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The current notion of the organization of molecules in a cholesteric phase is fairly well substantiated in the case of low-molecular-weight compounds. However, this question is open to discussion in the case of double-stranded nucleic acids. In this work, an attempt to compare the well-known data on the structure of cholesteric phases formed by double-stranded DNA molecules and the results of experimental modeling obtained by the authors has been undertaken. The comparison brings leads to assumption regarding the high probability of the existence of both short-range (positional) and long-range (orientational) order in the arrangement of double-stranded DNA molecules in the liquid crystalline phase. The presence of the orientational order, i.e., the rotation of quasinematic layers of double-stranded DNA molecules through a small angle, determines the formation of a spatially twisted (cholesteric) structure with specific physical and chemical properties. In addition, these results prompt a suggestion on the mode of the ordering of dsDNA molecules in liquid-crystalline dispersion particles and allow these particles to be considered candidate biosensing units.

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The answer to a question on the organization of molecules in a cholesteric phase is well enough proved in case of low molecular mass compounds. However, in case of double-stranded nucleic acids molecules the unequivocal answer to such question is a subject of discussions. In this work an attempt to generalize the well known literary data on the structure of the cholesteric phase formed by double-stranded DNA molecules was undertaken. Besides the experimental results of authors describing the packing of these molecules in the cholesteric liquid-crystalline dispersion particles are added to these data. Comparison of the results obtained offers the possibility to come out with an assumption of high probability of the existence of both the short-range positional and long-range orientational order in arrangement of double-stranded DNA molecules in a liquid-crystalline phase, and in the particles of dispersions of this phase generated under certain conditions. The occurrence of the orientational order, i.e. rotation of 'quasinematic' layers of double-stranded DNA molecules by a small angle, defines the formation of spatially twisted (cholesteric) structure with characteristic for it physical and chemical properties.

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The formation of cholesteric liquid-crystalline dispersions formed by double-stranded DNA molecules, handled by positively charged superparamagnetic cobalt ferrite nanoparticles, as well as action of these nanoparticles on DNA dispersion, are considered. The binding of magnetic nanoparticles to the linear double-stranded DNA in solution of high ionic strength (0.3 M NaCl) and subsequent phase exclusion of these complexes from polyethylene glycol-containing solutions lead to their inability to form dispersions, whose particles do possess the spatially twisted arrangement of neighboring double-stranded DNA molecules. The action of magnetic nanoparticles on DNA dispersion (one magnetic nanoparticle per one double-stranded DNA molecule) results in such "perturbation" of DNA structure at sites of magnetic nanoparticles binding that the regular spatial structure of DNA dispersion particles "blows up"; this process is accompanied by disappearance of both abnormal optical activity and characteristic Bragg maximum on the small-angle X-ray scattering curve. Allowing with the fact that the physicochemical properties of the DNA liquid-crystalline dispersion particles reflect features of spatial organization of these molecules in chromosomes of primitive organisms, it is possible, that the found effect can have the relevant biological consequences.

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The interaction between gold nanoparticles and particles of cholesteric liquid-crystalline dispersions formed by double-stranded DNA and poly(I)×poly(C) molecules is considered. It is shown that small-sized (~ 2 nm) gold nanoparticles induce two different structural processes. First, they facilitate the reorganization of the spatial cholesteric structure of the particles into a nematic one. This process is accompanied by a fast decrease in the amplitude of an abnormal band in the CD spectrum. Second, they induce cluster formation in a "free space" between neighboring nucleic acid molecules fixed in the structure of the quasinematic layers of liquid-crystalline particles. This process is accompanied by slow development of the surface plasmon resonance band in the visible region of the absorption spectrum. Various factors influencing these processes are outlined. Some assumptions concerning the possible mechanism(s) of fixation of gold nanoparticles between the neighboring double-stranded nucleic acid molecules in quasinematic layers are formulated.

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Structure of cholesteric liquid-crystalline dispersions (CLCDs) formed by double-stranded DNA molecules and treated with gadolinium salts was studied by small-angle X-ray scattering (SAXS). The obtained SAXS data open the way for structural modeling of these complexes to obtain a reasonable explanation for the correlated decrease in amplitude of an abnormal negative band in the circular dichroism (CD) spectra and the characteristic Bragg peak in the experimental small-angle X-ray scattering curves observed on treatment of CLCD by gadolinium salts. Model simulations of different kinds of structural organizations of the DNA-gadolinium complex were performed using novel SAXS data analysis methods in combination with several new, complementary modeling techniques, enabling us to build low-resolution three-dimensional structural models of DNA-gadolinium complexes fixed in CLCD particles. The obtained models allow us to suggest that a change takes place in the helical twist of quasinematic layers formed by these molecules at high concentrations of gadolinium salt. This change in the twist can be used to explain the experimentally observed increase in amplitude of an abnormal band in the CD spectra of DNA CLCD.

