Structural polymorphism of liquid-crystalline dispersions of double-stranded DNA complexed with synthetic polycations

Linear double-stranded DNA molecules interact with positively charged polyconidine molecules in aqueous salt solutions to yield liquid-crystalline dispersions (LCDs) with a mean particle diameter of ～6000 Å. The packing density of (DNA-polycation) complexes differs among LCD particles formed at different ionic strengths. X-ray data on the liquid-crystalline phases of (DNA-polyconidine) complexes formed under different conditions were compared with a phase diagram, reflecting polymorphism of liquid crystals of linear double-stranded DNA. It was shown that LCD was hexagonal at 0.15 M ≤ C _NaCl < 0.4 M and cholesteric at 0.4 M ≤ C _NaCl < 0.55 M. Cholesteric LCD displayed abnormal optical activity in the circular dichroism spectrum. A similar situation was observed with poly(2,5-ionene), another polycation differing in chemical structure from polyconidine. The results demonstrated structural polymorphism of (DNA-polycation) LCDs. It was assumed that the packing mode of (DNA-polycation) complexes in LCD particles can be regulated by changing NaCl concentration. The mechanism generating the cholesteric liquid-crystalline state of DNA in a narrow range of NaCl concentrations is discussed.     

Liquid-crystalline dispersions formed by the complexes of linear double-stranded DNA molecules with dendrimers

The specific features of liquid-crystalline dispersions formed by double-stranded DNA molecules interacting with polypropylenimine dendrimers of five generations (G1—G5) in aqueous saline solutions of various ionic strengths were studied. It was demonstrated that the binding of dendrimer molecules to DNA led to the formation of dispersions independently of solution ionic strength and dendrimer structure. By the example of a generation 4 dendrimer, it was shown that the shape of dispersion particles of the (DNA-dendrimer G4) complex were close to a sphere with a diameter of 300–400 nm. The boundary conditions (ionic strength of solution and molecular mass of dendrimer) for the formation of optically active (cholesteric) and optically inactive (DNA-dendrimer) dispersions were determined by circular dichroism spectroscopy. The dispersions formed by dendrimers G1–G3 and G5 were optically inactive. Dendrimers G4 formed liquid-crystalline dispersions of two types. Cholesteric liquid-crystalline dispersions were formed in high ionic strength solutions (μ > 0.4), whereas the dispersions formed in low and intermediate ionic strength solutions (μ < 0.4) lacked an intense negative band in their circular dichroism spectra. The effect of molecular crowding on both the (DNA-dendrimer G4) binding efficiency and the pattern of spatial packing of the (DNA-dendrimer G4) complexes in the liquid-crystalline dispersion particles was demonstrated. The factors determining the structural polymorphism of the liquid-crystalline dispersions of (DNA-dendrimer) complexes are postulated.     

DNA liquid-crystalline dispersion particles as a basis for sensitive biosensor elements

The data on the morphology, structural parameters, and abnormal optical properties of particles of cholesteric liquid-crystalline dispersions of double-stranded DNA are reviewed. The general principles of the creation and operation of biosensing units based on particles of these suspensions, including dispersed particles immobilized in hydrogels, are described. Examples demonstrating the analytical potentialities of liquid-crystalline biosensing units are given. A method for constructing "sandwich"-type biosensing units based on the particles of liquid-crystalline dispersion formed from molecules of DNA-polycation complexes is described.     

Temperature-induced changes of the packing of double-stranded linear DNA molecules in particles of liquid-crystalline dispersions

The circular dichroism spectra of liquid-crystalline dispersions obtained by phase exclusion of linear double-stranded DNA molecules from aqueous saline solutions of polyethylene glycol (120 ≤ C_PEG ≤ 300 mg/mL) have been investigated. The formation of liquid-crystalline dispersions at polyethylene glycol concentrations ranging from 120 to 200 mg/mL was accompanied by the emergence of an abnormal negative band in the spectrum of circular dichroism; this is indicative of cholesteric packing of the double stranded DNA molecules in the particles of the dispersion. Liquid-crystalline dispersions formed at PEG concentrations higher than 220 mg/mL and room temperature did not show any abnormal bands in the circular dichroism spectra; this is indicative of hexagonal packing of double-stranded DNA molecules in the particles of the dispersions. Heating of optically inactive liquid crystal dispersions induced a transition of the dispersions into a different state accompanied by the emergence of an abnormal negative band in the spectrum of circular dichroism. This transition is considered within the concept of the transformation of a hexagonal packing of DNA molecules into a cholesteric packing. A qualitative mechanism of such a transition is proposed that is formulated in the terms of the “quasinematic” layers of double-stranded DNA molecules that change their spatial orientation under the competing influences of the osmotic pressure of the solvent, orientational elasticity of the cholesteric packing, and thermal fluctuations.     

