Rare-earth-cation-induced change in the cholesteric twisting of neighboring nucleic acid molecules

Certain physicochemical characteristics of particles of the cholesteric liquid-crystal dispersions of complexes of double-stranded nucleic acids with rare earth elements have been determined. It is shown for the first time that the binding of the rare earth cations to linear nucleic acid molecules ordered in the structure of particles of the cholesteric liquid crystal dispersions is accompanied not only by amplification of the abnormal band in the circular dichroism spectrum, but also by the disappearance of the characteristic maximum on the X-ray scattering curves for small angles. The (cholesteric 1-cholesteric 2) transition induced by rare earth cations is an example of the operation of a microscopic machine consisting of spatially ordered nucleic acid molecules. Particles of the cholesteric liquid crystal dispersions of nucleic acid complexes with rare earth elements hold the abnormal optical properties for a long time.     

核酸与有机小分子反应机理的荧光特性研究

核酸与有机小分子的反应机理对认识核酸的结构与功能具有重要作用,也是揭示核酸的生物功能与一些药物的作用机制的重要途径。研究核酸与有机小分子之间的相互作用对生命过程的模拟和生命本质的探索具有十分重要的意义,并对近年来该领域采用的荧光光谱法进行了综述,从温度、双分子猝灭过程的速率常数、荧光寿命以及吸收光谱的变化等方面作了论述,从而确定了核酸与有机小分子(染料和药物)之间相互作用的荧光猝灭类型;总结了结合常数、荧光给体-受体间的作用距离、作用力类型及结合方式的多种求算方法,并分别阐述了核酸与染料及药物在不同结合数下生成常数的计算方法。这对研究核酸与有机小分子之间的作用机理、开发新的核酸探针以及以核酸为靶标的药物分子的设计有一定的指导意义。     

Theory for cholesteric ordering in lyotropic liquid crystals

Summary This paper presents an investigation of the chiral dispersion interaction between macromolecules in the solvent which is considered as a dielectric medium. In particular the results of the molecular statistical theory are reported. The expression for the helical pitch as a function of temperature on the solvent dielectric constant is used to interpret the experimental data. Moreover, the effect of the solvent chirality on the cholesteric ordering in polymer liquid crystals is considered. Finally the cholesteric ordering in the solution of chiral micelles is discussed. Work presented at the First USSR-Italy Bilateral Meeting on Liquid Crystals held in Portonovo, Ancona (Italy), September 30–October 2, 1987.     

Liquid-crystalline phases formed by DNA duplexes containing pyrophosphate groups

We have studied the interaction between synthetic DNA molecules containing pyrophosphate (PP) groups in various positions, which makes it possible to control the charge distribution along the DNA chain. The PP groups were either symmetrically arranged at the ends or at the center of DNA molecules or uniformly distributed along these molecules. It is shown that, similar to nonmodified DNA, the synthetic PP-modified DNA molecules can form cholesteric liquid crystals. Minima of the pair interaction potential are found, conditions of the symmetry of this potential are formulated, and the dependence of conformation angles on the effective charge is determined. The results of calculations show that the system exhibits polymorphism (i.e., several phases of cholesteric liquid crystals can exist in DNA solutions).     

Symmetry of electrostatic interaction between pyrophosphate DNA molecules

We study chiral electrostatic interaction between artificial ideal homopolymer DNA-like molecules in which a number of phosphate groups of the sugar-phosphate backbone are exchanged for the pyrophosphate ones. We employ a model in which the DNA is considered as a one-dimensional lattice of dipoles and charges corresponding to base pairs and (pyro)phosphate groups, respectively. The interaction between molecules of the DNA is described by a pair potential U of electrostatic forces between the two sets of dipoles and charges belonging to respective lattices describing the molecules. Minima of the potential U indicate orientational ordering of the molecules and thus liquid crystalline phases of the DNA. We use numerical methods for finding the set of minima in conjunction with symmetries verified by the potential U . The symmetries form a non-commutative group of 8th order, S . Using the group S we suggest a classification of liquid crystalline phases of the DNA, which allows several cholesteric phases, that is polymorphism. Pyrophosphate forms of the DNA could clarify the role played by charges in their liquid crystalline phases, and open experimental research, important for nano-technological and bio-medical applications.     

A coarse-grained model of the effective interaction for charged amino acid residues and its application to formation of GCN4-pLI tetramer

ABSTRACT

We present a simple coarse-grained model of the effective interaction for charged amino acid residues, such as Glu and Lys, in a water solvent. The free-energy profile as a function of the distance between two charged amino acid side-chain analogues in an explicit water solvent is calculated with all-atom molecular dynamics simulation and thermodynamic integration method. The calculated free-energy profile is applied to the coarse-grained potential of the effective interaction between two amino acid residues. The Langevin dynamics simulations with our coarse-grained potential are performed for association of a small protein complex, GCN4-pLI tetramer. The tetramer conformation reproduced by our coarse-grained model is similar to the X-ray crystallographic structure. We show that the effective interaction between charged amino acid residues stabilises association and orientation of protein complex. We also investigate the association pathways of GCN4-pLI tetramer.     