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Physics, Moscow, RussiaWe consider cholesteric liquid-crystalline DNA dispersions, and show thatpolymeric (Dau-Cu) complexes, the so-called bridges, between pairs of DNA molecules may generate a super liquid-crystalline structure (BR-phase), charachterized by a soliton lattice of the spatial distribution of theorder parameter. The BR-phase could have a layered spatial structure andan abnormal optical activity that could have a bearing upon the intenseCD-band observed in DNA-dispersions.

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The double-stranded molecules of nucleic acids (NA) of B- and A-families fixed in the structure of cholesteric liquid-crystalline dispersions, formed as a result of phase exclusion of these molecules from polymer-containing solution, have been used as 'building blocks' for the molecular design. Using the formation of polymeric chelate bridges between NA molecules, three-dimensional structures consisting of alternating NA, anthracycline and copper ions, were created. The formation of the polymeric chelate bridges allows one to stabilize the initial spatial mode of ordering of neighboring NA molecules in a form of so-called 'molecular constructions', immobilize these constructions onto supporting film and evaluate their sizes and shape. The creation of NA molecular constructions is accompanied by an 'extra-increase' in the amplitude of the bands in the CD spectra, despite the initial sense of cholesteric twisting characteristic of liquid-crystalline dispersions. Destroying of polymeric chelate bridges between NA molecules by action of biologically relevant compounds results in disintegration of NA liquid-crystalline molecular constructions. Three-dimensional NA molecular construction can be used as a microscopic size multifunctional chemical unit (chip) for biological or chemical needs.

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Double-stranded DNA fixed in a cholesteric liquid-crystalline dispersion was used for generating an ordered supramolecular structure in the presence of anthracycline and copper (II) ions. The structure is stable in a water-salt solution and does not require poly(ethyleneglycol).The ordered network can be immobilized on the surface of a polymeric film, and may collapse in the presence of biologically and pharmacologically relevant compounds. Accordingly, the DNA-based liquid-crystalline network represents the basis to obtain novel highly sensitive biosensing units.

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The formation of three-dimensional structures of double-stranded nucleic acid and polynucleotide molecules, fixed in the structure of liquid-crystalline dispersions and bridged by polymeric chelate complexes is described. The bridging elements consist of alternating daunomycin molecules and copper ions. It is shown that these bridges between nucleic acid molecules stabilize cholesteric structures of the DNA liquid-crystalline dispersion. The formation of polymeric chelate bridges is accompanied by a remarkable increase of the intense circular dichroism (CD) band characteristic of the DNA-daunomycin cholesterics. These bridges are destabilized by a number of biologically relevant compounds and macromolecules, such as ascorbic acid, homocarnosine, bovine serum albumin and lysozyme. The dramatic change in the optical activity of the liquid-crystalline dispersions upon addition of these compounds makes them easily detectable. The sensitivity of the method, in the range of analytic concentration 10(-4)-10(-8) M, depends on the nature of the compound being tested. The response of bridged DNA structures to biological effectors observed here foresees their further development as biosensor devices for detecting the presence of biologically and pharmacologically relevant compounds.

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The formation of liquid-crystalline dispersions (L.C.D.) from double-stranded DNA and polynucleotide (NA) molecules complexed with a number of anthracycline derivatives was investigated. These drugs form two types of complexes (complex I and complex II) with NA, which differ in the mode of drug orientation in respect to the NA helical axis. When complex II forms, addition of copper ions causes bridging of neighboring NA molecules through polymeric copper-anthracycline links (Figure 1). This results in an extra-increase in the amplitude of the intense CD band, characteristic for complex II, in the drug absorption region. Comparison of data obtained for different analogs and derivatives of daunomycin, has shown that the presence of 4 coordinating oxygen atoms at positions 5,6 and 11,12 (or 1,12) of the anthracycline ring system represents the basic prerequisite for the formation of a long polymeric chelate bridge after addition of copper ions. A second requirement relates to the chemical and stereochemical properties of sugar residues at position 7. These are important for proper positioning of the neighboring anthracycline aglycones in the polymeric chelate bridges and for spatial fixation of Cu2+ ions. Base sequence of double-stranded polynucleotides plays, if any, a minor role in polymeric chelate bridge formation. The question concerning the sterical orientation of two neighbouring antracyclines in the linking bridges, formed between NA molecules fixed in the liquid-crystalline structure, remains open.

