[Evaluation of cytotocicity and efficiency of antioxidant protection of hydrophilic derivatives of 2,4,6-trialkylphenols in Escherichia coli cells].

The effects of five new derivatives of 2,6-dialkyl-4-propylphenole containing in para-radical different ionogenic groups (-SO3Na, -S-SO3Na, -S-(NH2)2Cl) in the presence and in the absence of hydrogen peroxide on the survival of E. coli AB1157 cells and its isogenic strain defective in repair enzyme genes were studied. Cell survival treated with hydrogen peroxide was remarkably increased in the presence of (3-(3,5-dimethyl-4-hydroxyphenyl)propyl)-1-sulphonate of sodium (Cl). Replacement of methyl ortho-radicals in the structure of Cl for tret-buthyl or cyclohexyl groups led to a decrease of the compounds ability to protect the cells from exogenic hydrogen peroxide. Between derivatives of 2,6-di-tret-buthylphenol the compound with thiosulphonate group demonstrated properties comparable with those for its sulphonate analog, then a chloride of isotiurone at concentration 3 mM completely suppressed the growth of cells in presence and in the absence of H2O2. Compound Cl may be considered as most perspective for detail analysis as antioxidant.

[The dependence of cytotoxicity and antioxidant activity of ammonii derivatives of alkylphenols upon percularities of their structure].

Effect of seven structurally similar N, N-dimethyl-(4-hydroxyaryl)alkylammonium chlorides in the presence and in the absence of hydrogen peroxide on the survival of E. coli cells AB1157 and its isogenic strain BH910 defective in genes of repair enzymes has been analyzed. Among the studied compounds only chloride of N,N-dimethyl-(3,5-dimethyl-4-hydroxybenzyl)ammonium (C1) has no cytotoxic properties and increases the survive of the cells of both strains in the presence of H2O2 better than trolox (water soluble analog of alpha-tocopherol). C1 analogs: 3-methyl-(5-di(tert-butyl)-4-hydroxybenzyl) and 3-(3,5-di(tert-butyl)-4-hydroxyphenyl)propyl)amines derivatives effectively protected from H2O2 only mutant cells BH910. Among the structural analogs of C1 cytotoxicity increases at substitution of methyl groups in aromatic cycle by tert-butyl and cyclohexyl groups. Only C1 among the seven new compounds is the most promising antioxidant for the subsequent more detailed analysis.

[The structure and mechanism of the action of type-IB DNA topoisomerases].

DNA topoisomerases responsible for the superspiralization of genomic DNA participate in almost all vitally important cell processes, including replication, transcription, and recombination, and are essential for normal cell functioning. The present review summarizes published data for type-IB topoisomerases. The results concerning the thermodynamic, structural, and kinetic aspects of the functioning of topoisomerases and the peculiarities of the mechanisms of their action have been analyzed for the first time.

[Antioxidative activity of thiophane [bis(3-(3,5-di-tert-butyl-4-hydroxyphenyl)propyl)sulfide].

The antioxidant activity, mutagenicity, and genotoxicity of bis(3-(3,5-di-tert-butyl-4-hydroxyphenyl)propyl)sulfide (thiophane) were studied using bacterial tests. The results of both an Ames test and SOS chromotest, as well as those studying the survival of E. coli cells deficient in enzymes responsible for the repair of DNA oxidative damage, testify to the fact that thiophane is not mutagenic and genotoxic, and it protects Salmonella typhimurium cells better than the well-known antioxidant trolox.

[DNA and oligosaccharides stimulate oligomerization of human milk lactoferrin].

