[Dynamics of penetration of "solid" nanoconstructions based on double-stranded DNA complexed with gadolinium into CHO cells].

Currently, neutron capture therapy is a promising cancer treatment. This method is based on the reaction of the thermal neutron capture by some non-radioactive elements (e.g., Gds57), which results in subsequent emission of electrons and gamma rays. An effective instrument for delivery of gadolinium into the tumor tissue are the particles of the "rigid" nanostructures (NS) based on double-stranded DNA complexes with gadolinium (NS-Gd). The local concentration of Gd in such nanostructures may reach 40%. To optimize the process of neutron capture therapy it is very important to investigate possible penetration mechanisms of NS-Gd particles into the tumor cells. In this work, the dynamics of interaction NS-Gd with cultivated chinese hamster ovary cells (CHO) was studied by confocal and electron microscopy. It is shown that NS-Gd are able to enter CHO cells. This process begins in about 1 hour after the start ofincubation. After 6 h NS-Gd particles were detected in almost all cells. A further increase of the incubation time does not lead to significant changes in cell morphology, although the number NS-Gd inside the cells increases. The plasma membrane of the cells remains intact. The NS-Gd particles, which entered the cells, remain inside the cells for a long time. The data obtained show that NS-Gd are relatively low-toxic and suggest that the presence of NS-Gd in the tumor cells does not prevent their division. The data obtained are important for improving the efficiency of the neutron capture therapy method.

[Structural nucleic acid nanotechnology: liquid-crystalline approach].

The properties of the particles of cholesteric liquid-crystalline dispersions formed by double-stranded DNA molecules obtained as a result of phase exclusion of these molecules from water-salt polymer-containing solutions are briefly described. Physicochemical properties of quasinematic layers of dispersion particles and double-stranded DNA molecules in their content are taken into account in the course of developing fundamental background of the liquid-crystalline approach to the DNA structural nanotechnology. According to different versions of this approach, which is based on intraparticle gelation of cholesteric liquid-crystalline dispersions, spatial structures (DNA nanoconstructions, "rigid" DNA particles) with unique properties, are created. By means of atomic force microscopy images of "rigid" DNA particles of different type are registered. Specific properties of metallic nanoparticles (in particular, gold nanoparticles) are considered while developing the other approach to DNA structural nanotechnology, which provides the basis for "metallized" DNA nanoconstructions.

[Linear clusters of gold nanoparticles in quasinematic layers of DNA liquid-crystalline dispersion particles].

The effects of small size (approximately 2 nm) gold nanoparticles on the properties of particles of cholesteric liquid-crystalline dispersions formed by double-stranded DNA molecules were analyzed. It has been shown that gold nanoparticles induce two different processes. First, they facilitate reorganization of the spatial cholesteric structure of dispersion particles to nematic one. This process is accompanied by the fast decrease in the amplitude of abnormal band in the CD spectrum. Second, they can form ensembles consisting of gold nanoparticles. This process is accompanied by the development and displacement of surface plasmon resonance band in the visible region of the absorption spectrum. The appearance of this band is analyzed by considering two different models of the formation of ensembles consisting of gold nanoparticles. By small-angle X-ray scattering we performed structural analysis of phases formed by DNA cholesteric liquid-crystalline dispersion particles treated with gold nanoparticles. As a result of this study it was possible to prove the formation of linear clusters of gold nanoparticles in the "free space" between the adjacent DNA molecules fixed in the quasinematic layers of liquid-crystalline particles. It has been hypothesized that the formation of linear clusters of gold nanoparticles is most likely related to DNA molecules, ordered in the spatial structure of quasinematic layers, and the toxicity of these nanoparticles in biological systems hypothesized.

[DNA sequence-specific ligands: XIV. Synthesis of fluorescent biologicaly active dimeric bisbenzimidazoles-DB(3, 4, 5, 7, 11)].

Five fluorescent symmetric dimeric bisbenzimidazoles DB(n) have been synthesized containing four 2,6-substited benzimidazole fragments and differ in length of oligomethylene linker (n=3, 4, 5, 7, 11) between the two bisbenzimidazole blocks. The ability of these dimeric bisbenzimidazoles to form complexes with double-stranded DNA (dsDNA) was shown by spectral methods. Upon binding to dsDNA DB(n) are localized in the minor groove. The DNA-methyltransferase Dnmt3a inhibition data are demonstrate the site-specific binding of dimeric bisbenzimidazoles DB(3) and DB(11) with oligonucleotide duplex.

[From liquid crystals to nanoconstructions of DNA].

This paper reviews data obtained in our Laboratory in the field of the liquid-crystalline dispersions of the double-stranded nucleic acids (DNA, RNA) and results of the analysis of behavior of these biopolymeric molecules in the quasinematic layers. The fundamental data obtained in this area were used as a background for creation of the DNA nanoconstructions, containing different "guest" (biologically active or/and chemical substances) molecules. Two theoretically possible ways for creation of the DNA nanoconstructions were compared. The unique properties of the nanoconstructions dictating the scope of their practical application are described.

