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Biomedical subjects

S A Strel'tsov

Publications and source records attributed to S A Strel'tsov.

At least 19 recordsLinked to original sources
PubMed1976

[Interaction of dansyl-dipeptidyl-tRNA with E. coli ribosomes].

Dansyl-dipeptidyl-tRNA is found to bind with ribosomes in the presence of polyU much more efficiently than AcPhe-tRNA. 30-80% OF introduced danysl-dipeptidyl-tRNA is in a complex with ribosomes and reacts with puromycin in the presence of 5 mM Mg2+. A significant binding of dansyl-dipeptidyl-tRNA both for acceptor and donor ribosome regions is observed in the presence of 10 mMg2+, unlike AcPhe-tRNA, which is capable of the binding only at 20 mM Mg2+. A peptide transfer from dansyl-dipeptidyl-tRNA on puromycin takes place at 10 mM Mg2+ in the absence of template, while AcPhe-tRNA efficiently interacts with puromycin only at 20 mM Mg2+. The data obtained suggest that the increase of hydrophobity of a peptide residue in peptidyl-tRNA increases its binding in peptidyl transferase of ribosomes.

Dansyl Compounds↗
PubMedDate not supplied

[Ligands with affinity to specific sequence of DNA base pairs. XII. The synthesis and cytological studies of dimeric Hoechst 33258 molecules].

We synthesized dimeric Hoechst dye molecules composed of two moieties of the Hoechst 33258 fluorescent dye phenolic hydroxy groups of which were tethered via pentamethylene, heptamethylene, or triethylene oxide linkers. A characteristic pattern of differential staining of chromosome preparations from human premonocytic leukemia HL60 cells was observed for all the three fluorescent dyes. The most contrast pattern was obtained for the bis-Hoechst analogue with the heptamethylene linker; its quality was comparable with the picture obtained in the case of chromosome staining with 4',6-diamidino-2-phenylindole. The ability to penetrate into the live human fibroblasts was studied for the three bis-Hoechst compounds. The fluorescence intensity of nuclei of live and fixed cells stained with the penta- and heptamethylene-linked bis-Hoechst analogues was found to differ only slightly, whereas the fluorescence of the nuclei of live cells stained with triethylene oxide-linked bis-Hoechst was considerably weaker than that of the fixed cells. The bis-Hoechst molecules are new promising fluorescent dyes that can both differentially stain chromosome preparations and penetrate through cell and nuclear membranes and effectively stain cell nuclei.

Base Pairing↗
PubMedDate not supplied

[Effect of supporting substrates on the structure of DNA and DNA-trivaline complexes studied by atomic force microscopy].

Linear DNA, circular DNA, and circular DNA complexes with trivaline (TV), a synthetic oligopeptide, were imaged by atomic force microscopy (AFM) using mica as a conventional supporting substrate and modified highly ordered pyrolytic graphite (HOPG) as an alternative substrate. A method of modifying the HOPG surface was developed that enabled the adsorption of DNA and DNA-TV complexes onto this surface. On mica, both purified DNA and DNA-TV complexes were shown to undergo significant structural distortions: DNA molecules decrease in height and DNA-TP displays substantial changes in the shape of its circular compact structures. Use of the HOPG support helps preserve the structural integrity of the complexes and increase the measured height of DNA molecules up to 2 nm. AFM with the HOPG support was shown to efficiently reveal the particular points of the complexes where, according to known models of their organization, a great number of bent DNA fibers meet. These results provide additional information on DNA organization in its complexes with TV and are also of methodological interest, since the use of the modified HOPG may widen the possibilities of AFM in studying DNA and its complexes with various ligands.

Adsorption↗
PubMedDate not supplied

[DNA-specific dimeric bisbenzimidazole].

A dimeric analogue of the fluorescent dye Hoechst 33258 was synthesized. It was shown to differentially stain human chromosome preparations and bind to double-stranded DNAs.

