[Design of oligonucleotide inhibitors of the human DNA-methyltransferase 1].

Mammalian DNA methyltransferase 1 (Dnmt1) is responsible for copying DNA methylation patterns during cell division. A number of studies demonstrate that Dnmt1 plays an important role in carcinogenesis, that causes, in particular, significant interest in searching for specific inhibitors of this enzyme. In the present study, with the purpose of design of oligonucleotide inhibitors of human Dnmt1, a number of single-, double-stranded and hairpin DNA-structures, containing canonical or modified enzyme recognition site 5'-CG were constructed on the basis of uniform 22 b sequence. It was shown, that such structural features as C:A-mismatch, phosphorothioates and hairpin are capable to incrementally increase oligonucleotide affinity to Dnmt1. The improvement of inhibitor properties were also achieved by substitution of target cytosine with 5,6-dihydro-5-azacytosine, 5-methyl-2-pyrimidinone and 6-methyl-pyrrolo-[2,3-d]-2-pyrimidinone. The concentrations of the most efficient oligonucleotides caused 50% inhibition of methylation of 1 microM conventional DNA substrate, polymer poly(dI-dC) * poly(dI-dC), were about 10(-7) M. In the equal in vitro conditions the constructed oligonucleotide inhibitors demonstrated much stronger effect compared to known inhibitors of Dnmt1, which were used as controls.

An examination of the ability of titanium dioxide nanoparticles and its conjugates with oligonucleotides to penetrate into eucariotis cells.

In this study we examine the possibility that TiO2 nanoparticles and their conjugates can penetrate into cultivated cells without any special transfection procedures. Oligonucleotides and their derivates were conjugated with the TiO2 nanoparticles, which were obtained as colloidal solutions at a concentration of TiO2 0.3M by TiCl4 hydrolysis. The electronic microscopy of various cell cultures (KCT, Vero, and MDCK) treated with nanoparticle solutions (20 µg/µl) showed that nanoparticles could enter the cells and accumulate in the vacuoles and phagosomes and form inclusions in cytoplasm. Thus, we demonstrated the penetration of TiO2 nanoparticles and their oligonucleotide conjugates into intracellular space without any auxiliary operations. Most other researches used electroporation techniques for similar purposes [1, 2, 5].

[Molecular enzymology of phage T4 Dam DNA-methyltransferase]. / Moleculiarnaia énzymologiia Dam-DNK-metiltranferazy faga T4.

The review reflects results of studies on the molecular mechanism of phage T4 Dam DNA-methyltransferase action. The enzyme (T4Dam) catalyzes methyl group transfer from S-adenosyl-l-methionine (AdoMet) to N6-adenine position in the palindromic recognition sequence GATC (EC 2.1.1.72). The enzyme subunit structure, substrate-binding and kinetic parameters for a wide range of native and modified oligonucleotide duplexes, as well as steady-state reaction kinetic scheme, included T4Dam isomerization to catalytically active form, are considered. The found mechanisms of DNA induced T4Dam dimerization, target base flipping, enzyme reorientation in an asymmetrically modified recognition sequence, effector action of reaction substrates and processive methylation of DNA substrates, containing more than one specific site, are discussed. The results obtained with T4Dam may be useful for understanding mechanisms of action of other homologous enzymes, most of all for specimens of numerous family of Dam DNA-methyltransferases.

[DNA-[N4-cytosine]-methyltransferase from Bacillus amyloliquefaciens: mechanism of action derived from steady state kinetics]. / DNK-[N4-tsitozin]-metiltransferaza iz Bacillus amyloliquefaciens: mekhanizm deistviia po dannym statsionarnoi kinetiki reaktsii.