[DNA sequence-specific ligands: XIII. New Dimeric Hoechst 33258 molecules, inhibitors of HIV-1 integrase in vitro].

Dimeric Hoechst 33258 molecules [dimeric bisbenzimidazoles (DBBIs)] that, upon binding, occupy one turn of the B form of DNA in the narrow groove were constructed by computer simulation. Three fluorescent DBBIs were synthesized; they consist of two bisbenzimidazole units tail-to-tail linked to phenolic hydroxy groups via penta- or heptamethylene or tri(ethylene glycol) spacers and have terminal positively charged N.N-dimethylaminopropyl carboxamide groups in the molecule. The absorption spectra of the DBBIs in the presence of different DNA concentrations showed a hypochromic effect and a small shift of the absorption band to longer wavelengths, which indicated the formation of a complex with DNA. The presence of an isobestic point in the spectrum indicates the formation of one type of DBBI-DNA complexes. The interaction of DBBIs with DNA was studied by CD using a cholesteric liquid-crystalline dispersion (CLD) of DNA. The appearance of a positive band in the absorption region of ligand chromophores in the CD spectrum of the DNA CLD indicates the formation of a DBBI-DNA complex in which ligand chromophores are arranged at an angle close to 54 degrees relative to the helix axis of DNA, which suggests the localization of the DBBI in the narrow groove of DNA. All the DBBIs were found to be in vitro inhibitors of HIV-1 DNA integrase in the 3'-processing reaction, and, of the three DBBIs, two dimers inhibit HIV-1 integrase even in submicromolar concentrations.

[Description of the binding of chitosan to DNA at different ionic strengths in terms of the theories of ion condensation and adsorption].

The binding of chitosan molecules to DNA in solutions of different ionic strength has been studied. The data were analyzed in terms of the model of ion condensation and the thermodynamic theory of the binding of protracted ligands to DNA. Combining these approaches made it possible to estimate the sterical and energetic characteristics of chitosan-DNA binding and establish the dependence of the chitosan-DNA binding constant on the ionic strength of solution.

[Complexes of gadolinium with linear and liquid-crystalline forms of DNA].

The binding of Gd3+ ions to linear double-stranded DNA molecules in water-salt solutions or in liquid-crystalline dispersions is accompanied by sharp changes in their optical and X-ray characteristics. Depending on the initial conditions of complex formation, the binding of Gd3+ ions either to DNA bases or phosphate groups occurs, which leads to changes in the properties of the liquid-crystalline dispersions. The packing of neighboring DNA molecules in particles of the liquid-crystalline dispersion of the complex DNA-Gd3+ depends strongly on the concentration of Gd3+ ions. This process is accompanied by a decrease in the amplitude of Bragg's reflection maximum. The unique properties of the developed material open the possibilities for its practical use.

[Formation of various types of complexes upon the interaction of anthraquinones with DNA]. / Obrazovanie kompleksov raznogo tipa pri vzaimodeistvii antrakhinonov s DNK.

The optical properties (circular and linear dichroism) of the 11 anthraquinone antibiotics complexed with DNA molecules under conditions giving rise to cholesteric liquid-crystalline dispersions were investigated. Complexes of compounds A911 and A912 with double-stranded linear or circular DNA molecules differ strongly in their properties from those of other anthraquinones. The possible reasons of these differences and their possible correlation with the biological activity of the A911 and A912 are discussed.

[Enzymatic cleavage of superhelical DNA in a liquid crystal state]. / Fermentativnoe rasshcheplenie superspiral'noi DNK v usloviiakh ee zhidkokristallicheskoi upakovki.

Superhelical pBR322 DNA molecules form liquid-crystalline dispersions in water-salt solutions containing poly(ethyleneglycol). The formation of the liquid-crystalline dispersions from superhelical DNA molecules results in the appearance of two sites inside the DNA molecules that are split by Micrococcal nuclease. The first site of digestion does not differ from the standard site split by this enzyme in water-salt solutions, whereas the second one represents a new site specific only for the DNA molecules forming liquid-crystalline dispersions. Splitting of the DNA molecule through the first site is accompanied by formation of its linear form; splitting of a new site results in the formation of two linear DNA fragments with molecular masses equal to half of the initial DNA molecules. Enzyme digestion of superhelical DNA molecules forming liquid-crystalline dispersions induces a reformation of the "nonspecific" space organization of dispersions to the cholesteric one. A hypothetic model for packing of the superhelical DNA molecules inside liquid-crystalline dispersions and its transformation under enzyme action is suggested.