Lactoferrin (LF), the glycoprotein transferring Fe+ ions, is contained in barrier liquids, human blood and milk. LF is an acute phase protein and one of the most important factors of nonspecific defense. The protein has unique set of biological functions. Using the methods of small-angle X-ray scattering and light-scattering it was shown for the first time that addition of DNA and oligosaccharides to LF with different level of initial oligomerization leads to an enhance in the oligomerization rate. 1M NaCl stimulates almost a complete dissociation of LF oligomeric complexes obtained in the pesence of DNA, oligosaccharides, or early founded oligomerization effectors (nucleotides). It was shown that LF oligomeric complexes obtained in the presence of different oligomerization effectors have different stability. Incubation with 50 mM MgCl2 leads to complete destruction of the protein complexes formed by ATP and oligosaccharide but partially dissociate the complexes with following formation of new in the case of AMP- and d(pT)10-dependent associates, which possess higher stability i n presence of the salt. A possible role of LF oligomerization for different biological functions of the protein is discussed.

[New promising antioxidants based on 2,6-dimethylphenol].

Three new sulfur-containing derivatives of 2,6-dimethylphenol were synthesized. Their antioxidative activity, mutagenicity, and genotoxicity were examined by bacterial tests and by calculating the dominant lethal mutations in murine embryonic cells. It was shown that all the compounds synthesized have a marked antioxidative effect and no genotoxic or mutagenic properties. One of the antioxidants, 4-(3-dodecylthiopropyl)-2,6-dimethylphenol, increases the survival of cells of both the wild-type Escherichia coli strain and bacterial strains defective in the genes of repair enzymes and has a more distinct antioxidative effect than the classic antioxidants alpha-tocopherol and trolox, increasing the survival of cells devoid of repair enzymes.

[Interactions of human ribosomal protein S3 with undamaged and damaged DNA].

Human S3 protein (hS3) is a structural component of the ribosome, which, in addition to its role in translation, possesses activities typical of some DNA repair enzymes. Recombinant hS3 purified from inclusion bodies and refolded under different conditions was investigated for its ability to bind and cleave oligodeoxyribonucleotide substrates containing different lesions abundant in cellular DNA (apurine/apyrimidine sites, uracil, 8-oxoguanine, 8-oxoadenine, 5,6-dihydrouracil, hypoxanthine). hS3 catalyzed cleavage of apurine/apyrimidine sites through beta-elimination mechanism forming a transient Schiff base covalent intermediate, but did not cleave substrates containing other lesions. Refolding of hS3 in the presence of Fe2+ and S2- ions did not increase its activity, despite the earlier suggestions that this protein could contain an iron-sulfur cluster. Binding of hS3 to DNA ligands containing oxidized and deaminated bases was less efficient than its binding to undamaged DNA. Therefore, the activity of hS3 on apurine/apyrimidine sites is not likely to be involved in the global in vivo DNA repair but could have a role in the repair in some specific locations in the genome.

[Interaction of single-stranded DNA with the second DNA-binding site of RecA nucleoprotein filament].

RecA protein first forms filament on single-stranded (ss) DNA forming the first DNA-binding site for interaction with this ssDNA a formation of the second site for interaction with double-stranded DNA occurs in parallel. Then the formed nucleoprotein filament interacts with molecules of double-stranded (ds) DNA but can also recognize ssDNA. The formed complex realizes a search of homology and exchange of homologous strands. We have studied recently the mechanism of RecA filamentation on ssDNA. Here a study of interaction of different DNAs with the second site of RecA filament using a method of stepwise increase of the ligand complicity was performed. The second site under recognition interacts with every nucleotide units of DNA-ligand forming contact with both internucleotide phosphate groups and bases of DNA. Pyrimidinic d(pC)n [Russian character: see text d(pT)n oligonucleotides interact with the second site of the RecA filament more effectively than with d(pA)n oligonucleotides. This occurs due to a more effective interaction of the RecA filament with 5'-terminal unit of pyrimidinic DNAs and to a difference in specific conformational changes of nucleoprotein filaments in the complex with purinic and pyrimidinic DNAs. A comparison of thermodynamic characteristics of DNA recognition by the first and the second sites of DNA recognition is carried out. It was shown that at n >10 d(pC)n d(pN)n interact with the second site weaker, that with the first site. The complexation of the second site with d(pA)n at n >20 is more effective than with the first site. The difference in the affinity of d(pA)n to the fist and second sites is increased monotonically with the enhancement of their length. Possible mechanisms of RecA-dependent search of homology and strand exchange are discussed.