Effect of dipole forces on the structure of the liquid phases of DNA

The dipole-dipole contribution to the energy of the pair interaction between DNA molecules has been calculated and analyzed. Rigid fragments of DNA, i.e., of a length of about the persistent length, which have discrete dipole moments of base pairs, are considered. For a given distance between the centers of mass of molecules, the energy of the dipole-dipole interaction is a function of three angular variables; the angles ?₁ and ?₂ between the central dipoles of both molecules and the z axis passing through the centers of the molecules, as well as the angle ξ between long axes of the molecules, are taken as these variables. It is shown that the dipole energy has minima when the mutual orientation of the molecules satisfies one of the following conditions: (i) ?₁ = ?₂ = 0 or (ii) ?₁ = ?₂ = π. The cholesteric twist angle ξ can be both positive and negative in dependence on the type of the minimum. For realistic cholesteric dispersion parameters, the dipole energy is only slightly lower than the experimentally known binding energy of the molecules in dispersion. The results allow the assumption that the dipole forces significantly affect the structure and other properties of DNA suspensions; in particular, they can lead to nontrivial texture phenomena, biaxial correlation, and multistability.     

基于功能性核酸识别的荧光各向异性分析方法与应用

荧光各向异性方法又称荧光偏振法,基于相互作用的分子结合前后发射光退偏振的不同而实现对相互作用的研究或对目标物的检测。20世纪50年代Gregorio Weber用荧光各向异性法研究了氮磺酰氯与牛血清白蛋白和卵清白蛋白的作用,开启了该方法在生物化学研究中应用的先河。而20世纪90年代开始的功能性核酸(FNAs,包括核酸适配体和核酸酶等)的发现与合成,使基于功能性核酸的传感得到了广泛的应用。核酸适配体能够特异性识别目标分子,基于核酸识别的荧光各向异性分析方法具有高选择性、高灵敏度、高通量等优势,在研究蛋白质、核酸和小分子的相互作用中起到重要作用,然而如何提高结合前后的荧光各向异性信号变化,尤其是小分子识别前后,在基于功能性核酸识别的分析方法发展中是一个挑战。介绍了基于功能性核酸识别的荧光各向异性的方法应用于检测蛋白质、核酸及其他在生命活动中起重要作用的小分子的基本原理及设计理念。     

Specific features of indirect interaction in an impurity graphene bilayer in the framework of the s-d model

The specific features of the Ruderman-Kittel-Kasuya-Yosida interaction in an impurity graphene bilayer have been calculated in the framework of the s-d model. Hydrogen atoms are considered as impurities. The calculations have demonstrated that the antiferromagnetic impurity-spin ordering is preferable at short distances, while as the distance increases, the ordering becomes ferromagnetic. The dependences of the exchange interaction constant on the problem parameters are shown.     

共振光散射技术测定核酸的研究进展

核酸分析是生命科学研究中最重要的技术之一。目前主要是应用核酸内源紫外吸收光谱的紫外分光光度法和基于荧光探针分子与核酸相互作用的荧光分光光度法。紫外分光光度法灵敏度低 ,荧光分光光度法试剂昂贵 ,有毒性。近年来 ,共振光散射技术在核酸分析中的应用得到了迅速的发展。核酸的共振光散射分析方法可以用普通的荧光分光光度计进行测定 ,应用安全、便宜的试剂获得很高的灵敏度。简要介绍了共振光散射分析的基本原理 ,并对近年来利用共振光散射技术分析核酸的研究进行了评述。内容主要包括利用有机染料分子作为核酸的共振光散射探针的分析方法 ;基于阳离子表面活性剂、金属离子及其络合物以及药物与核酸相互作用的分析方法 ;核酸形成大粒子的散射分析方法。     

The re-entrant cholesteric phase of DNA

The character of packing of double-stranded DNA molecules in particles of liquid-crystal dispersions formed as a result of the phase exclusion of DNA molecules from aqueous salt polyethylene glycol solutions has been estimated by comparing the circular dichroism (CD) spectra of these dispersions recorded at different osmotic pressures and temperatures. It is shown that the first cycle of heating of dispersion particles with hexagonally packed double-stranded DNA molecules leads to the occurrence of abnormal optical activity of these particles, which manifests itself in the form of a strong negative CD band, characteristic of DNA cholesterics. Moreover, subsequent cooling is accompanied by a further increase in the abnormal optical activity, which indicates the existence of the “hexagonal → cholesteric packing” phase transition, controlled by both the osmotic pressure of the solution and its temperature. The result obtained can be described in terms of “quasi-nematic” layers composed of orientationally ordered DNA molecules in the structure of dispersion particles. There are two possible ways of packing for these layers, which determine their hexagonal or cholesteric spatial structure. The second heating → cooling cycle confirms these results and is indicative of possible differences in the packing of double-stranded DNA molecules in the hexagonal phase, which depend on the osmotic pressure of the solution.     

