arXiv subjects

S. M. Perepelytsya

Publications and source records attributed to S. M. Perepelytsya.

10 recordsLinked to original sources

arXiv2020

Low-frequency vibrations of water molecules in minor groove of the DNA double helix

The dynamics of the structured water molecules in the hydration shell of the DNA double helix is of paramount importance for the understanding of many biological mechanisms. In particular, the vibrational dynamics of a water spine that is formed in the DNA minor groove is the aim of the present study. Within the framework of the developed phenomenological model, based on the approach of DNA conformational vibrations, the modes of H-bond stretching, backbone vibrations, and water translational vibrations have been established. The calculated frequencies of translation vibrations of water molecules vary from 167 to 205 cm$^{-1}$ depending on the nucleotide sequence. The mode of water vibrations higher than the modes of internal conformational vibrations of DNA. The calculated frequencies of water vibrations have shown a sufficient agreement with the experimental low-frequency vibrational spectra of DNA. The obtained modes of water vibrations are observed in the same region of the vibrational spectra of DNA as translation vibrations of water molecules in the bulk phase. To distinguish the vibrations of water molecules in the DNA minor groove from those in the bulk water, the dynamics of DNA with heavy water was also considered. The results have shown that in the case of heavy water the frequencies of vibrations decrease for about 10 cm$^{-1}$ that may be used in the experiment to identify the mode of water vibrations in the spine of hydration in DNA minor groove.

q-bio.BM↗

arXiv2020

Dynamics of K$^+$ counterions around DNA double helix in the external electric field: a molecular dynamics study

The structure of DNA double helix is stabilized by metal counterions condensed to a diffuse layer around the macromolecule. The dynamics of counterions in real conditions is governed by the electric fields from DNA and other biological macromolecules. In the present work the molecular dynamics study {was} performed for the system of DNA double helix with neutralizing K$^+$ counterions and for the system of KCl salt solution in the external electric field of different strength (up to 32 mV/Å). The analysis of ionic conductivities of these systems {has shown} that the counterions around the DNA double helix are slowed down compared with KCl salt solution. The calculated {values of ion mobility} are within (0.05$÷$0.4) mS/cm depending on the orientation of the external electric field relatively to the double helix. Under the electric field parallel to the macromolecule K$^+$ counterions move along the grooves of the double helix staying longer in the places with narrower minor groove. Under the electric field perpendicular to the macromolecule the dynamics of counterions is less affected by DNA atoms, and starting with the electric field values about 30 mV/Å the double helix undergoes a phase transition from double-stranded to single-strand state.

physics.bio-ph↗

arXiv2020

Molecular dynamics study of the competitive binding of hydrogen peroxide and water molecules with the DNA phosphate groups

The hydrogen peroxide is present in the living cell at small concentrations that increase under the action of the heavy ion beams in the process of anticancer therapy. The interactions of hydrogen peroxide with DNA, proteins and other biological molecules are poorly understood. In the present work the competitive binding of the hydrogen peroxide and water molecules with the DNA double helix backbone has been studied using the molecular dynamics method. The simulations have been carried out for the DNA double helix in a water solution with hydrogen peroxide molecules and Na$^{+}$ counterions. The obtained radial distribution functions of counterions, H$_2$O$_2$ and H$_2$O molecules with respect to the oxygen atoms of DNA phosphate groups have been used for the analysis of the formation of different complexes. The calculated mean residence times show that a hydrogen peroxide molecule stays at least twice as long near the phosphate group (up to 7 ps) than a water molecule (about 3 ps). The hydrogen peroxide molecules form more stable complexes with the phosphate groups of the DNA backbone than water molecules do.

q-bio.BM↗

arXiv2015

To understanding of the mechanisms of DNA deactivation in ion therapy of cancer cells

Changes in the medium of biological cell nucleus under ion beam action is considered as a possible cause of cell functioning disruption in the living body. As the most long-lived molecular product appeared in the cell after the passage of high energy ions, the hydrogen peroxide molecule is picked out. The possibility of the formation of stable complexes of hydrogen peroxide molecules with active sites of DNA nonspecific recognition (phosphate groups of the double helix backbone) is studied, and the formation of stable DNA-peroxide complexes is considered. Due to the negative charge on the oxygen atoms of DNA phosphate group in solution the counterions that under natural conditions neutralize the double helix have been also taken into consideration. The complexes consisting of oxygen atoms of DNA phosphate group, H$_2$O$_2$ and H$_2$O molecules, and Na$^{+}$ counterion have been considered. Energy of the complexes have been determined based on the electrostatic and van der Waals interactions within the approach of atom-atom potential functions. The stability of various configurations of molecular complexes has been estimated. It has been found that hydrogen peroxide molecules can form the stable complexes with phosphate groups of DNA and counterions which are no less stable than the complexes with water molecules. It is shown that the formation of stable complexes of H$_2$O$_2$--Na$^{+}$--PO$_{4}^{-}$ can be detected experimentally by the observation of specific DNA vibrations in the low-frequency Raman spectra. The interaction of H$_2 $O$_2$ molecule with phosphate group of the double helix backbone can block the processes of DNA biological functioning and induce the deactivation of the genetic apparatus of the cell. Thus, the new channel of high-energy ions action on living cell has been proposed.

