T4-DNA ligase: substrate properties of synthetic DNA-duplexes with structural anomalies

Structural defects, affecting T4 DNA ligase function, were revealed with the help of synthetic DNA duplexes, containing modifications at single nick. Changes of configuration at C2' and C3' atoms of furanose in the acceptor terminus lead to total blocking of the nick sealing activity of T4 DNA ligase. On the contrary, substitution of 3'-terminal deoxyribonucleotide for ribonucleotide doesn't affect the enzyme's action. The duplex looses all of it's substrate activity if the next from the nick G.C pair is substituted for the noncomplementary G.C pair. In DNA duplexes containing an unpaired base in the nick, elimination of the extrahelical nucleotide proceeds the ligation step. In these cases the duplex substrate activity decreases depending on the extent of extrahelical base stacking into the double stranded DNA.     

Self-consistent quasineutral dust structures

Distributions of the dusty plasma parameters (electron, ion, and dust densities; dust grain charge; and ion drift velocity) in quasineutral dust structures whose dimensions are much greater than the mean free path of the ions in their interactions with neutral particles are calculated numerically under conditions such that ionization sources are located outside the structures. Planar, cylindrical, and spherical structures are investigated. It is shown that static equilibrium structures are governed by a single (basic) parameter: the electrostatic potential drop between the center of the structure and its boundary. It is found that the maximum value of the basic parameter (in energy units) does not exceed the electron temperature. The basic parameter also determines the total number of dust grains in the structure and the power of external ionization sources that are necessary to sustain this structure. The fact that the basic parameter varies within a limited range allows one to consider all the possible structures with a given dimensionality (planar, cylindrical, and spherical).     

Helical structures in complex plasma II: Collective interaction

The conditions for the formation and stability of quasi-crystal helical structures formed of charged dust grains of equal size in a complex plasma are investigated. A study is made of both the transverse confinement of such structures by means of an external parabolic potential well and the possibility of their self-confinement or confinement by the field of the smaller background grains. It is shown that, in the presence of dissipation, any initial random distribution of dust grains in a cylindrical external potential evolves into an equilibrium helical structure with a constant pitch angle. It is found that, when the external control parameter is smoothly varied, the pitch angle of the helix changes abruptly and the structure of the quasi-crystal undergoes bifurcations, during which the number of interwoven helices changes. The smaller the confinement parameter and the weaker the attractive forces between the grains, the larger the number of bifurcations. In addition, it is found that, because of the attraction (both noncollective and collective) between the dust grains, stable helical structures may exist not only at zero value of the external confinement parameter, but also at a negative one, and that the collective interaction between the grains not only increases the number of bifurcations but also changes their character.     

Structural and kinetic aspects of chemical reactions in DNA duplexes. Information on DNA local structure obtained from chemical ligation data.

Chemical ligation of oligonucleotides in double-stranded helices has been considered in its structural-kinetic aspect. A study was made of (i) two series of DNA duplexes with various arrangements of reacting groups in the ligation junction induced by mispairing or by alteration of furanose structure (the replacement of dT unit with rU, aU, IU, xU, dxT ones) and of (ii) eight synthetic water-soluble carbodiimides with different substituents at N1 and N3 atoms. We assumed that some information on the local structure of modified sites in the duplex can be obtained from kinetic parameters of oligonucleotide coupling reaction. The ratio of kinetic constants k3/(k2 + k3) for productive and nonproductive decomposition of the activated phosphomonoester derivative apparently reflects the reaction site structure: for a given duplex this parameter is virtually independent of the condensing agent composition. Based on the analysis of the chemical ligation kinetics a suggestion has been made about the conformation of some modified units in the double helix.     

Mutagenesis, directed by artificial oligonucleotide analogs. I. Participation of ribonucleotide fragments in DNA replication and repair

The mutation system has been developed to study the mutagenic properties of modified oligonucleotide analogs. The mutagenic properties of oligonucleotides containing one ribonucleotide have been examined. The presence of a ribonucleotide is shown not to induce any mutations. But when the oligonucleotide induces two marker deletions detached by 6 nucleotides they may be repaired separately, in this case the deletion bordering with the ribonucleotide is predominantly repaired.     

Spectral properties of an N-pole helical structure consisting of like-charged equal-size dust grains

The oscillations and stability of an N-pole helical structure that consists of like-charged equal-size dust grains and is confined in a plasma in an axisymmetric potential well are studied theoretically. Self-confining structures, as well as their linear collective modes corresponding to three coupled types of grain displacements (change in the radius of the structure, change in the distance between neighboring lattice planes of the structure, and angular displacements in the lattice planes), are found. On the whole, the coupled oscillations have the form of wormlike perturbations. Dispersion relations for the oscillation modes of helical structures composed of N interwoven helices are derived and solved numerically.     

Nonlinear equilibrium spherical dust structures I: Basic equations and criterion for the existence of self-organized structures

Basic equations for dust structures are formulated that account for the balance of the forces, plasma fluxes, and grain charges with allowance for nonlinearity in the screening of individual grains and possible violation of quasineutrality due to the interaction of collective fields with plasma fluxes. A theory of non-linear drag forces exerted by plasma fluxes on dust grains is developed for moderate drift flux velocities, higher than the mean ion thermal velocity but much lower than the acoustic speed. It is shown that equilibrium dust structures have finite sizes and negative charges and that they can exist only in a certain range of intensities of external fluxes on their surfaces. When there is no additional volume ionization, the size of the structures is determined by the intensity of the external flux. A study is made of a weakly ionized dusty plasma in which the interaction of its components with neutral gas atoms plays a major role. The ion, electron, and dust density distributions, as well as the distributions of the dust grain charges and plasma fluxes, are calculated self-consistently as functions of the distance from the center of a structure.     

Nonlinear equilibrium spherical dust structures II: Dependence of equilibrium states on volume ionization,number of trapped dust grains,and neutral gas pressure

A study is made of how equilibrium spherical dust structures depend on the volume ionization power, the neutral gas pressure, the number of trapped dust grains, and the ion-to-electron temperature ratio. It is shown that the structures are charged negatively and their charge is determined by the floating potential, which depends on the radius of the structure and on the ion temperature. The structures are charged mainly by absorbing a plasma flux. Conditions are determined under which the polarization fields and charges out-side the structures change sign, indicating the presence of overscreening effects, previously known only for individual dust grains. It is shown that overscreening outside the structures results exclusively from the plasma fluxes that are generated by the structure itself and are required to maintain it in equilibrium.     

Nonlinear screening of dust grains and structurization of dusty plasma: II. formation and stability of dust structures

The second part of the review on dust structures (the first part was published in Plasma Phys. Rep. 39, 515 (2013)) is devoted to experimental and theoretical studies on the stability of structures and their formation from the initially uniform dusty plasma components. The applicability limits of theoretical results and the role played by nonlinearity in the screening of dust grains are considered. The importance of nonlinearity is demonstrated by using numerous laboratory observations of planar clusters and volumetric dust structures. The simplest compact agglomerates of dust grains in the form of stable planar clusters are discussed. The universal character of instability resulting in the structurization of an initially uniform dusty plasma is shown. The fundamental correlations described in the first part of the review, supplemented with effects of dust inertia and dust friction by the neutral gas, are use to analyze structurization instability. The history of the development of theoretical ideas on the physics of the cluster formation for different types of interaction between dust grains is described.