Influence of Ca 2+ cations on low pH‐induced DNA structural transitions

Dostál

Misselwitz

et al. 2005

J. Raman Spectrosc.

Raman spectra of calf thymus DNA were measured in the pH interval 6.4 to 3.45 in the presence of divalent manganese ions. pH-dependent protonation of AT and GC base pairs and conformational changes were indicated in the spectra. Protonation of adenine residues becomes obvious at pH 4.4 and continues upon lowering the pH to 3.45. Adenine protonation is connected with the disruption of AT base pairs. Protonation of GC base pairs is indicated at somewhat lower pH than that of AT base pairs, namely at pH 3.8, and continues upon lowering the pH to 3.45. At pH 3.8 unstacking of thymine residues is indicated, and spectral markers for the unstacking of adenine and cytosine were found at pH 3.45. Changes of the DNA backbone are indicated by spectral changes of conformational marker bands at 898 and 1423 cm −1 .

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

DNA structure at low pH values, in the presence of Mn2+ ions: a Raman study

Dostál

Misselwitz

et al. 2005

J. Raman Spectrosc.

“…1 An equilibrium mixture of B-DNA has been found, with an altered conformation and intermediate structure, proving the possible significance of alternative DNA structures for biological processes. In such mechanisms, the pH manifests itself as a powerful and sensitive tool for regulation.…”

Section: Introductionmentioning

confidence: 96%

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

Morari

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.

“…The values of the global relaxation time suggest also the existence of a vibrational relaxation time, because the reorientational movement is much more slower for the DNA macromolecule in aqueous solution. Particularly, the absence of reorientational broadening [13,[15][16][17], the cytosine ring breathing mode at 787 cm −1 [7,16,[18][19][20], the DNA backbone PO 2 − symmetric stretching vibration at 1094 cm −1 [12,16,19], the purines (dA, dG) and pyrimidines (dT, dC) residues band at 1376 cm −1 [17][18][19], the guanine (N-7) and adenine rings vibration at 1489 cm −1 [16,17] and the purines (dG, dA) 1578 cm −1 vibration ( [21] and references therein) of calf-thymus DNA, at different Mn 2+ ions concentrations, in the presence of Na + ions, are summarized in Tables 1, 2 and 4, 5, respectively.…”

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

confidence: 99%

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.