physics.bio-ph↗

arXiv2015

Structuring of counterions around dna double helix: a molecular dynamics study

Structuring of DNA counterions around the double helix has been studied by the molecular dynamics method. A DNA dodecamer d(CGCGAATTCGCG) in water solution with the alkali metal counterions Na$^{+}$, K$^{+}$, and Cs$^{+}$ has been simulated. The systems have been considered in the regimes without excess salt and with different salts (0.5 M of NaCl, KCl or CsCl) added. The results have showed that the Na$^{+}$ counterions interact with the phosphate groups directly from outside of the double helix and via water molecules at the top edge of DNA minor groove. The potassium ions are mostly localized in the grooves of the double helix, and the cesium ions penetrate deeply inside the minor groove being bonded directly to the atoms of nucleic bases. Due to the electrostatic repulsion the chlorine ions tend to be localized at large distances from the DNA polyanion, but some Cl$^{-}$ anions have been detected near atomic groups of the double helix forming electrically neutral pairs with counterions already condensed on DNA. The DNA sites, where counterions are incorporated, are characterized by local changes of double helix structure. The lifetime of Na$^{+}$ and K$^{+}$ in complex with DNA atomic groups is less than 0.5 ns, while in the case of the cesium ions it may reach several nanoseconds. In this time scale, the Cs$^{+}$ counterions form a structured system of charges in the DNA minor groove that can be considered as ionic lattice.

q-bio.BM↗

arXiv2014

Effect of ionic ordering in conductivity experiments of DNA aqueous solutions

The effects of ionic ordering in DNA water solutions are studied by conductivity experiments. The conductivity measurements are performed for the solutions of DNA with KCl salt in the temperature range from 28 to 70 C. Salt concentration vary from 0 to 2 M. The conductivity of solutions without DNA but with the same concentration of KCl salt are also performed. The results show that in case of salt free solution of DNA the melting process of the double helix is observed, while in case of DNA solution with added salt the macromolecule denaturation is not featured. For salt concentrations lower than some critical one (0.4 M) the conductivity of DNA solution is higher than the conductivity of KCl water solution without DNA. Starting from the critical concentration the conductivity of KCl solution is higher than the conductivity of DNA solution with added salt. For description of the experimental data phenomenological model is elaborated basing on electrolyte theory. In framework of the developed model a mechanism of counterion ordering is introduced. According to this mechanism under the low salt concentrations electrical conductivity of the system is caused by counterions of DNA ion-hydrate shell. Increasing the amount of salt to the critical concentration counterions condense on DNA polyanion. Further increase of salt concentration leads to the formation of DNA-salt complexes that decreases the conductivity of the system.

q-bio.BM↗

arXiv2013

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

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.

q-bio.BM↗

arXiv2010

Intensities of the Raman bands in the low-frequency spectra of DNA with light and heavy counterions

The approach for calculation of the mode intensities of DNA conformational vibrations in the Raman spectra is developed. It is based on the valence-optic theory and the model for description of conformational vibrations of DNA with counterions. The calculations for Na- and Cs-DNA low-frequency Raman spectra show that the vibrations of DNA backbone chains near 15 cm-1 have the greatest intensity. In the spectrum of Na-DNA at frequency range upper than 40 cm-1 the modes of H-bond stretching in base pairs have the greatest intensities, while the modes of ion-phosphate vibrations have the lowest intensity. In Cs-DNA spectra at this frequency range the mode of ion-phosphate vibrations is prominent. Its intensity is much higher than the intensities of Na-DNA modes of this spectra range. Other modes of Cs-DNA have much lower intensities than in the case of Na-DNA. The comparison of our calculations with the experimental data shows that developed approach gives the understanding of the sensitivity of DNA low-frequency Raman bands to the neutralization of the double helix by light and heavy counterions.

q-bio.BM↗

arXiv2008

Observation of the DNA ion-phosphate vibrations

The low-frequency Raman spectra of Na-and Cs-DNA water solutions have been studied to determine the mode of counterion vibrations with respect to phosphate groups of the DNA double helix. The obtained spectra are characterized by the water band near 180 cm-1 and by several DNA bands near 100 cm-1. The main difference between Na- and Cs-DNA spectra is observed in case of the band 100 cm-1. In Cs-DNA spectra this band has about twice higher intensity than in Na-DNA spectra. The comparison of obtained spectra with the calculated frequencies of Na- and Cs-DNA conformational vibrations [Perepelytsya S.M., Volkov S.N. Eur. Phys. J. E. 24, 261 (2007)] show that the band 100 cm-1 in the spectra of Cs-DNA is formed by the modes of both H-bond stretching vibrations and vibrations of caesium counterions, while in Na-DNA spectra the band 100 cm-1 is formed by the mode of H-bond stretching vibrations only. The modes of sodium counterion vibrations have a frequency 180 cm-1, and they do not rise above the water band. Thus, the increase in intensity of the band 100 cm-1 in the spectra of Cs-DNA as compared with Na-DNA is caused by the mode of ion-phosphate vibrations.

q-bio.BM↗

arXiv2004

Ion-Phosphate Mode in the DNA Low-Frequency Spectra

The vibrational dynamics of a DNA molecule with counterions neutralizing the charged phosphate groups have been studied. With the help of elaborated model the conformational vibrations of the DNA double helix with alkaline metal ions have been described both qualitatively and quantitatively. For the complexes of DNA with counterions Li+, Na+, K+, Rb+ and Cs+ the normal modes have been found, and a mode characterized by the most notable ion displacements with respect to the DNA backbone has been determined. The frequency of counterion vibrations has been established to decrease as the ion mass increases. The results of theoretical calculation have been showed to be in good agreement with the experimental data of Raman spectroscopy.

q-bio.BM↗