arXiv subjects

S. N. Volkov

Publications and source records attributed to S. N. Volkov.

14 recordsLinked to original sources

arXiv2020

Interaction of hydrogen peroxide molecules with non-specific DNA recognition sites

Ion beam therapy is one of the most progressive methods in cancer treatment. Studies of the water radiolysis process show that the most long-living species that occur in the medium of a biological cell under the action of ionizing irradiation are hydrogen peroxide (H$_2$O$_2$) molecules. But the role of H$_2$O$_2$ molecules in the DNA deactivation of cancer cells in ion beam therapy has not been determined yet. In the present paper, the competitive interaction of hydrogen peroxide and water molecules with atomic groups of non-specific DNA recognition sites (phosphate groups PO$_4$) is investigated. The interaction energies and optimized spatial configurations of the considered molecular complexes are calculated with the help of molecular mechanics method and quantum chemistry approach. The results show that the H$_2$O$_2$ molecule can form a complex with the PO$_4$ group (with and without a sodium counterion) that is more energetically stable than the same complex with the water molecule. Formation of such complexes can block genetic information transfer processes in cancer cells and can be an important factor during ion beam therapy treatment.

physics.bio-ph↗

arXiv2020

Conformational impact on deformation of DNA TATA-box

The theoretical study of deformability of special sequence of DNA double helix TATA-box is presentated. The paper elaborates on the mechanisms of abnormal deformation of DNA TATA-box double helix that cannot be explained using the standard mechanical model of polymer molecules (WLC) and needs more detailed modeling. Analyzing of DNA TATA-box deformation it is shown the molucule can undergo significant deformations due to its property of the structural polymorphism, that is, possibility of the double helix fragment to exist in more then one conformations. In addition to elastic components (bending, twisting), the presented model includes the following deformation features: possibility of conformation rearrangement of the shapes of the sugar rings, effects of a specific nucleotide sequence and anisotropy, the coupling between components. Presented model allows describe abnormal deformation based on physical special fitures of double helix inner structure.

physics.bio-ph↗

arXiv2020

The effect of DNA conformation changes on the coupling of the macromolecule deformation components

The model of the deformation of DNA macromolecule is developed with the accounting of two types of components of deformation: external and internal. External components describe the bend, twist and stretch of the double helix. The internal component - the conformational mobility inside of the double helix. In the work the deformation of DNA macromolecule is considered taking into account the coupling of the external component (of deformation) with the internal component (of conformational change). Under the task consideration the macromolecule twist-stretch coupling and coupling between twist and internal component are taken into account. The solution obtained in these conditions for the deformation components allows changing the character of respond in stretch component on unwind (overwind) in dependence on the applied force to twist component. The changing of the character of deformation from compression to tension achieving of critical untwisting force (and vise versa the changing of the character of deformation from overwind to unwind at critical tension force)is known from the single molecular experiments. The nature of such unexpected behavior of double helix have clarified in the present work by including in consideration the internal component. The obtained solutions and their conformity to experimental results show the essential role of coupling between internal and external components in the double helix conformational mechanics under action force in pN range.

cond-mat.soft↗

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↗

arXiv2017

Possible scenarios of DNA double helix unzipping process

Analysis of single-molecule micromanipulation experiments of DNA unzipping process shows some features of the force-distance curve, namely two consequent plateaus in the area of ${\sim}12-14pN$ dependent on nucleotide sequence structure, as well as peaks appearance in the plateau area, to which it was not paid essential attention earlier. Using atom-atom potential function method the estimations of Watson-Crick base pairs opening energies are made. On the basis of this results two possible scenarios of the DNA double helix unzipping process are proposed. According to the first scenario DNA unzipping takes place slowly and as equilibrium process, with small difference between two plateaus on the unzipping curve. In this case firstly base pairs transit into the 'pre-opened' metastable state along the 'opening' pathway and then open along the 'stretch' pathway. Our estimations show that an important factor for the realization of this scenario is the existence of double-stranded DNA coil in the unopened part of DNA. The second scenario is characterized by higher opening force. In this scenario base pairs open directly along the 'stretch' pathway as non-equilibrium process. The conditions of the first scenario realization show that it can play a key role in the understanding of the DNA unzipping in vivo during transcription and genetic information transfer processes.

