Conformational vibrations of ionic lattice in DNA: Manifestation in the low-frequency Raman spectra

Abstract

Conformational vibrations of DNA with counterions neutralizing the phosphate groups of the double helix backbone are studied within the framework of phenomenological approach developed. The counterions are considered to be localized in two possible positions: near the phosphate groups of the double helix backbone, and between the phosphate groups in DNA minor groove. For the description of DNA conformational vibrations the structure of counterions tethered to the phosphate groups of double helix backbone is represented as an ionic lattice. Using the developed approach the frequencies and Raman intensities for DNA with Na +, Cs +, and Mg 2+ counterions in different positions are calculated. As a result the manifestations of influence of counterion type and their position on the low-frequency Raman spectra (< 200 cm − 1 ) are determined. The obtained spectrum of DNA with Na + counterions near phosphate group is characterized by intensive modes of internal conformational vibrations of the double helix (from 60 to 110 cm − 1 ), while modes of ion-phosphate vibrations (near 170 cm − 1 ) have low intensity. In case of DNA with Cs + counterions near phosphate groups the mode of ion-phosphate vibrations (near 115 cm − 1 ) is the most prominent, with other modes of DNA conformational vibrations being low-intensive. The spectra of DNA with Mg 2+ counterions between phosphate groups are described by the high intensity of the internal modes of the double helix (from 60 to 120 cm − 1 ) that was found to be essentially dependent on the minor groove width. The obtained low-frequency Raman spectra provide a way to determine the type of counterions and its position with respect to phosphate groups.