Kinetic analysis of methyl group transfer from S-adenosyl-L-methionine (SAM) to the 5'-GGATCC recognition site catalyzed by the DNA-[N4-cytosine]-methyltransferase from Bacillus amyloliquefaciens [EC 2.1.1.113] has shown that the dependence of the rate of methylation of the 20-meric substrate duplex on SAM and DNA concentration are normally hyperbolic, and the maximal rate is attained upon enzyme saturation with both substrates. No substrate inhibition is observed even at concentrations many times higher than the Km values (0.107 microM for DNA and 1.45 microM for SAM), which means that no nonreactive enzyme-substrate complexes are formed during the reaction. The overall pattern of product inhibition corresponds to an ordered steady-state mechanism following the sequence SAM decreases DNA decreases metDNA increases SAH increases (S-adenosyl-L-homocysteine). However, more detailed numerical analysis of the aggregate experimental data admits an alternative order of substrate binding, DNA decreases SAM decreases, though this route is an order of magnitude slower.

[The kinetic mechanism of phage T4 DNA-[N6-adenine]-methyltransferase]. / Kineticheskii mekhanizm deistviia DNK-[N6-adenin]-metiltransferazy faga T4.

Kinetic analysis of methyl group transfer from S-adenosyl-L-methionine (SAM) to the GATC recognition site catalyzed by the phage T4 DNA-[N6-adenine]-methyltransferase (MTase) [EC 2.1.1.72] showed that the reverse reaction is at least 500 times slower than the direct one. The overall pattern of product inhibition corresponds to an ordered steady-state mechanism following the sequence SAM decreases DNA decreases metDNA increases SAH increases (S-adenosyl-L-homocysteine). Pronounced inhibition was observed at high concentrations of the 20-meric substrate duplex, which may be attributed to formation of a dead-end complex MTase-SAH-DNA. In contrast, high SAM concentrations proportionally accelerated the reaction. Thus, the reaction may include a stage whereby the binding of SAM and the release of SAH are united into one concerted event. Computer fitting of alternative kinetic schemes to the aggregate of experimental data revealed that the most plausible mechanism involves isomerization of the enzyme.

[DNA-(N4-cytosine)-methyltransferase from Bacillus amyloliquefaciens: kinetic and substrate binding properties]. / DNK-(N4-tsitozin)-metiltransferaza iz Bacillus amyloliquefaciens: kineticheskie i substrat-sviazyvaiushchie svoistva.

Interaction of DNA-(N4-cytosine)-methyltransferase from the Bacillus amyloliquefaciens (BamHI MTase, 49 kDa) with a 20-mer oligonucleotide duplex containing the palindrome recognition site GGATCC was studied by methods of steady-state and presteady-state kinetics of the methyl group transfer, gel retardation, and crosslinking of the enzyme subunits with glutaric aldehyde. In steady-state conditions, BamHI MTase displays a simple kinetic behavior toward a 20-mer oligonucleotide substrate. A linear dependence was observed for the reaction rate on the enzyme concentration and a Michaelis dependence of the reaction rate on the concentration of both substrates: S-adenosyl-L-methionine (SAM), the methyl group donor, and DNA, the methyl group acceptor. In independent experiments, the concentration of the 20-mer duplex or SAM was changed, the enzyme concentration being substantially lower then the concentrations of substrates. The kcat values determined in these conditions are in good agreement with one another and approximately equal to 0.05 s-1. The Km values for the duplex and SAM are 0.35 and 1.6 microM, respectively. An analysis of single turnover kinetics (at limiting concentration of the 20-mer oligonucleotide duplex) revealed the following characteristics of the BamHI MTase-dependent methylation of DNA. The value of rate constant of the DNA methylation step at the enzyme saturating concentration is on average 0.085 s-1, which is only 1.6 times higher than the value determined in steady-state conditions. Only one of two target cytidine residues was methylated in the course of the enzyme single turnover, which coincides with the earlier data on EcoRI MTase. Regardless of the order of the enzyme preincubation with SAM and DNA, both curves for the single turnover methylation are comparable. These results are consistent with the model of the random order of the productive ternary enzyme-substrate complex formation. In contrast to the relatively simple kinetic behavior of BamHI MTase in the steady-state reaction are the data on the enzyme binding of DNA. In gel retardation experiments, there was no stoichiometrically simple complexes with the oligonucleotide duplex even at low enzyme concentrations. The molecular mass of the complexes was so high that they did not enter 12% PAG. In experiments on crosslinking of the BamHI MTase subunits, it was shown that the enzyme in a free state exists as a dimer. Introduction of substoichiometric amounts of DNA into the reaction mixture results in pronounced multimerization of the enzyme. However, addition of SAM in saturating concentration at an excess of the oligonucleotide duplex over BamHI MTase converts most of the enzyme into a monomeric state.