physics.bio-ph↗

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↗

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↗

arXiv2010

Local-field excitations in 2D lattices of resonant atoms

We study excitations of the local field (locsitons) in nanoscale two-dimensional (2D) lattices of strongly interacting resonant atoms and various unusual effects associated with them. Locsitons in low-dimensional systems and the resulting spatial strata and more complex patterns on a scale of just a few atoms were predicted by us earlier [A. E. Kaplan and S. N. Volkov, Phys. Rev. Lett., v. 101, 133902 (2008)]. These effects present a radical departure from the classical Lorentz-Lorenz theory of the local field (LF), which assumes that the LF is virtually uniform on this scale. We demonstrate that the strata and patterns in the 2D lattices may be described as an interference of plane-wave locsitons, build an analytic model for such unbounded locsitons, and derive and analyze dispersion relations for the locsitons in an equilateral triangular lattice. We draw useful analogies between one-dimensional and 2D locsitons, but also show that the 2D case enables locsitons with the most diverse and unusual properties. Using the nearest-neighbor approximation, we find the locsiton frequency band for different mutual orientations of the lattice and the incident field. We demonstrate a formation of distinct vector locsiton patterns consisting of multiple vortices in the LF distribution and suggest a way to design finite 2D lattices that exhibit such patterns at certain frequencies. We illustrate the role of lattice defects in supporting localized locsitons and also demonstrate the existence of "magic shapes", for which the LF suppression at the exact atomic resonance is cancelled.

physics.optics↗

arXiv2009

Nanostratification of optical excitation in self-interacting 1D arrays

The major assumption of the Lorentz-Lorenz theory about uniformity of local fields and atomic polarization in dense material does not hold in finite groups of atoms, as we reported earlier [A. E. Kaplan and S. N. Volkov, Phys. Rev. Lett., v. 101, 133902 (2008)]. The uniformity is broken at sub-wavelength scale, where the system may exhibit strong stratification of local field and dipole polarization, with the strata period being much shorter than the incident wavelength. In this paper, we further develop and advance that theory for the most fundamental case of one-dimensional arrays, and study nanoscale excitation of so called "locsitons" and their standing waves (strata) that result in size-related resonances and related large field enhancement in finite arrays of atoms. The locsitons may have a whole spectrum of spatial frequencies, ranging from long waves, to an extent reminiscent of ferromagnetic domains, -- to super-short waves, with neighboring atoms alternating their polarizations, which are reminiscent of antiferromagnetic spin patterns. Of great interest is the new kind of "hybrid" modes of excitation, greatly departing from any magnetic analogies. We also study differences between Ising-like near-neighbor approximation and the case where each atom interacts with all other atoms in the array. We find an infinite number of "exponential eigenmodes" in the lossless system in the latter case. At certain "magic" numbers of atoms in the array, the system may exhibit self-induced (but linear in the field) cancellation of resonant local-field suppression. We also studied nonlinear modes of locsitons and found optical bistability and hysteresis in an infinite array for the simplest modes.

physics.optics↗

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

Conformational transformations of DNA macromolecule in heteronomous conformation

To understand the mechanism of TATA-box conformational transformations we model structure mobility and find the types of conformational excitations of DNA macromolecule in heteronomous conformation. We have constructed the two-component model for describing DNA conformational transformation with simultaneous transitions in the furanos rings of the monomer link. Internal component describes the change of the base pair position in the double helix. External component describes the displacement of mass center of the monomer link. Nonlinearity of the system is accounted with a form of potential energy describing C3'-C2' and C2'-C3' sugars transitions in monomer link, and interrelation between monomer conformational transition and macromolecule deformation. The comparison of our results with experimental data allows to confirm that the localized conformational excitations may realise in DNA TATA-box. These excitations cause the deformation of the macromolecule fragment.

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↗

arXiv2003

Modeling DNA Conformational Transformations on the Mesoscopic Scales

The approach for the description of the DNA conformational transformations on the mesoscopic scales in the frame of the double helix is presented. Due to consideration of the joint motions of DNA structural elements along the conformational pathways the models for different transformations may be constructed in the unifying two-component form. One component of the model is the degree of freedom of the elastic rod and another component -- the effective coordinate of the conformational transformation. The internal and external model components are interrelated, as it is characteristic for the DNA structure organization. It is shown that the kinetic energy of the conformational transformation of heterogeneous DNA may be put in homogeneous form. In the frame of the developed approach the static excitations of the DNA structure under the transitions between the stable states are found for internal and external components. The comparison of the data obtained with the experiment on intrinsic DNA deformability shows good qualitative agreement. The conclusion is made that the found excitations in the DNA structure may be classificated as the static conformational solitons.

q-bio.BM↗