Dynamics of ion-phosphate lattice of DNA in left-handed double helix form

TL;DR

This study models the vibrational dynamics of Z-DNA with counterions, calculating Raman spectra and identifying ion-specific vibrational modes, especially highlighting the influence of magnesium ions on low-frequency spectra.

Contribution

Develops a phenomenological model of ion-phosphate lattice vibrations in Z-DNA, predicting Raman spectra and ion-specific vibrational modes, including a new Mg2+ mode at 150 cm-1.

Findings

Identifies a new Mg2+ ion vibrational mode at 150 cm-1.

Shows Raman mode intensities depend on magnesium ion concentration.

Model predictions align well with experimental Raman spectra.

Abstract

The conformational vibrations of Z-DNA with counterions are studied in framework of phenomenological model developed. The structure of left-handed double helix with counterions neutralizing the negatively charged phosphate groups of DNA is considered as the ion-phosphate lattice. The frequencies and Raman intensities for the modes of Z-DNA with Na+ and Mg2+ ions are calculated, and the low-frequency Raman spectra are built. At the spectra range about the frequency 150 cm-1 new mode of ion-phosphate vibrations is found, which characterizes the vibrations of Mg2+ counterions. The results of our calculations show that the intensities of Z-DNA modes are sensitive to the concentration of magnesium counterions. The obtained results describe well the experimental Raman spectra of Z-DNA.