[Interactions of pro- and eukaryotic DNA repair enzymes with oligodeoxyribonucleotides containing clustered lesions].

Interactions of oxoGuanine-DNA glycosylases from Escherichia coli (Fpg) and human (OGG1) and abasic site endonucleases from yeast (Apnl) and E. coli (Nfo) with oligodeoxyribonucleotides containing oxoGuanine (oxoG) and tetrahydrofuran (F, a stable analog of an abasic site) separated by various numbers of nucleotides have been studied. Inhibitor analysis has shown that the affinity of Fpg for single-stranded ligands does not depend on the relative positions of oxoG and F lesions. KM and kcat values have been determined for all double-stranded substrates and all enzymes under study. The effect of introducing the second lesion was strongly dependent on the relative positions of the lesions and the nature of the enzyme. The highest drop in the affinity (1.6-148-fold) and the reaction rate (4.8-58-fold) has been observed with Fpg and OGG1 for substrates containing F immediately 5' or 3' adjacent to oxoG. Introduction of the second lesion barely changed the KM values for Apnl and Nfo substrates. At the same time, the reaction rates were 5-10-fold lower for substrates containing two adjacent lesions. For all enzymes studied, increasing the distance between two lesions in duplex DNA reduced the effect of the lesion in KM and kcat values.

[DNA-hydrolyzing IgG antibodies from the blood of patients with acquired immune deficiency syndrome].

DNAase activity of 110 samples of IgG from the blood of AIDS patients was analyzed. It was shown that the relative activity of preparations varies very much from patient to patient, but 96% preparations show detectable level of DNAase activity. Several rigid criteria were applied and it was shown that DNAase activity is an intrinsic property of antibodies from AIDS patients. It was shown that catalytic activity could posses not only intact IgG, but also separated light chains of polyclonal antibodies. The abzymes catalyze DNA hydrolysis effectively in a wild range of pH (5.0-9.5). K(M) and V(MaKC) values of antibody-dependent hydrolysis of DNA was estimated.

[The effect of nucleotides on oligomeric state of human lactoferrin].

A polyfunctional protein lactoferrin (LF) which is present in human barrier fluids, blood and milk and this protein of acute phase is responsible for nonspecific cells defense against microbial and viral infection and cancer diseases. Using the methods of small-angle X-ray scattering and light-scattering it was shown that LF in solution exists in oligomeric state. The level of LF oligomerization depends upon its concentration and time of keeping of no frozen neutral protein solutions. At the concentrations comparable with those in human milk (1-6 mg/ml) the average inertial radius values (Rg) of LF can reach 100-450 angstroms, while Rg for monomer LF form is 26.7 angstroms. LF was shown to complex with different nucleotides and hydrolyze them. The addition of ATP and AMP to LF demonstrating any level of oligomerization leads to increase of oligomerization processes and enhancement of the Rg values up to 600-700 angstroms According to different models of LF monomer association to its oligomeric forms (sphere, plate, cylinder) the oligomeric complexes demonstrate high Rg values which can contain from several tens up to several thousands of LF monomers. A possible role of LF oligomerization for different biological functions of the protein is discussed.

[Interactions of human 8-oxoguanine-DNA glycosylase with single- and double-stranded DNA].

Interactions of human 8-oxoguanine-DNA glycosylase (hOGG1) with single- and double-stranded oligodeoxyribonucleotides (ODN) have been studied by the method of stepwise increase in ligand complexity. The ODNs have been found to inhibit the glycosylase-catalyzed reaction competitively. The K1 values have been determined for a set of ODNs. All units of non-specific DNA within the enzyme footprint have been shown to interact with the protein globule in an additive manner. An increase in the d(pN)n length (n) by one unit caused a monotonous 1.4-1.5-fold increase in their affinity for the glycosylase ODN until n = 10, mostly due to weak nonspecific contacts of the enzyme and the sugar-phosphate backbone. The weak nonspecific additive interactions contributed about five orders of magnitude in the affinity of hOGG1 for specific DNA (Kd approximately 10(-5) M), whereas introduction of a 8-oxoguanine residue added about three orders of magnitude to this affinity (Kd approximately 10(-8) M). Quantitative features of recognition of specific DNA by the enzyme are analyzed.