Effect of dipole-dipole interaction in a solvent on the electronic spectra of three-component solutions

Electronic spectra of three-component solutions are calculated on the basis of a model, which makes it possible to incorporate the interaction between the molecules of a polar solvent, including the case of dielectric saturation. It is shown that the use of the theory of three-component solutions, which disregards the interaction between the molecules of a polar solvent, can lead to an overestimation of the efficiency with which an activator interacts with the molecules of a polar solvent. Translated from Zhurnal Prikladnoi Spektroskopii, Vol. 67, No. 1, pp. 38–41, January–February, 2000.     

Statistical screening in aP,T-invariant model

It is shown that in theP, T-invariant model with the mixed Chern-Simons term the interaction of charge carriers leads to effective changing of their statistics, which depends on distance between them. In particular, in the limit of large distances fermions effectively turn into bosons.     

On the existence of the thermodynamic limit for classical systems with nonspherical potentials

It is shown, that the configurational partition function for a classical system of molecules interacting with nonspherical pair potential is proportionals to the configurational partition function for a system of particles interacting with temperature-dependent spherical k-body potentials (k ?2). Therefore, the thermodynamic limit for nonspherical molecules exists if the effective k-body interaction is stable and tempered. A number of criteria for the nonspherical potential are developed which ensure these properties. In case the nonsphericity is small in a certain sense, stability and temperedness of the angle-averaged nonspherical potential are sufficient to ensure thermodynamic behaviour.     

荧光光谱法测定核酸的研究

研究了花菁Ⅱ与核酸的相互作用,发现在核酸的存在下,花菁Ⅱ的荧光被明显地猝灭,且猝灭程度与核酸的浓度存在良好的线性关系.     

Statistical analysis of spectra of single impurity molecules and dynamics of disordered solids: II. Manifestation of interaction of two-level systems with impurity molecules at different distances

Manifestations in the spectra of impurity chromophore molecules in a disordered solid matrix of the interaction of these molecules with two-level systems (TLSs) of the matrix are analyzed. The characteristic distances within the limits of which the interaction between TLSs and an impurity molecule leads, in the main, to either splitting or broadening of the spectrum, as well as the distance beginning with which this interaction is practically undetectable, are determined. Information about the effective value of the minimal distance between impurity molecules and TLSs, which is caused by nonzero sizes of the molecules and the TLSs, is presented. The analysis is performed by a statistical processing of experimental and model spectra of single tetra-tert-butylterrylene molecules in amorphous polyisobutylene at a temperature of 2 K, when the contribution of quasi-local low-frequency vibrational modes of the matrix to these spectra can be neglected.     

Interaction between solute molecules in medium density solvents

Solvation properties of solutes in supercritical, medium density solvents have been analysed using hypernetted-chain theory with the emphasis on the solvent-mediated interaction between solute molecules. The solvent and solute molecules are Lennard-Jones particles, and the solute is present at infinite dilution. Also a pair of solute molecules separated by different distances has been considered using reference interaction site model theory. Mainly, solvents at two typical densities (1.09_pc and 2.91_pc; pc is the critical density) that are in medium and high density regions, respectively, are treated. The temperature is set at 1.04T_C (T_c is the critical temperature). When the solute size is larger than the solvent size and the strength of the solute-solvent attractive interaction is greater than that of the solvent-solvent in the medium density region, the solvent structure confined between a pair of solute molecules is largely different from that near a single solute molecule. The confined solvent becomes denser and more stabilized as the distance between the solute molecules decreases, and an attractive interaction is induced between them. The interaction becomes even more attractive as the strength of the solute-solvent attractive interaction increases. The observations are qualitatively different from those in the high density region. Another high density region, which is well below the critical temperature, has been considered, but the behaviour observed is similar to that in the high density region above the critical temperature.     

The microscopic theory for BPI and BPII of the blue phase

A statistical theory of the blue phase of chiral liquid crystal is proposed. The form of the interaction potential between molecules is assumed to be the same as that used in the theory for cholesteric phase. Using the cell model of the liquid statistical theory, we deduced the distribution function of single molecule. The free energy of the system obtained has the same form as that of the Ginzberg－Landau phenomenology theory. The order-parameter tensors of BPI and BPII phases we calculated can be compared with the experimental results.     

Formation of annihilating pairs from molecules of aromatic compounds in n-paraffin matrices

The formation of annihilating pairs from molecules of aromatic compounds incorporated into the crystal lattice of n-paraffins has been studied. It has been established that annihilating pairs can be formed both from the molecules incorporated into adjacent unit cells according to the replacement principle and from the molecules incorporated with intervals of one or two unit cells of the crystal lattice of the matrix.. It has been shown that the influence of the solvent on the annihilation rate of triplet excitations of aromatic compounds is associated with the dependence of the degree of overlapping of electron clouds of interacting molecules and the distances between them on the solvent.