[Single turnover kinetics of phage T4 DNA-(N6-adenine)methyltransferase]. / Kinetika odnogo oborota metilirovaniia DNK-(N6-adenin)-metiltransferazoi faga T4.

Interaction of T4 DNA-(N6-adenine)-methyltransferase [EC 2.1.1] was studied with a variety of synthetic oligonucleotide substrates containing the native recognition site GATC or its modified variants. The data obtained in the decisecond and second intervals of the reaction course allowed for the first time the substrate methylation rates to be compared with the parameters of the steady-state reaction. It was established that the substrate reaction proceeds in two stages. Because it is shown that in steady-state conditions T4 MTase forms a dimeric structure, the following sequence of events is assumed. Upon collision of a T4 MTase monomer with an oligonucleotide duplex, an asymmetrical complex forms in which the enzyme randomly oriented relative to one of the strands of the specific recognition site catalyzes a fast transfer of the methyl group from S-adenosylmethionine to the adenosine residue (k1 = 0.21 s-1). Simultaneously, a second T4 MTase subunit is added to the complex, providing for the continuation of the reaction. In the course of a second stage, which is by an order of magnitude slower (k2 = 0.023 s-1 for duplex with the native site), the dimeric T4 MTase switches over to the second strand and the methylation of the second residue, target. The rate of the methyl group transfer from donor, S-adenosylmethionine, to DNA is much higher than the overall rate of the T4 MTase-catalyzed steady-state reaction, although this difference is considerably less than that shown for EcoRI Mtase. Substitutions of bases and deletions in the recognition site affect the substrate parameters in different fashions. When the GAT sequence is disrupted, the proportion of the initial productive enzyme-substrate complexes is usually sharply reduced. The flipping of the adenosine residue, a target for the modification in the recognition site, revealed by fluorescence titration, upon interaction with the enzyme supports the existing notions about the involvement of such a DNA deformation in reactions catalyzed by various DNA-MTases.

[Oligomerization of DNA-(adenine-N6)-methyltransferase from phage T4 and its effect on the catalytic characteristics of the enzyme]. / Oligomerizatsiia DNK-(adenin-N6)-metiltransferazy faga T4 i ee vliianie na katalitcheskie kharakteristiki fermenta.

The structural and catalytic properties of the phage T4 DNA-(adenine-N6)-methyltransferase (EC 2.1.1.72) were studied at different enzyme-substrate concentration ratios by chemical cross-linking of the protein subunits and by measuring the presteady state kinetics of the reactions. Various structural states of the methyltransferase were correlated with its catalytic activity, and it was shown that the oligomeric forms of the enzyme are catalytically active but are characterized by the reaction parameters different from those of the monomer.

[Effect of S-adenosyl-L-methionine and its analogs on site-specific binding DNA-(adenine-N6)-methyltransferase from T4 phage to the oligonucleotide substrate]. / Vliianie S-adenozil-L-metionina i ego analogov na sait-spetsificheskoe sviazyvanie DNK-(adenin-N6)-metiltransferazy faga T4 s oligonukleotidnym substratom.