[A compact form of DNA in solution. III. Influence of the ion composition of the solution on the compactization process of double-stranded DNA in the presence of peg]. / Kompaktnaia forma DNK v rastvore III. Vliianie ionnogo sostava rastvora na protsess kompaktizatsii dvukhtsepochechnoi DNK v prisutstvii polietilenglikolia

The data showing the features of the DNA compactization process in PEG-containing solutions of chlorides of different alkaline metals (LiCl, KCl, RbCl and CsCl) and an ammonium salt (CH3-(CH2)17-N-(CH3)3Br) are presented. The data indicate that the formation of a compact form of the double-stranded DNA in PEG-containing water-salt solutions depends not only on the PEG concentration and ionic strength but on tha cation nature as well. The compactization occurs most easily in the presence of Na+-ions. This indicates a specific character of interaction between Na+-ions and DNA phosphate groups which may be due to an optimum structural fit between the hydrated Na+-ions and orientation of the phosphate groups in the DNA molecule. The nature of forces involved in the processes of the intramolecular compactization and intermolecular aggregation of double-stranded DNA molecules in water-salt solution is discussed. The difference between the effect of Na+ and that of K+-ions on the compactization process at the ionic strengths close to physiological values makes it possible to suggest that the changes of the tertiary structure of double-stranded DNA which accompany its function in vivo may take place under conditions of a decreased water activity at the expense of relatively slight changes in ion composition of the water surrounding DNA.

[Liquid crystals and liquid crystal dispersions of DNA-daunomycin complexes]. / Zhidkie kristally i zhidkokristallicheskie dispersii kompleksov DNK-daunomitsin.

The X-ray and optical properties as well as the textures of liquid crystals formed of DNA molecules bound in complex with an anthracycline antibiotic daunomycin were investigated. It was shown that DNA.daunomycin complexes, depending on the extent of alteration of the DNA secondary structure by daunomycin, could yield two types of cholesterics differing in the direction of their spatial twisting as well as nematics. Liquid-crystalline dispersions of DNA.daunomycin complexes have CD spectra with "mirror" bands depending on daunomycin concentration. "Testing" of the orientation of daunomycin molecules on the DNA in liquid-crystalline particles suggested two types of binding.

[Nucleic acids as a basis for creating biosensors]. / Nukleonovye kisloty kak osnova dlia sozdaniia biosensorov.

Here we present a brief conception of biosensors. Structural peculiarities and properties of single- and double-stranded nucleic acids that are to be taken into account when creating biosensors on the basis of these biomolecules are considered. On the example of two biologically active compounds a possibility is shown for constructing biosensors on the basis of liquid-crystalline dispersions of low molecular mass DNA and on the basis of liquid-crystalline DNA dispersions immobilized due to their inclusion into the synthetic polymeric matrix.

[Relationship between the molecular structure of aqueous solutions of polyethylene glycol and the compactness of double-stranded DNA molecules]. / O sviazi mezhdu molekuliarnym stroenii vodnykh rastvorov poliétilenglikolia i kompaktizatsiei dvukhtsepochechnykh molekul DNK.

The dependence of viscosity of the water solutions of poly(ethylene glycol) (PEG) on the molecular weight has been studied. It has been shown that there is a "transitional" region in PEG properties which accounts for the formation of fluctuation polymer network of the PEG molecules. It has been shown that the "transitional" region in properties of PEG which appears at a certain concentration of PEG (CtrPEG) is characteristic of the PEG preparations with molecular weights exceeding 600 and dependence of the value of CtrPEG on the molecular weight of PEG was obtained. Compactization of double-stranded DNA molecules in PEG-containing water-salt solutions has been studied and the dependence of the value of CcrPEG, . i.e. the concentration of PEG at which the compact particles of DNA appear in the solution, on the molecular weight of PEG was obtained. The correlation between these two dependences reflecting quite different physico-chemical processes shows that the double-stranded DNA molecules are constrained within the polymer network of the PEG molecules. The influence of ionic strength and ionic composition of the solution on the formation of a compact form was investigated. The transition of the DNA molecules from a linear to a compact state may occur only at a definite value of ionic strength of the solution. This transition may occur at the change of K+ for Na+ cations (at a constant value of CPEG). The extent of compactization of the DNA molecules in PEG-containing water-salt solutions is monitored by the molecular structure and by the ionic strength of the solvent. It is supposed that the peculiarities of compactization of the DNA molecules in PEG-containing water-salt solutions reflect some characteristics of conformational transitions of the DNA molecules which occur in vivo.

[Restructuring of the spatial organization of circular DNA molecules in liquid crystal dispersions]. / Perestroenie prostranstvennoi organizatsii kol'tsevykh molekul DNK v zhidkokristallicheskikh dispersiiakh.

