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

2008 ◽  
Vol 22 (6) ◽  
pp. 475-489 ◽  
Author(s):  
Cristina M. Muntean ◽  
Ioan Bratu
Keyword(s):  
Relaxation Time ◽  
Vibrational Energy ◽  
Raman Band ◽  
Relaxation Times ◽  
Low Ph ◽  
Calf Thymus Dna ◽  
Relaxation Processes ◽  
Molecular Subgroups ◽  
Limit Values ◽  
Calf Thymus

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.

scholarly journals Subpicosecond dynamics in calf-thymus DNA, in the presence of Zn2+ions: A Raman spectroscopic study

2009 ◽  
Vol 23 (3-4) ◽  
pp. 141-154 ◽  
Author(s):  
Cristina M. Muntean ◽  
Ioan Bratu ◽  
Konstantinos Nalpantidis ◽  
Monica A. P. Purcaru
Keyword(s):  
Vibrational Energy ◽  
Raman Band ◽  
Relaxation Times ◽  
Calf Thymus Dna ◽  
Relaxation Processes ◽  
Molecular Subgroups ◽  
Molecular Subgroup ◽  
Limit Values ◽  
Calf Thymus ◽  
Solvent Molecules

In this paper the Raman total half bandwidths of calf-thymus DNA vibrations have been measured as a function of Zn2+ions concentration, in the presence of a constant concentration of Na+ions, respectively. The dependencies of the total half bandwidths and of the global relaxation times, on DNA molecular subgroup structure and on Zn2+ions concentration, are reported. It is shown that changes in the subpicosecond dynamics of molecular subgroups in ZnDNA complexes can be monitored with Raman spectroscopy.Particularly, the Raman band parameters for the vibrations at 729 cm−1(dA), 792 cm−1(dC, dT and 5'-C–O–P–O–C-3' network), 1094 cm−1(DNA backbone PO2−symmetric stretching), 1377 cm−1(dA, dT, dC), 1489 cm−1(the guanine N-7 and adenine rings) and 1581 cm−1(dG, dA) of ZnDNA complexes, in the presence of Zn2+ions concentrations that varied between 0 and 250 mM, are presented. In our study, the full widths at half-maximum (FWHM) of the bands in calf-thymus DNA complexes are typically in the wavenumber range from 10 to 50 cm−1. It can be observed that the molecular relaxation processes studied in this work, have a global relaxation time smaller than 0.94 ps and larger than 0.21 ps. The limit values are characterizing the dA and dG residues, respectively (vibrations at 729 cm−1and 1489 cm−1).Binding of Zn2+ions to double helical calf-thymus DNA results for some vibrations in smaller global relaxation times and larger bandwidths, respectively, possible as a consequence of the increased interaction of the base moieties with the solvent molecules in unstacked structures.The fastest and the slowest dynamics for different DNA structural subgroups and different Zn2+ions concentrations, respectively, have been analyzed.A comparison between different time scales of the vibrational energy transfer processes, characterizing the ZnDNA structural subgroups has been given.We have found that metal ion's type and concentration are modulators for the (sub)picosecond dynamics of calf thymus DNA molecular subgroups.

scholarly journals 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 ◽  
Vol 21 (4) ◽  
pp. 193-204 ◽  
Author(s):  
Cristina M. Muntean ◽  
Ioan Bratu
Keyword(s):  
Molecular Dynamics ◽  
Vibrational Energy ◽  
Divalent Cations ◽  
Relaxation Times ◽  
Helical Structure ◽  
Low Ph ◽  
Calf Thymus Dna ◽  
Relaxation Processes ◽  
Molecular Subgroup ◽  
Calf Thymus

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.

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

2008 ◽  
Vol 22 (5) ◽  
pp. 345-359 ◽  
Author(s):  
Cristina M. Muntean ◽  
Ioan Bratu
Keyword(s):  
Molecular Dynamics ◽  
Structural Changes ◽  
Vibrational Energy ◽  
Raman Band ◽  
Relaxation Times ◽  
Ion Concentration ◽  
Calf Thymus Dna ◽  
Relaxation Processes ◽  
Molecular Relaxation ◽  
Calf Thymus

In this paper the Raman total half bandwidths of calf-thymus DNA vibrations have been measured as a function of Mn2+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 Mn2+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 cm-1(dA), 787 cm-1(dC), 1094 cm-1(PO2-), 1376 cm-1(dA, dG, dT, dC), 1489 cm-1(dG, dA) and 1578 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 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.Mn2+-induced DNA structural changes result for the vibrations at 729 cm-1and 787 cm-1in smaller global relaxation times, and larger half bandwidths, respectively, as compared to the starting value of 0 mM Mn2+. 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-1is 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 Mn2+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-1of the DNA backbone PO2-symmetric stretching vibration is faster upon increasing the Mn2+ions concentration between 0–600 mM and seems not to be influenced by the Na+ions content, specific to our experimental conditions.

