Distributions of circular DNA according its topological states

A distinctive feature of closed circular DNA molecules is their particular topological state, which cannot be altered by any conformational rearrangement short of breaking at least one strand. This topological constraint opens unique possibilities for experimental studies of the distributions of topological states created in different ways. Primarily, the equilibrium distributions of topological properties are considered in the review. It is described how such distributions can be obtained and measured experimentally, and how they can be computed. Comparison of the calculated and measured equilibrium distributions over the linking number of complementary strands, equilibrium fractions of knots and links formed by circular molecules has provided much valuable information about the properties of the double helix. Study of the steady-state fraction of knots and links created by type II DNA topoisomerases has revealed a surprising property of the enzymes: their ability to reduce these fractions considerably below the equilibrium level.     

Elements of structural organization of the transcribed area of the ribosomal repeat (rDNA) in human peripheral blood lymphocytes

The rDNA transcribed region (TR) was tested for accessibility to RsaI recognizing 15 TR sites, DNase I, and photoinducible arylazide (N-(4-azido-2-hydroxybenzoyl)-N,N'-diaminoheptane acetate) in isolated nuclei and, with arylazide, in intact cells. Arylazide entered cells well and did not appreciably affect the chromatin structure. Its photolysis products efficiently modified DNA in accessible sites. Single-strand breaks made by DNase I were not transformed in double-stranded in rDNA TR, suggesting the necessity of denaturing electrophoresis for such an analysis. About 70% of all rDNA copies proved poorly inaccessible to endonucleases and arylazide, the accessibility being higher in their 18S and 5.8S rRNA gene regions than in the regions of the external transcribed spacers (ETSs) and the 28S rRNA gene. Proteinase K disrupted this structure, and the corresponding copies were extracted from nuclei. This explained why in situ hybridization occasionally fails to reveal rDNA in the nucleolar fibrillar center (FC) on electron microscopic preparations. In other rDNA copies, TR (excluding 5'-ETS) was accessible to nucleases and arylazide. These copies were not extracted from nuclei treated with proteinase K. Some of their RsaI sites were protected by tightly bound proteins. Seven such regions were identified in TR. Possible association of the molecular structure, nucleolar location, and functional state of rDNA is discussed.     

Study of molecular mechanisms of translation initiation in mammals using in vitro reconstruction of initiation complexes

Papers on the mechanisms of translation initiation in mammals studied by reconstruction of initiation complexes from individual components are reviewed. The author points to the constraints of this approach and to the pitfalls ignoring which one might come to erroneous conclusions and even artifacts. In addition, some methods employed in the field as well as some technical problems are discussed in the paper, together with the means of obviating them. The review could be a guidebook for newcomers into this quite labor-consuming field.     

Functional compartmentation of the translation apparatus and channeling of tRNA/aminoacyl-tRNA in cells of higher eukaryotes

Literature data and authors' results in the field of structure-function organization of the translation apparatus in higher eukaryotes are considered. Proof is presented of the channeling of tRNA/aminoacyl-tRNA in the course of eukaryotic protein synthesis. The concept of the shuttle role of elongation factor eEF1A is grounded; the factor, being in a GTP-bound form, delivers aminoacyl-tRNA to the ribosome and then, in the GDP form after hydrolysis of GTP on the ribosome, forms a complex with the deacylated tRNA and delivers it to the aminoacyl-tRNA synthetase. The notion of translational compartment is defined.     

Calculation of DNA condensation, caused by adsorption of ligands

A method for calculating the curves of DNA transition from linear to condensed state upon binding of condensing ligands has been developed. The character of the transition and ligand concentration necessary for condensation have been shown to be governed by the length of DNA molecule, energy and stoichiometry parameters of DNA-ligand complex (equilibrium constant between linear and condensed form in the absence of ligands, constants for ligand binding to linear and condensed forms, the number of base pairs covered by one ligand, etc.). The results of the calculations indicate that only slight difference in the free energies of these states in free DNA (less than 6 cal/mole(bp) for DNA of 500 bp long) is sufficient for the existence of stable linear state in the absence of ligands (in free DNA) and the formation of stable condensed state upon complexation.     

Construction of peptide mimetics of an epitope of the human immunodeficiency virus (HIV-1) gp41 protein, recognized by virus-neutralizing antibodies 2F5

A phase peptide library was screened with virus-neutralizing monoclonal antibodies (MCA) 2F5 which recognize a conserved epitope of HIV-1 gp41. Phages that expose peptides specifically binding with MCA 2F5 were selected by ELISA. Amino acid sequence analysis revealed a homology to region 662-671 of HIV-1 HB10 gp160 for most peptides. The major role in recognition was ascribed to Asp-664, Lys-665, and Trp-666. The epitope-mimicking peptides were tested for immunogenicity. Antibodies to gp41 were detected in serum of immunized rabbits.     

Comparative evaluation of the efficacy of Borrelia indication in ixodes ticks (Ixodidae) using dark field microscopy and polymerase chain reaction (PCR)

Indication of Borrelia (B. burgdorferi sensu lato) in 205 adult unfed I. persulcatus ticks from a natural focus was carried out simultaneously by methods of PCR and dark-field microscopy of vital preparations. PCR method revealed Borrelia prevalence in considerable number of ticks, in which Borrelia were not found by microscopy of 250 microscopic fields in a preparation from each individual tick. At the same time, PCR method didn't give positive results for approximately 8% of ticks, which contained rather high concentration of Borrelia (more than 10 per 100 microscopic fields). In general, PCR method doesn't have advantages in comparison with a microscopy of vital preparations for study the Borrelia prevalence in ticks.     

On the development of body-wall musculature Diplostomum chromatophorum metacercariae (Trematoda: Diplostomidae)

The body-wall musculature of invasive cercariae and metacercariae of Diplostomum chromatophorum at different intervals after the penetration into the experimental intermediate host Cyprinus carpio (1, 3, 5, 6, 7, 10, 12, 20, 34, 40 days) has been investigated with the help of TEM technique. During the first 10 days after the invasion (in conditions of our experiment), the cercarial subtegumental muscle fibres degenerate. These muscles are replaced by newly formed ones. Mass differentiation of myoblasts beneath the tegument was observed in 7-10-day-old metacercariae. Obtained data indicate the metamorphosis of body-wall musculature during the morphogenesis in Diplostomum chromatophorum metacercariae.     

Epigenetic cell reactions induced by ionizing radiation

The importance of radiation modification of epigenetic activity in the general mechanism of radiobiological reactions is proved. The inheritable epigenetic changes induced by irradiation are one of the basic reasons of formation of the remote radiation pathology. It is noted that epigenetic inheritable changes of cells have the determined character distinguishing them from mutation changes, being individual and not directed. It is underlined the ability of ionizing radiation to modify a level of spontaneous genetic instability inherited in a number of cell generations on the epigenetic mechanism.     

Asymmetric responses of epicardial and endocardial fibers of the dog atrium to cholinergic effects

The ACh shortened the AP in canine epicardial and endocardial cells, the effect being more obvious in the latter. The findings suggest that 4-aminophyridine-sensitive transient outward current is expressed in canine atrial epicardial and endocardial cells, that the ACh exerts direct effects on epicardial and endocardial AP duration, that differential responses of epicardial and endocardial AP duration to the ACh may alter the gradient of repolarisation across the atrial wall and contribute to the vagus-indoced atrial flutter and fibrillation.