Benzimidazoles↗
PubMedDate not supplied

[New physical interpretation of S-shaped curves: competition between various types of binding of ligands with DNA].

In studies of interactions of ligands with nucleic acid molecules, S-shaped curves are often obtained. In this work we show that the sigmoidal shape of the curves is due to a competition of ligand molecules for DNA binding sites. If a ligand that binds to DNA can form two types of complexes with the binding constants K1 and K2 and binding site sizes L1 and L2, respectively, then in the event that K1 < K2 and L1 < L2, the dependence of the concentration of complexes of the first type on the concentration of the ligand added to solution can be S-shaped.

Binding Sites↗
PubMedDate not supplied

[Interaction of topotecan--a DNA topoisomerase inhibitor--with dual-stranded polydeoxyribonucleotides. I. Dimerization of topotecan in solution].

Behavior of topotecan, DNA topoisomerase I inhibitor, was studied in aqueous solutions by optical methods. Topotecan absorption spectra were recorded in the pH range 0.5-11.5 and its pKa were determined. Quantum chemical calculations were made for all charge states of the topotecan molecule in lactone and carboxylate form. The calculated absorption maxima agree well with the experimental data. Protonation of the topotecan D ring (pKa = 3.6) was revealed. Comparison of experimental and calculated data showed topotecan structure with a proton at the oxygen atom at C16a rather than N4 to be the most preferable. Topotecan molecules were shown to form dimers at concentrations above 10(-5) M. Topotecan dimerization is accompanied by an increase in the pKa of hydroxy group of the A ring from 6.5 ([TPT] = 10(-6) M) to 7.1 ([TPT] = 10(-4) M), which indicates participation of this group in dimer stabilization, perhaps due to intermolecular hydrogen bonding with N1 of the B ring of a neighboring molecule. Probable dimer structures were proposed. The topotecan dimerization constant was determined, K = (4.0 +/- 0.7) x 10(3) M-1.

Dimerization↗
PubMedDate not supplied

[Thermodynamic model of the formation of bridges between nucleic acid molecules in a liquid crystal].

A thermodynamic model of the formation of bridges consisting of alternating daunomycin molecules and copper ions and connecting neighboring nucleic acid molecules in a particle of a liquid crystalline dispersion was constructed. The model is based on the conception that ligands are adsorbed on lattices of reaction centers which are formed in a liquid crystal at a particular spatial arrangement of adjacent nucleic acid molecules (phasing). Equations were derived that describe typical experimentally obtained S-shaped dependences of bridge concentration on the concentration of copper ions and daunomycin molecules in an initial solution. It was shown that dependences of this kind take place in two variants of the adsorption model: when the binding of daunomycin with adjacent nucleic acid molecules is considered to be independent on the formation of bridges and when bridges compete with single daunomycin molecules for the sites on adjacent nucleic acid molecules.

Algorithms↗
PubMedDate not supplied

[Interaction of topotecan, DNA topoisomerase I inhibitor, with double-stranded polydeoxyribonucleotides. III. Binding at the minor groove].

Interaction of topotecan (TPT) with calf thymus DNA, coliphage T4 DNA, and poly(dG-dC). poly(dG-dC) was studied by optical (linear flow dichroism, UV-vis spectroscopy) and quantum chemical methods. The linear dichroism (LD) signal of TPT bound to DNA was shown to have positive sign in the range 260-295 nm. This means that the plane of quinoline fragment (rings A and B) of TPT molecule form an angle lower 54 degrees with the long axis of DNA, and hence TPT molecule can not intercalate between DNA base pairs. TPT was established to bind to calf thymus DNA as readily as to coliphage T4 DNA whose all cytosines in the major groove were glycosylated at the 5th position. Consequently, the DNA major groove does not participate in TPT binding. TPT molecule was shown to compete with distamycin for binding sites in the minor groove of DNA and poly(dG-dC). poly(dG-dC). Thus, it was demonstrated for the first time that TPT binds to DNA at its minor groove.