Cell cycle of bone marrow CD34+ cells during autoimmune disease development in MRLMpJ/lpr mice.

The development of autoimmune disease in Fas-deficient MRLMpJ/lpr mice is associated with a relative decrease in the content of bone marrow CD34+ cells, which can attest to intensification of migration of early hemopoietic precursors from the bone marrow. The intensity of CD34+ apoptosis is high in young healthy MRLMpJ/lpr mice in comparison with the control, but decreases during the development of autoimmune disease. Proliferative activity of CD34+ cell population surpassed the control in all mouse groups, except AID2. The detected shifts in quantitative and qualitative parameters of CD34+ cells attest to an important role of stem hemopoietic precursors in the formation of autoimmune disease in MRLMpJ/lpr mice.

[Physico-chemical basis of RecA nucleo-protein filament formation on single].

The analysis of RecA protein playing a central role in homologous recombination of E. coli with single-stranded DNAs of various structure and length on quantitative level is carried out for the first time. It was shown that weak additive interactions between protein monomers of filament and different structural elements of DNA provide DNA recognition. Orthophosphate and dNMPs (I50 = 12-20 mM) were shown to be the minimal inhibitors of RecA filamentation on d(pN)20. The lengthening of homooligonucleotides from d(pN)2 to d(pN)20 by one unit leads to monotonic increase in the affinity by a factor approximately 2 (factor f) due to weak additive contacts of RecA with every internucleoside phosphate group of DNA (f = 1.56) and specific interactions with each of T and C bases (f = 1.32). RecA filament does not practically interact with bases of d(pA)n, but contacts with internucleoside phosphate groups of the first turn (n < 10; f = 2.1) more effective than with additional turns of d(pA)n (n > 10; f = 1.3). The affinity of RecA protein for d(pN)n, containing typical and a number of different modified bases depends on a type of base, peculiarities of DNA structure and conformation of its sugar-phosphate backbone. The affinity is increased significantly if the bases contain exocyclic proton accepting groups. The possible reasons of preferable complexation of RecA with DNA of definite structure and length are analyzed. The mechanism of single-stranded DNA recognition by RecA and hypothetical mechanism of homological DNA strands exchange are proposed.

[Interaction of HIV-1 reverse transcriptase with new minor groove ligands and their conjugates with oligonucleotides].

The influence of new non-natural regular minor groove binders (MGB), containing 2-4 imidazole, pyrrole or thiazole residues, and their conjugates with oligonucleotides, on the polymerization reaction catalyzed by HIV-1 reverse transcriptase was analyzed. Various model template-primer complexes: poly(A)-oligo(U), poly(A)-oligo(dT), poly(dA)-oligo(U), poly(dA)-oligo(dT) and activated DNA were used. The concentration of oligopeptides, giving 50% inhibition (I50) of the RT-dependent polymerization reaction, was shown to depend strongly on the structure of template-primer complexes, number and type of the heterocycle rings in the MGBs analyzed. The range of I50 for the most of the compounds studied is 7.7 x 10(-3)-1.0 x 10(-5) M. The affinity of MGB is minimal for poly(A)-oligo(U). However, some of imidazole and pyrrole-containing MGBs demonstrated unusually high affinity (I50 = 3 x 10(-9)-4 x 10(-8) M) to the above template-primer in complex with RT. The affinity of conjugates of thiazolecarboxamides with oligonucleotides complementary or partially complementary to the template, is 1-4 orders higher compared to free thiazolecarboxamides. The possible reasons of the dependence of I50 values upon the structure of the template-primer complexes, the structure of MGB, and their conjugates with oligonucleotides are discussed.