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

2009 ◽  
Vol 23 (5-6) ◽  
pp. 281-289 ◽  
Author(s):  
Cristina M. Muntean ◽  
Ioan Bratu
Keyword(s):  
Relaxation Time ◽  
Genomic Dna ◽  
Vibrational Energy ◽  
Raman Band ◽  
Dynamical Behavior ◽  
Relaxation Processes ◽  
Molecular Subgroups ◽  
Molecular Relaxation ◽  
Leaf Tissues ◽  
Genomic Dnas

In this paper the Raman total half bandwidths of eight genomic DNAs from leaf tissues [potato (Solanum tuberosumL.), sword fern (Nephrolepis exaltataL.), scopolia (Scopolia carniolicaJacq.), redwood (Sequoia sempervirensD. Don. Endl.), orchids (Cymbidium × hybrida), chrysanthemum (Dendranthema grandifloraRamat.) and common sundew (Drosera rotundifoliaL.)] 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 cm−1(deoxyribose, dA), 1047 cm−1(CO stretching C‒O‒P‒O‒C, dG), 1089 cm−1(P—O symmetric stretching of PO2‒), 1124 cm−1(dA), 1272 cm−1(dC, dG, dT), 1276 cm−1(dC), 1455 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−1takes 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.

Relaxation Time Spectrum, Elasticity, and Viscosity of Rubber. I

1954 ◽  
Vol 27 (1) ◽  
pp. 36-54 ◽  
Author(s):  
W. Kuhn ◽  
O. Künzle ◽  
A. Preissmann
Keyword(s):  
Relaxation Time ◽  
Relaxation Times ◽  
Time Spectrum ◽  
Test Sample ◽  
Elastic Behavior ◽  
Relaxation Processes ◽  
Relaxation Time Spectrum ◽  
Restoring Force ◽  
Constant Length ◽  
Rapid Deformation

Abstract By rapid deformation of a medium in which linear molecules are present, various changes are produced simultaneously in the latter. These changes are more or less independent of one another, and can release independently and totally or partially by rearrangement of valence distances and valence angles in the chain molecules. By virtue of such relaxation processes, a portion of the stress originating in the rapid deformation disappears, with a changing time requirement for the various portions. A relaxation time spectrum is thus formed. The relaxation time spectrum consists of a finite number of restoring force mechanisms with proper relaxation times or of a continuous spectrum. Both the creep curves (the dependence of the length of a body on time at constant load), and stress relaxation (decay of the stress observed in test sample kept at constant length after rapid deformation), as well as the total visco-elastic behavior, especially the behavior at constant periodic deformation of the test sample, are determined by the relaxation time spectrum. The appropriate Quantitative relationships were derived.

Ultrasonic dispersion in gaseous sulphur dioxide

1957 ◽  
Vol 243 (1232) ◽  
pp. 78-83 ◽  
Keyword(s):  
Relaxation Time ◽  
Sulphur Dioxide ◽  
Major Part ◽  
Vibrational Energy ◽  
Vibrational Mode ◽  
Relaxation Times ◽  
Ultrasonic Waves ◽  
Ultrasonic Frequency ◽  
Ultrasonic Dispersion ◽  
Dispersion Zone

The velocity of ultrasonic waves has been measured in gaseous sulphur dioxide at 20, 102 and 200° C for values of f/p ranging from 200 kcs -1 atm -1 to 7 Mcs -1 atm -1 . ( f is the ultrasonic frequency, p the pressure.) Dispersion involving the major part of the vibrational specific heat was found at all temperatures. Each dispersion zone corresponds to two distinct relaxation times differing by a factor of ten. The lower relaxation time corresponds with activation of the lowest (519 cm -1 ) vibrational mode, the higher to activation of the remainder of the vibrational energy. The conditions giving rise to a double relaxation process are discussed.

Molecular Transformations in DNA under the Influence of UV-radiation

2020 ◽  
Vol 04 ◽  
Author(s):  
Vigen G. Barkhudaryan ◽  
Gayane V. Ananyan ◽  
Nelli H. Karapetyan
Keyword(s):  
Uv Radiation ◽  
Uv Irradiation ◽  
Absorption Spectroscopy ◽  
Calf Thymus Dna ◽  
Dilute Solutions ◽  
Concentrated Solutions ◽  
Buffer Solution ◽  
Low Concentration ◽  
Calf Thymus ◽  
Dna Solutions

Background: The processes of destruction and crosslinking of macromolecules occur simultaneously under the influence of ultraviolet (UV) radiation in synthetic polymers, dry DNA and their concentrated solutions. Objective: The effect of UV radiation on calf thymus DNA in dilute solutions subjected to UV- irradiation was studied in this work. Method: The calf thymus DNA was studied in dilute solutions using viscometry, absorption spectroscopy and electrophoresis. Results: It was shown, that at a low concentration of DNA in the buffer solution ([DNA] = 85 μg / ml) under the influence of UV radiation, the processes of destruction of macromolecules and an increase in their flexibility predominate, which is accompanied by a gradual decrease in the viscosity of their solution. In addition, due to the low concentration of the solution, intramolecular crosslinking of macromolecules predominates, which also reduces their size and, consequently, the viscosity of the solution. Conclusion: It was concluded, that in dilute DNA solutions, due to the predominance of the processes of intramolecular crosslinking of macromolecules over intermolecular, only constant processes of decreasing the sizes of DNA macromolecules occur. As a result, its solubility remains virtually unchanged during UV irradiation. The described comments are also excellently confirmed by the results of absorption spectroscopy and electrophoresis

