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

Abstract

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 .

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

“…The behaviour of the Raman band parameters of 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] at 150 mM NaCl (0.660 ps), being comparable with the value at 200 mM Mn 2+ (0.643 ps). The fastest dynamics is observed for the vibrations at 1489, 1578 cm −1 around 300 mM Mn 2+ in the case of DNA samples at 10 mM NaCl (global relaxation times 0.523 ps for the 1489 cm −1 band and 0.607 ps for the 1578 cm −1 band, respectively).…”

“…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.…”

The influence of divalent metal ions on low pH induced LacDNA structural changes as probed with UV resonance Raman spectroscopy

“…Wavenumber positions of the major peaks are presented in Figs 3 and 4, respectively, being in accordance with those given previously in the literature. [1,5,11,19,20,[23][24][25][26][27][28][29][30][31][32] Table 1 presents a detailed comparative analysis of the UV (275 nm) resonance Raman markers of the six LacDNA complexes, the corresponding single-stranded oligonucleotides (SS1 and SS2) and the proper sum of spectra of single oligonucleotides. Proposed UVRR band assignments found in the literature for similar compounds are also included.…”

The Peculiar Response of DNA Hydrogel Fibers to a Salt and pH Stimulus

“…The peak occurring at 1 094 cm À1 arises from the PO 2 -group symmetrical stretching vibration along the DNA backbone. [16] The intensity of this band decreased at pH ¼ 2 ( Figure 4A(a)). This indicates that a partial protonation of the DNA backbone phosphate groups occurred, leading to a contraction of the DNA hydrogel fibers at pH ¼ 2, resulting in the disappearance of the PO À 2 symmetrical Raman line ( Figure 4A(b)).…”

“…This indicates that a partial protonation of the DNA backbone phosphate groups occurred, leading to a contraction of the DNA hydrogel fibers at pH ¼ 2, resulting in the disappearance of the PO À 2 symmetrical Raman line ( Figure 4A(b)). Moreover, the disappearance of the peaks occurring at 1 488, [16] 1 559, [15] and 1 578 cm À1 [15] indicates that the hydrogen bonds of the base pairs of the DNA were completely broken, suggesting a denaturing of the DNA at pH ¼ 2.…”