[Human milk lactoferrin hydrolyzes nucleoside-5'-triphosphates].

Lactoferrin (LF) is a main iron-transfering glycoprotein of human barrier body fluids, blood and milk. LF, a protein of the acute phase, is responsible for nonspecific cells defense against microbial and viral infection and cancer diseases. LF is an important component of the passive immunity of newborns system. LF, an extremely polyfunctional protein, is the object of intensive investigations. In this work electrophoretically homogeneous LF from human milk was prepared. Affinity chromatography of LF on Blue Sepharose separated the protein into several distinct isoforms with different affinities to this resin. Two of this isoforms possess nucleoside-5'-triphosphate-hydrolyzing activity. Using several methods including in-gel ATPase activity assays, we show that ATP (and others NTP) hydrolysis is an intrinsic property of LF, and that LF is the major ATPase of human milk. It was shown that ATP-hydrolyzing site is located in C-lobe of LF.

[The role of weak specific and nonspecific interactions in recognition and conversation by enzymes of long DNA]. / Rol' slabykh spetsificheskikh i nespetsificheskikh vzaimodeistvii v uznavanii i prevrashchenii fermentami protiazhennykh DNK.

According to a currently accepted model, enzymes engage in high-rate sliding along DNA when searching for specific recognition sequences or structural elements (modified nucleotides, breaks, single-stranded DNA fragments, etc.). Such sliding requires these enzymes to possess sufficiently high affinity for DNA of any sequence. Thus, significant differences in the enzymes' affinity for specific and nonspecific DNA sequences cannot be expected, and formation of a complex between an enzyme and its target DNA unlikely contributes significantly in the enzyme specificity. To elucidate the factors providing the specificity we have analyzed many DNA replication, DNA repair, topoisomerization, integration, and recombination enzymes using a number of physicochemical methods, including a method of stepwise increase in ligand complexity developed in our laboratory. It was shown that high affinity of all studied enzymes for long DNA is provided by formation of many weak contacts of the enzymes with all nucleotide units covered by protein globules. Contacts of positively charged amino acid residues with internucleotide phosphate groups contribute most to such interactions; the contribution of each contact is very small and the full contact interface usually resembles interactions between oppositely charged biopolymer surfaces. In some cases significant contribution to the affinity is made through hydrophobic and/or van der Waals interactions of the enzymes with nucleobases. Overall, depending on the enzyme, such nonspecific interactions provide 5-8 orders of the enzyme affinity for DNA. Specific interactions of enzymes with long DNA, in contrast to contacts of enzymes with small ligands, are usually weak and comparable in efficiency with weak nonspecific contacts. The sum of specific interactions most often provides approximately one and rarely two orders of the affinity. According to structural data, DNA binding to any of the investigated enzymes is followed by a stage of DNA conformation adjustment including partial or complete DNA melting, deformation of its backbone, stretching, compression, bending or kinking, eversion of nucleotides from the DNA helix, etc. The full set of such changes is characteristic for each individual enzyme. The fact that all enzyme-dependent changes in DNA are effected through weak specific rather than strong interactions is very important. Enzyme-specific changes in DNA conformation are required for effective adjustment of reacting orbitals with accuracy about 10-15 degrees, which is possible only for specific DNA. A transition from nonspecific to specific DNA leads to an increase in the reaction rate (kcat) by 4-8 orders of magnitude. Thus, the stages of DNA conformation adjustment and catalysis proper provide the high specificity of enzyme action.

[Antibodies to DNA in the blood of patients with tick-borne encephalitis]. / Antitela k DNK v krovi bol'nykh kleshchevym éntsefalitom.