Ce(IV)-mediated formation of benzenediazonium ion from a non-aminoazo dye, 1-phenylazo-2-hydroxy-naphthalene (Sudan I) and its binding to DNA

1989 ◽  
Vol 54 (7) ◽  
pp. 2021-2026
Author(s):  
Marie Stiborová ◽  
Befekadu Asfaw ◽  
Pavel Anzenbacher
Keyword(s):  
Azo Dyes ◽  
Acidic Medium ◽  
Model System ◽  
Calf Thymus Dna ◽  
Suitable Model ◽  
Principal Product ◽  
Calf Thymus ◽  
Sudan I ◽  
A Minor

Ce(IV) ions in acidic medium convert a carcinogenic non-aminoazo dye, 1-phenylazo-2-hydroxy-naphthalene (Sudan I) into an ultimate carcinogen, which binds to calf thymus DNA. The principal product of Sudan I oxidation by the Ce(IV) system is the benzenediazonium ion. A minor product is the dihydroxyderivative of Sudan I, 1-(4-hydroxyphenylazo)-2,6-dihydroxynaphthalene. Other minor coloured products (yellow and brown) were not identified. The principal product (the benzenediazonium ion) is responsible for the carcinogenicity of Sudan I, as it covalently binds to DNA. Ce(IV) ions in acidic medium represent a suitable model system, which imitates the activation route of carcinogenic azo dyes.

scholarly journals T2 mapping of the peritumoral infiltration zone of glioblastoma and anaplastic astrocytoma

2021 ◽  
pp. 197140092198932
Author(s):  
Timo Alexander Auer ◽  
Maike Kern ◽  
Uli Fehrenbach ◽  
Yasemin Tanyldizi ◽  
Martin Misch ◽  
...  
Keyword(s):  
Relaxation Time ◽  
Isocitrate Dehydrogenase ◽  
Anaplastic Astrocytoma ◽  
T2 Mapping ◽  
Relaxation Times ◽  
Region Of Interest ◽  
World Health ◽  
High Grade ◽  
High Grade Gliomas ◽  
Health Organization

Purpose To characterise peritumoral zones in glioblastoma and anaplastic astrocytoma evaluating T2 values using T2 mapping sequences. Materials and methods In this study, 41 patients with histopathologically confirmed World Health Organization high grade gliomas and preoperative magnetic resonance imaging examinations were retrospectively identified and enrolled. High grade gliomas were differentiated: (a) by grade, glioblastoma versus anaplastic astrocytoma; and (b) by isocitrate dehydrogenase mutational state, mutated versus wildtype. T2 map relaxation times were assessed from the tumour centre to peritumoral zones by means of a region of interest and calculated pixelwise by using a fit model. Results Significant differences between T2 values evaluated from the tumour centre to the peritumoral zone were found between glioblastoma and anaplastic astrocytoma, showing a higher decrease in signal intensity (T2 value) from tumour centre to periphery for glioblastoma ( P = 0.0049 – fit-model: glioblastoma –25.02± 19.89 (–54–10); anaplastic astrocytoma –5.57±22.94 (–51–47)). Similar results were found when the cohort was subdivided by their isocitrate dehydrogenase profile, showing an increased drawdown from tumour centre to periphery for wildtype in comparison to mutated isocitrate dehydrogenase ( P = 0.0430 – fit model: isocitrate dehydrogenase wildtype –10.35±16.20 (–51) – 0; isocitrate dehydrogenase mutated 12.14±21.24 (–15–47)). A strong statistical proof for both subgroup analyses ( P = 0.9987 – glioblastoma R2 0.93±0.08; anaplastic astrocytoma R2 0.94±0.15) was found. Conclusion Peritumoral T2 mapping relaxation time tissue behaviour of glioblastoma differs from anaplastic astrocytoma. Significant differences in T2 values, using T2 mapping relaxation time, were found between glioblastoma and anaplastic astrocytoma, capturing the tumour centre to the peritumoral zone. A similar curve progression from tumour centre to peritumoral zone was found for isocitrate dehydrogenase wildtype high grade gliomas in comparison to isocitrate dehydrogenase mutated high grade gliomas. This finding is in accordance with the biologically more aggressive behaviour of isocitrate dehydrogenase wildtype in comparison to isocitrate dehydrogenase mutated high grade gliomas. These results emphasize the potential of mapping techniques to reflect the tissue composition of high grade gliomas.

Investigation of Anti-Cancer Drug Nimustine Interaction with Calf Thymus DNA

MAPAN ◽  
2016 ◽  
Vol 31 (3) ◽  
pp. 169-175 ◽  
Author(s):  
Deepti Chadha ◽  
Shweta Agarwal ◽  
Ranjana Mehrotra
Keyword(s):  
Calf Thymus Dna ◽  
Cancer Drug ◽  
Calf Thymus ◽  
Anti Cancer
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