The change in the spatial structure of superhelical and nicked DNA molecules in liquid-crystalline dispersions under micrococcal nuclease treatment was studied. Micrococcal nuclease digestion leads to restructuring from the "nonspecific" packing of circular DNA in dispersion particles to the cholesteric one. The transition is described by the Kolmogorov-Avramy equation; however, the parameters of the equation are essentially different for the different topological forms of circular DNA. The liquid-crystalline state of DNA expands the range of the solvent properties (ionic conditions etc.) under which the micrococcal nuclease action remain highly efficient.

[Compact form of DNA in solution. X. Peculiarities of circular dichroism spectra of DNA compact particles forming polyethylene glycol-containing water-salt solutions]. / Kompaktnaia forma DNK v rastvore. X. Osobennosti spektrov krugovogo dikhroizma kompaktnykh chastits DNK sformirovannykh v vodno-solevykh rastvorakh, Soderzhashchikh polietilenglikol'.

The experimental data indicating that the amplitude of the negative band in CD spectra of DNA compact particles forming in PEG-containing water-salt solutions intensifies with the decrease of DNA molecular weight are presented. This effect is not explained by the light scattering on the compact particles. The presence of the negative band in CD spectrum of DNA compact particles is interpreted as result of formation of dichrographic-active "microcrystalline" region ("domains") (if DNA compact particles are formed from double-stranded molecules with unaltered secondary structure); it is also supposed that the number of these regions in the particle and their dichrographic activity doesn't depend on the particles size. This interpretation is in agreement with experimental data on the increase of the number of compact particles with the decrease of DNA molecular weight. Proportionality coefficient in the linear dependence of the amplitude of negative band on the size of DNA compact particles in solution depends apparently on dichrographic activity of "microcrystalline" regions, and this activity is connected with structural peculiarities of initial DNA molecules.

[Formation of liquid-crystalline dispersions of double-stranded DNA-chitosan complexes]. / Obrazovanie zhidkokristallicheskikh dispersii kompleksov dvukhtsepochechnoi DNK s khitozanom.

Right-handed helical double-stranded DNA molecules were shown to interact with chitosans to form under certain conditions (chitosan molecular weight, content of amino groups, distance between amino groups, ionic strength and pH of solution) cholesteric liquid-crystalline dispersions characterized by abnormal positive band in CD spectrum in the absorption region of DNA nitrogen bases. Conditions were found for the appearance of intense negative band in CD spectrum upon dispersion formation. In some cases, no intense band appeared in CD spectrum in spite of dispersion formation. These results indicate not only the multiple forms of liquid-crystalline dispersions of DNA-chitosan complexes but also a possibility to control the spatial properties of these complexes. The multiplicity of liquid-crystalline forms of DNA-chitosan complexes was attempted to explain by the effect of character of dipoles distribution over the surface of DNA molecules on the sense of spatial twist of cholesteric liquid crystals resulting from molecules of the complexes.

[Effect of intercalators on the properties of liquid-crystalline dispersions of nucleic acid-chitosan complex]. / Vliianie interkaliatorov na svoistva zhidkokristallicheskikh dispersii kompleksa NK-khitosan.

Molecules of deoxyribonucleic acid and synthetic polydeoxyribonucleotides (NA) in the particles of liquid-crystalline dispersions resulting from interaction with chitosan are accessible to interaction with intercalators. The intercalation is accompanied by alteration in the direction of spatial twist of cholesterics of NA-chitosan complexes. This effect is absent in the case of "classical" cholesterics produced from NA molecules via phase exclusion, i.e., the cholesteric structure of NA-chitosan complex is very "labile" as distinct from "classical" cholesteric NA.

[Some X-ray diffraction parameters of liquid-crystalline dispersions of nucleic acid-chitosan complexes ]. / Nekotorye rentgenograficheskie parametry zhidkokristallicheskikh dispersii kompleksov NK-khitosan.

Liquid-crystalline dispersions of nucleic acid-chitosan complexes (NA-chitosan) possess optical and X-ray diffraction properties different from those of "classical" cholesterics. It is possible that positive charge distribution (distance between charges, chitosan conformation, etc.) in the polymeric chain of chitosan molecule combining with NA molecule is the factor that affects the spatial structure of resulting dispersions.

[Molecular construction (superstructures) with adjustable properties based on double-stranded nucleic acids]. / Molekuliarnye konstruktsii (superstruktury) s reguliruemymi svoistvami na osnove dvukhtsepochechnykh nukleinovykh kislot.

Formation of molecular construction that consists of double-stranded molecules of nucleic acids (or synthetic polynucleotides) located at the distance 30-50 A in the spatial structure of particles of their cholesteric liquidcrystalline dispersion and crosslinked by polymeric chelate bridges is described. The resulting superstructure, which possesses peculiar physicochemical properties, could be used as integral biosensor whose properties depend on temperature, the presence of chemical or biologically active compounds of different nature, etc.