Formation of liquid-crystalline dispersions of double-stranded DNA-chitosan complexes

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.     

Formation of Liquid-Crystalline Dispersions of Double-Stranded DNA–Chitosan Complexes

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.     

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 (～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.     

The formation of liquid-crystalline dispersions of DNA-chitosan complexes under the conditions of molecular crowding

The formation of liquid-crystalline dispersions from DNA-chitosan complexes in polyethyleneglycol-containing solutions was studied. It was shown that the molecular crowding affects neither the efficiency of binding of chitosan molecules to DNA nor the mode of spatial packing of DNA-chitosan complexes in particles of liquid-crystalline dispersions.     

Re-entrant cholesteric phase in DNA liquid-crystalline dispersion particles

In this research, we observe and rationalize theoretically the transition from hexagonal to cholesteric packing of double-stranded (ds) DNA in dispersion particles. The samples were obtained by phase exclusion of linear ds DNA molecules from water-salt solutions of poly(ethylene glycol)—PEG—with concentrations ranging from 120 mg ml^?1 to 300 mg ml^?1. In the range of PEG concentrations from 120 mg ml^?1 to 220 mg ml^?1 at room temperature, we find ds DNA molecule packing, typical of classical cholesterics. The corresponding parameters for dispersion particles obtained at concentrations greater than 220 mg ml^?1 indicate hexagonal packing of the ds DNA molecules. However, slightly counter-intuitively, the cholesteric-like packing reappears upon the heating of dispersions with hexagonal packing of ds DNA molecules. This transition occurs when the PEG concentration is larger than 220 mg ml^?1. The obtained new cholesteric structure differs from the classical cholesterics observed in the PEG concentration range 120–220 mg ml^?1 (hence, the term ‘re-entrant’). Our conclusions are based on the measurements of circular dichroism spectra, X-ray scattering curves and textures of liquid-crystalline phases. We propose a qualitative (similar to the Lindemann criterion for melting of conventional crystals) explanation of this phenomenon in terms of partial melting of so-called quasinematic layers formed by the DNA molecules. The quasinematic layers change their spatial orientation as a result of the competition between the osmotic pressure of the solvent (favoring dense, unidirectional alignment of ds DNA molecules) and twist Frank orientation energy of adjacent layers (favoring cholesteric-like molecular packing).     

Nanoconstructions based on double-stranded nucleic acids

We describe the formation and properties of nanoconstruction that consists of the double-stranded DNA molecules located at distance of 35-50 A in the spatial structure of particles of their cholesteric liquid-crystalline dispersions and cross-linked by artificial nanobridges. The resulting nanostructures possess the peculiar spatial and optical properties.     

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.     

Enzymatic cleavage of superhelical DNA in a liquid crystal state]

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.     

Effect of intercalators on the properties of liquid-crystalline dispersions of nucleic acid-chitosan complex

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.     

Retention of gold nanoparticles in the structure of quasinematic layers formed by DNA molecules

Gold nanoparticles are shown to get incorporated into double-stranded DNA molecules forming quasinematic layers in the cholesteric liquid-crystalline dispersion particles. The process of nanoparticle incorporation results in distortion in an ordered arrangement of the neighboring dsDNA molecules in a layer and in global spatial structure of particles of the dispersion, which may be one of the possible causes of the genotoxicity of gold nanoparticles.     

Particles of liquid-crystalline dispersions formed by (nucleic acid-rare earth element) complexes as a potential platform for neutron capture therapy

Microscopic size particles of the cholesteric double-stranded DNA (RNA) liquid-crystalline dispersions, containing the ions of the rare earth elements in their content, have been obtained for the first time. The properties of these particles differ from those of classical DNA cholesterics noticeably. The local concentration of the rare earth elements in a particle reaches 200 mg/ml. The particles of the liquid-crystalline dispersion of the (DNA-gadolinium) complex maintain the properties for a long time. The combination of the microscopic size of particles, high concentration of gadolinium in particles and their stability opens a way to practical application of this new biomaterial.     

Effect of platinum(II) chemotherapeutic agents on properties of DNA liquid crystals

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.     

Novel Cholesteric Phase in Dispersions of Nucleic Acids due to Polymeric Chelate Bridges

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.     

SAXS-data-based structural modeling of DNA–gadolinium complexes fixed in particles of cholesteric liquid-crystalline dispersions

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.