Zn²⁺–DNA interactions in aqueous systems: A Raman spectroscopic study

Abstract

The influence of Zn2+ions on the structure of natural calf thymus DNA was studied by Raman spectroscopy. Measurements were done at room temperature and pH 6.2±0.1, in the presence of 10 mM Na+, and of Zn2+in a concentration range varying between 0 and 250 mM, respectively. No condensation of DNA was observed.As judging from the marker bands near 681 cm−1(dG), 729 cm−1(dA), 752 cm−1(dT), and 787 cm−1(dC, dT) altered nucleoside conformations in these residues are supposed to occur, in different intervals of Zn2+ions concentration. Changes in the conformational marker centered around 835 cm−1, upon Zn2+binding to DNA, were detected. Binding of zinc(II) ions to the charged phosphate groups of DNA, stabilizing the double helical structure, is indicated in the spectra. We have found that binding of metal ions at N3 of cytosine takes place at zinc(II) concentrations between 150–250 mM and interaction of Zn2+ions with adenine is observed in a concentration range from 10 to 250 mM. Binding of zinc(II) ions to N7 of guanine and, possibly, in a lesser extent to adenine was also observed as indicated by the Raman marker bands near 1490 and 1581 cm−1. There is no intensity change of the band at 1668 cm−1, suggesting no change in their base pairing and no change induced in the structure of water by Zn2+cations. No evidence for DNA melting was identified.

Surface‐enhanced Raman spectroscopy of genomic DNA from in vitro grown plant species

“…This mediumintensity band is due to a complex vibrational mode involving the deoxyribose-linked phosphodiester network (5 C-O-P-O-C3 ) of B-DNA. [19,20] This band is absent in our present SERS dataset of plant DNAs and this observation might be connected with the adsorption properties of DNA to the silver surface of the nanoparticles.…”

“…[18] The spectral interval 600-800 cm −1 contains Raman bands that originate from vibrations involving concerted ring stretching motions (ring breathing) of purine or pyrimidine residues, often in combination with stretching of the glycosidic bond and possibly also stretching of bonds within the linked deoxyribose ring. [19,20] These bands thus combine the relatively high Raman intensity typical for base residue vibrations with the sensitivity in wavenumber value expected from changes in glycosyl torsion angle and/or deoxyribose ring pucker (C2 -endo vs C3 -endo). [19,20] The band appearing at 685 cm −1 , in the case of DNA extracted from Exacum and Malus species, is a diagnostic of C2 -endo-anti conformation of dG.…”

“…[19,20] These bands thus combine the relatively high Raman intensity typical for base residue vibrations with the sensitivity in wavenumber value expected from changes in glycosyl torsion angle and/or deoxyribose ring pucker (C2 -endo vs C3 -endo). [19,20] The band appearing at 685 cm −1 , in the case of DNA extracted from Exacum and Malus species, is a diagnostic of C2 -endo-anti conformation of dG. However, it is possible that the wavenumber shift to higher values observed for this peak in the SERS spectra, as compared with previous normal Raman literature, might be due to the interaction of the metallic substrate with DNA molecules.…”

“…SERS wavenumbers (cm −1 ) and tentative assignments of genomic DNA from leaves of different plant species[2,3,15,17,19,25] …”

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.…”