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The interaction of daunomycin molecules with double-stranded DNA in the liquid-crystalline state was investigated. It was shown that at a certain extent of daunomycin binding a change of the mechanism of anthracycline orientation with reference to the DNA chain occurs. This is testified by the alteration of the sense of spatial packing of the DNA molecules in liquid-crystalline dispersions formed as a result of phase separation in poly(ethyleneglycol)-containing solutions, as well as by the onset of the reaction of daunomycin with divalent copper ions. Using this reaction, polymeric (daunomycin-copper) chelate cross-links between the DNA molecules fixed in the liquid-crystalline dispersions were formed. The length of such cross-links as adjusted by the distance between the DNA molecules, which, in turn, depends on the concentration of poly(ethyleneglycol) used for phase separation. The above molecular building mechanism may lead to new interesting applications.

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The formation of cholesteric liquid-crystalline dispersions from DNA-daunomycin complexes in water-salt polyethyleneglycol-containing solutions was investigated. In the case of nonclassical complex formation between DNA and daunomycin (DAU), reactive groups of DAU were used for the formation of polymeric chelate complex with divalent copper ions (-DAU-Cu-...-Cu-DAU-), located between neighboring double-stranded DNA molecules, fixed in spatial structure of liquid-crystalline dispersions. The formation of polymeric chelate complex does not depend upon the sense of helicoidal twist of DNA cholesterics. A many-fold increase in the CD band in the DAU absorption region is specific to this process. A reduction of the divalent copper ions as a result of a redox-process is accompanied by destroying of structure of polymeric chelate complex between DNA molecules and by disappearance of the abnormal CD band in daunomycin absorption region.

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The preparations of chicken erythrocyte linear double-stranded DNA and superhelical plasmid pBR322 DNA were irradiated by continuous low-intensity UV radiation (I = 25-50 W/m2, lambda = 254 nm) as well as by high-intensity picosecond laser UV radiation (I = 10(11)-10(13) W/m2, lambda = 266 nm). The effect of DNA secondary structure alterations on the formation of liquid-crystalline dispersions from UV-irradiated DNA preparations was studied. It was shown that in the case of linear DNA, watching the disappearance of abnormal optical activity characteristic for cholesteric liquid crystal we managed to detect the presence of photochemical alterations in DNA irradiated by low-intensity UV radiation at an absorbed energy of more than 20 quanta per nucleotide. In the case of superhelical DNA using enzyme treatment of liquid-crystalline dispersions and monitoring the appearance of abnormal optical activity, we detected the presence of photochemical alterations in DNA molecules after low-intensity UV irradiation at an absorbed energy of less than 4 quanta per nucleotide. Under the latter approach using picosecond UV laser irradiation at three different light intensities we were able to distinguish the different mechanisms of fine alterations in DNA secondary structure at an absorbed energy value of about 3 quanta per nucleotide.

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We have investigated the X-ray and optical properties (CD spectra and polarization microscopy) of liquid-crystalline phases and dispersions formed on pretreatment of low molecular weight DNA with the platinum(II) coordination complexes, cis-diammine-dichloroplatinum(II) (DDP), 2,2'-bipyridinedichloroplatinum(II) (1) and 2,2'-bipyridineethylenediammineplatinum(II) (2). It is demonstrated that the platination of DNA leads to the ordering of neighbouring molecules of DNA in liquid-crystalline phases being diminished. The intense bands observed in the CD spectra of liquid-crystalline dispersions prepared from DNA pretreated with 1 or 2 can be used to determine the orientation of the latter compounds with respect to the helical axis of the DNA and to detect distortions in the secondary structure of DNA. The possible causes of the appearance of the intense bands in the CD spectra of liquid-crystalline phases and alterations in the manner of packing of the molecules of DNA within them are discussed.

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In the presence of polyethyleneglycol water-salt solutions, DNA is condensed to a kind of mesophase (liquid crystals). The peculiar properties of this phase caused by anisotropic orientations have been analyzed by circular dichroism (CD) of condensed particles of DNA complexed with dyes, i.e. anthracycline antibiotics (daunomycin, aclacinomycin A), actinomycin, and ethidium bromide. The anthracycline complexes show intense CD bands in the visible and the UV region. Daunomycin induces a typical reversal of the sign of these CD bands with increasing occupation of the double helix contrary to the other ligands. This characteristic effect and its partial reversal after removal of daunomycin from the condensed particles can be the result of the change of the direction of the mesophase helical twist owing to an energy change of interaction between DNA molecules, and partially to a modification of base-plane inclination (tilt), too. This new type of DNA complex state is characterized in detail.

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Formation of compact particles from linear DNA-anthracycline complexes is accompanied by appearance of intense bands in the CD spectra in the region of absorption of DNA bases (UV-region) and in the region of absorption of anthracycline chromophores (visible region). The intense (positive or negative) bands in the region of anthracycline absorption demonstrate an ordered helical location of anthracycline molecules on the DNA template. This fact, in its turn, is related to formation of the DNA superstructure in PEG-containing water-salt solutions with a long-range orientation of nitrogen bases. Possible types of DNA superstructures and the relation between the local- and the long-range order of bases in the DNA superstructure are discussed.

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