19] and references therein).…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2011

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Abstract. In this work the SERS total half bandwidths of five genomic DNAs from in vitro-grown apple leaf tissues (Malus domestica Borkh., Fam Rosaceae, cvs. Florina, Rebra, Goldrush, Romus 3 and Romus 4) have been measured. We have shown that surface-enhanced Raman scattering can be used to study the fast subpicosecond dynamics of DNA in the proximity of a metallic surface. The dependencies of the total half bandwidths and of the global relaxation times, on DNA molecular subgroup structure, on the type of genomic apple plant DNA and on time, are reported. An example of the time-dependence of SERS band parameters of DNA, in the proximity of silver nanoparticles, has been given. It is shown that changes in the subpicosecond surface dynamics of molecular subgroups in genomic DNAs from in vitro-grown apple leaf tissues can be monitored with surface-enhanced Raman spectroscopy.Particularly O)] of genomic DNAs from apple leaves are presented. In our study, the full widths at half-maximum (FWHM) of the bands in genomic DNAs from in vitro-grown apple leaf tissues are typically in the wavenumber range from 14 to 52 cm −1 . Besides, it can be observed that molecular relaxation processes studied in this work, have a global relaxation time smaller than 0.76 ps and larger than 0.20 ps.A comparison between different ranges of FT-Raman and SERS band parameters of DNA extracted from leaf tissues, respectively, is given.We have found that the bands of DNA from Romus 3 and Rebra cultivars are suitable for studying the dynamical behaviour of molecular subgroups, in genomic nucleic acids extracted from in vitro-grown apple plants.

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IR Study on the Relaxation of the Phosphate Group of 5‘-dCMP in²H₂O and H₂O Solutions

Cited by 14 publications

References 103 publications

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

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

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

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

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IR Study on the Relaxation of the Phosphate Group of 5‘-dCMP in2H2O and H2O Solutions

Cited by 14 publications

References 103 publications

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

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

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

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

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IR Study on the Relaxation of the Phosphate Group of 5‘-dCMP in²H₂O and H₂O Solutions

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