Yu. M. Yevdokimov

Invite Article: The Liquid-Crystalline Phases of Double-Stranded Nucleic Acids in Vitro and in Vivo

Abstract This article describes the state of and progress in experimental studies of liquid crystals of naturally occurring nucleic acids and synthetic polynucleotides. The areas considered in this review include: (i) the liquid-crystalline phase of nucleic acids in aqueous salt solutions, (ii) the liquid-crystalline phase of nucleic acids in aqueous polymer solutions, (iii) the liquid-crystalline phase of nucleic acids in living systems. Some unsolved problems which are of interest from both a physicochemical and a biological point of view are discussed.

Invited Article Liquid-crystalline dispersions of nucleic acids

Abstract The formation and properties of dispersions of double stranded natural and synthetic nucleic acids are described. Evidence is given for the liquid-crystalline state of the nucleic acid within the dispersed droplets in these phases. The exploitation of nucleic acid dispersions in biosensors is discussed.

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.

Formation of polymeric chelate bridges between double-stranded DNA molecules fixed in spatial structure of liquid-crystalline dispersions

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.

Two types of temperature induced transitions of poly(I) · poly(C) liquid crystals

Abstract Small-angle X-ray scattering curves, CD. spectra and textures of the liquid-crystalline phase formed from poly(I) · poly(C) in water-salt solutions containing poly(ethyleneglycol) have been obtained at different temperatures. It was found that heating the poly(I) · poly(C) liquid-crystalline phase is accompanied by two types of transitions, the first being cholesteric → compensated structure → cholesteric and the second being cholesteric → isotropic state transition. The latter transition takes place at a temperature which corresponds to that of separation of chains of a double-stranded poly(I) · poly(C) molecule. The temperature dependence of the abnormally high optical activity of poly(I) · poly(C) liquid crystals allows us to estimate the order parameter of poly(I) · poly(C) molecules in both the liquid-crystalline phase and the liquid-crystalline microphases.

Bovine sperm chromatin is not protected from the effects of ultrasmall gold nanoparticles

The response of ejaculated bovine spermatozoa to gold nanoparticles was studied by the standard method of nuclear chromatin decondensation in vitro. After the treatment of semen samples with a hydrosol containing gold nanoparticles with an average diameter of ∼3.0 nm and a concentration of 1 × 1015 particles/mL, the ability of sperm nuclei to decondense in the presence of sodium dodecyl sulfate (SDS) and dithiothreitol (DTT) dramatically changed compared to the control. The frequencies of gametes with nondecondensed (“intact”), partially decondensed, and completely decondensed nuclei correlated as 40: 32: 28% and 0: 36: 64% in the experiment and the control, respectively. Moreover, the appearance of a sufficiently large number of gametes with destructed and almost completely destroyed nuclei was noticed in the spermatozoa treated with gold nanoparticles. This article suggests the putative mechanisms of action of ultrasmall gold nanoparticles on the structural and functional integrity of the deoxyribonucleoprotein (DNP) complex of mature male gametes.

Analytical capacity of the DNA liquid-crystalline dispersions as biosensing units

Abstract The main theoretical principles used for creating biosensing units based on the liquid-crystalline dispersions formed from the linear double-stranded DNA molecules are considered in this paper. A broad range of analytical abilities of these units is illustrated. These units are capable of detecting various biologically active compounds influencing the DNA secondary structure. A new ‘sandwich-type’ of biosensing unit based on the liquid-crystalline (DNA-daunomycin) complexes is also proposed. Some unsolved problems are outlined.

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.

Magnetic Properties of Copper as a Constituent of Nanobridges Formed between Spatially Fixed Deoxyribonucleic Acid Molecules

The number of copper ions as constituents of a nanobridge that links two deoxyribonucleic acid (DNA) molecules that are fixed in a particle of a liquid-crystalline dispersion has been evaluated from the measurements of the magnetic susceptibility of particles in the liquid-crystalline dispersion of DNA. It has been shown that the experimental data are consistent with both theoretical assumptions on the possible structure of a nanobridge and a thermodynamic model that describes the formation of these bridges.

Double-stranded nucleic acids in liquid-crystalline dispersions as building blocks for cross-linked supramolecular structures.

Abstract 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