Using fluorescence of 2-aminopurine-substituted oligonucleotide duplexes, "flipping" of the target base in the process of interaction of T4 DNA-(adenine-N6)-methyltransferase (EC 2.1.1.72) with the substrate double-stranded DNA was revealed. It was shown that S-adenosyl-L-methionine, the methyl group donor, induces the reorientation of the enzyme relative to the asymmetrically modified recognition site.

[Experimental study of therapeutical properties and safety of king crab collagenase-containing ointment]. / Eksperimental'noe izuchenie lechebnykh svoistv mazi, soderzhashchei kollagenazu kamchatskogo kraba.

The effects of ointment containing king crab (Paralithodes camtschatica) collagenase on intact skin, thermal, and pyonecrotic wounds were studied in rats by using hematological, biochemical, immunological, and morphological methods. The ointment for the skin and viscera was shown to be safe. It is highly effective in debriding the infected wounds. Different concentrations of collagenase were tested. The concentration of collagenase was recommended to be 0.2 mg/g ointment for use.

[Use of collase for culturing cells]. / Primenenie kollazy dlia kul'tivirovaniia kletok.

Collase, an enzymatic preparation made from crab hepatopancreas, was used as a dissociative reagent in preparation of primary cell cultures and for detachment of continuous cells from the substrate during reinoculation. Collase was found to increase viable cell harvest by 2 to 2.5 times in comparison with trypsin and had a less detrimental effect on the cells which retained their proliferative activity, morphology, productivity, and sensitivity to viruses.

[Identification of the gene for the immunodominant p35 protein from vaccinia virus]. / Identifikatsiia gena immunodominantnogo belka p35 virusa ospovaktsiny.

A major immunodominant envelope protein p35 of vaccina virus was purified by means of extraction from virions with detergent NP-40. The protein was cleaved with CNBr, four homogenous peptides were isolated and their N-terminal amino acid sequences were determined. Computer search in a protein sequences data bank revealed that the immunodominant protein p35 of vaccinia virus is encoded by H3 gene in HindIII-H fragment of vaccinia virus genome.

[Aggregation of tryptophanyl-tRNA synthetase depending on temperature. Study by a low-angle scatter x-ray method]. / Zavisiashchaia ot temperatury agregatsiia triptofanil-tRNK-sintetazy. Issledovanie metodom malouglovogo rentgenovskogo rasseianiia.

By means of small angle X-ray scattering, an aggregation of beef pancreas Trp-tRNA synthetase (EC 6.1.1.2) was observed at physiological temperatures. A Trp-tRNA synthetase preparation which is homogeneous after PAGE in beta-ME-SDS was found to be heterogeneous in particle sizes even at low (4-8 degrees C) temperature. At heating up to 30-45 degrees C, the oligomer sizes increased as well as its proportion depending on the incubation time and temperature; very large aggregates were observed 10 times exceeding the sizes of initial particles. Cooling to 20 degrees C caused no disaggregation due to disulphide bond formation between associated subunits of Trp-tRNA synthetase. A hypothesis is proposed that the aggregation of bovine Trp-tRNA synthetase evaluated in vitro and not observed earlier with any aminoacyl-tRNA synthetases of unicellular organisms might serve as one of the mechanisms of its compartmentation in pancreas.

Amino acid sequence determination of vaccinia virus immunodominant protein p35 and identification of the gene.

A major immunodominant envelope protein of vaccinia virus (protein p35) was purified by extraction from virions with the nonionic detergent Nonidet P-40. The protein was cleaved with cyanogen bromide. Four homogeneous peptides were isolated and their N-terminal amino acid sequences determined. A computer search of a protein-sequence data bank revealed complete identity of the determined sequences with sequences 44-63, 144-149, 154-165, and 224-238 of ORF H3 of the HindIII-H fragment of the vaccinia virus genome (Rosel et al 1986). It has therefore been established that the immunodominant protein p35 of vaccinia virus is encoded by the gene in the HindIII-H fragment of the vaccinia virus genome.