Raman microspectroscopic study on low‐pH‐induced DNA structural transitions in the presence of magnesium ions

2003

Biopolymers

Self Cite

Large changes in the Raman spectra of calf thymus DNA are observed upon lowering the pH. In order to gain a better insight into these effects, several simulations of the Raman spectra of the guanine-cytosine (GC) Watson-Crick and Hoogsteen base pairs are performed. By comparing the Raman bands of GC base pairs in calf thymus DNA at high and low pH with the theoretical simulations of GC base pairs, it is found that the intensity changes in the theoretical bands located between 400 and 1000 cm(-1) are small compared to the experimental ones. The behavior of the cytosine band at 1257 cm(-1) upon lowering the pH is not reproduced in the GC theoretical spectra. The bands located above 1300 cm(-1) in the theoretical spectra display intensity changes that are similar to those found for GC base pairs in calf thymus DNA spectra.

Section: Introductionmentioning

confidence: 97%

mentioning

confidence: 97%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Numerical simulations of Raman spectra of guanine‐cytosine Watson–Crick and protonated Hoogsteen base pairs

Morari

2003

Biopolymers

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“…Based on our data, the global relaxation time of the band near 1094 cm −1 of the DNA backbone PO 2 − symmetric stretching vibration [22,23], has a tendency to decrease upon increasing the Mn…”

Section: CM Muntean and I Bratu / (Sub)picosecond Dynamics In Mndnmentioning

confidence: 70%

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

Bratu

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.

Raman microspectroscopic study of effects of Na(I) and Mg(II) ions on low pH induced DNA structural changes

Segers-Nolten

2003

Biopolymers

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In this work a confocal Raman microspectrometer is used to investigate the influence of Na(+) and Mg(2+) ions on the DNA structural changes induced by low pH. Measurements are carried out on calf thymus DNA at neutral pH (7) and pH 3 in the presence of low and high concentrations of Na(+) and Mg(2+) ions, respectively. It is found that low concentrations of Na(+) ions do not protect DNA against binding of H(+). High concentrations of monovalent ions can prevent protonation of the DNA double helix. Our Raman spectra show that low concentrations of Mg(2+) ions partly protect DNA against protonation of cytosine (line at 1262 cm(-1)) but do not protect adenine and guanine N(7) against binding of H(+) (characteristic lines at 1304 and 1488 cm(-1), respectively). High concentrations of Mg(2+) can prevent protonation of cytosine and protonation of adenine (disruption of AT pairs). By analyzing the line at 1488 cm(-1), which obtains most of its intensity from a guanine vibration, high magnesium salt protect the N(7) of guanine against protonation. A high salt concentration can prevent protonation of guanine, cytosine, and adenine in DNA. Higher salt concentrations cause less DNA protonation than lower salt concentrations. Magnesium ions are found to be more effective in protecting DNA against binding of H(+) as compared with calcium ions presented in a previous study. Divalent metal cations (Mg(2+), Ca(2+)) are more effective in protecting DNA against protonation than monovalent ions (Na(+)).