A comparison of relative levels of autoantibodies (Abs) to both native (n) and denatured (d) DNA in the blood of 55 patients with tick-borne encephalitis (TBE) was carried out. 31% of patients with TBE was shown to have an increased level Abs to nDNA and 40% of patients demonstrate increased level of Abs to dDNA. The percent of TBE patients with increased concentration of anti-nDNA Abs higher then that in patients with multiple sclerosis (18%) and some other autoimmune diseases (6-18%), but comparable with that for patients with systemic lupus erythematosus (38%) and polymyositis (42%). In contrast to patients with systemic lupus erythematosus and multiple sclerosis, the level of Abs to nDNA in patients with TBE is higher than the level of Abs to dDNA. Correlation coefficients of Ab levels to both n- and dDNA were estimated for group of patients in whole and for separate subgroups with different type of disease (temperature reaction, feverishness and meningitis). Analysis of correlation between titres of anti-DNA Abs and three standard biochemical markers of TBE (activity of aspartate- and alanine-aminotransferases, and concentration of whole bilirubin) for 22 patients with TBE was carried out. Statistically significant correlation was revealed only between the level of Abs to nDNA and activities of aspartate- and alanine-aminotransferases, correlation coefficients are equal to +0.44 and +0.48, respectively.

[Association between DNA antibodies levels in the blood of patients with multiple sclerosis and clinical presentation of the disease]. / Urovni antitel k DNK v krovi bol'nykh rasseiannym sklerozom v zavisimosti ot klinicheskikh kharakteristik zabolevaniia.

Multiple sclerosis (MS) as an autoimmune disease is characterized by occurrence of high titres of antibodies (AB) to cell structures and autoantigens. Various AB-mediated effector mechanisms can participate directly in the pathogenesis of demyelinisation damaging myelin, oligodendrocytes and nervous fibres. Antinuclear AB, including anti-DNA AB are an example of activation of humoral immunity in MS. Pathogenetic and clinical value of these AB is investigated insufficiently. The aim of this study was estimation of the AB titers in MS patients from two populations of Russia in relation to clinical features of MS. Results of examination of 83 patients with definite MS from Novosibirsk and Moscow (49 and 34 patients) are analyzed. Groups of comparison consisted of healthy donors and patients with SLE of the same age. Use of identical methods in the analysis of the data received in two various populations made the data objective as much as possible and revealed the strongest clinico-biochemical associations. Levels of AB to both native and denaturated DNA were studied. Comparison of several test-systems showed that the system produced by "Specialized scientific Labs" Company has the best sensitivity. In two populations of MS patients the levels of AB in plasma were similar and associated between each other, higher than in donors, but lower than in SLE patients. In both groups MS patients with secondary progressive MS had higher percent of samples of plasma with average and high levels of AB. In the Novosibirsk group associations of levels of AB with parameters of disease severety (EDSS and a number of FS scales) were seen. In the Moscow group levels of AB to DNA were significantly associated with time from the disease onset to certain level of disability (EDSS 3); both the analysis of average values and the correlation analysis showed a weak association of AB to DNA level and MS duration. The data testify that AB to DNA play a more important role in MS pathogenesis than was considered earlier. Catalytic AB as a part of anti-DNA AB may play a special role.

[The mechanism of supercoiled DNA recognition by eukaryotic type I topoisomerases. II. A comparison of the enzyme interaction with specific and nonspecific oligonucleotides]. / Mekhanizm uznavaniia superskruchennoi DNK éukarioticheskimi topoizomerazami pervogo tipa II. Sravnenie vzaimodeistviia fermentov so spetsificheskimi i nespetsificheskimi oligonukleotidami.

Data on the interaction of DNA type I topoisomerases from the murine and human placenta cells with specific and nonspecific oligonucleotides of various structures and lengths are summarized. The relative contributions of various contacts between the enzymes and DNA that have previously been detected by X-ray analysis to the total affinity of the topoisomerases for DNA substrates are estimated. Factors that determine the differences in the enzyme interactions with specific and nonspecific single- and double-stranded DNAs are revealed. The results of the X-ray analysis of human DNA topoisomerase I are interpreted taking into account data on the comprehensive thermodynamic and kinetic analysis of the enzyme interaction with the specific and nonspecific DNAs.