Base Pairing↗
PubMedDate not supplied

[Interaction of topotecan, DNA topoisomerase I inhibitor, with double-stranded polydeoxyribonucleotides. 4. Topotecan binds preferably to the GC base pairs of DNA].

Interaction of topotecan (TPT) with synthetic double-stranded polydeoxyribonucleotides has been studied in solutions of low ionic strength at pH = 6.8 by linear flow dichroism (LD), circular dichroism (CD), UV-Vis absorption and Raman spectroscopy. The complexes of TPT with poly(dG-dC).poly(dG-dC), poly(dG).poly(dC), poly(dA-dC).poly(dG-dT), poly(dA).poly(dT) and previously studied by us complexes of TPT with calf thymus DNA and coliphage T4 DNA have been shown to have negative LD in the long-wavelength absorption band of TPT, whereas the complex of TPT with poly(dA-dT).poly(dA-dT) has positive LD in this absorption band of TPT. Thus, there are two different types of TPT complexes with the polymers. TPT has been established to bind preferably to GC base pairs because its affinity to the polymers of different GC composition decreases in the following order: poly(dG-dC).poly(dG-dC) > poly(dG).poly(dC) > poly(dA-dC).poly(dG-dT) > poly(dA).poly(dT). The presence of DNA has been shown to shift monomer-dimer equilibrium in TPT solutions toward dimer formation. Several duplexes of the synthetic polynucleotides bound together by the bridges of TPT dimers may participate in the formation of the studied type of TPT-polynucleotide complexes. Molecular models of TPT complex with linear and ring supercoiled DNAs and with deoxyguanosine have been considered. TPT (and presumably all camptothecin family) proved to be a representative of a new class of DNA-specific ligands whose biological action is associated with formation of dimeric bridges between two DNA duplexes.

Base Pairing↗
PubMedDate not supplied

[Interaction of topotecan-a DNA topoisomerase I inhibitor-with dual-stranded polydeoxyribonucleotides. V. Topotecan is able to cause single- and double-strand breaks in ring superhelical DNA in the absence of enzyme].

Temperature, concentration, and time dependence for the emergence of breaks in the sugar-phosphate backbone in a circular supercoiled DNA (scDNA) was studied for the first time in the presence of topotecan (TPT) and in the absence of human DNA topoisomerase I (topo I). Because TPT is a comptothecin (CPT) derivative, it is the first example for the ability of molecules of CPT family to cause double-stranded breaks in scDNA in the absence of the enzyme. The experiments were carried out in low ionic strength solutions (10 mM sodium cacodylate) at neutral pH (6.8). Incubation time necessary for the appearance of double-stranded breaks in scDNA in the presence of TPT correlated with the time of formation of strong TPT-DNA complex. A model was suggested for the complex composed of two crossed DNA duplexes bound through a bridge of two dimers of TPT lactone form. According to this model, two carbonyl groups of D rings of different TPT dimers form hydrogen bonds with 2-amino groups of guanines located in the neighboring base pairs of diverse strands of one of DNA duplexes. At the same time, two other carbonyl groups of D rings of TPT dimers form hydrogen bonds with 2-amino groups of guanines spaced five bp apart in the same strand of the second DNA duplex.

DNA Damage↗
PubMedDate not supplied

[Interaction of trivaline with single-stranded polyribonucleotides].

Binding of tripeptide H-Val3-(NH)2-Dns (TVP) to polyribonucleotides was studied by fluorescence methods, circular and flow linear dichroism, equilibrium dialysis and electron microscopy. It was found that TVP binds to poly(U) in monomer, dimer and tetramer forms with binding constants of about 10(3), 40, 18.10(4) M, respectively. The cooperativity parameter for peptide dimer binding is 2000. The peptide forms tetramer complexes with poly(A), poly(C), poly(G) also. The formation of a complex between the peptide tetramer and nucleic acid is accompanied by a significant increase in the fluorescence intensity. The cooperative binding of TVP dimers to poly(U), poly(A), poly(C) is accompanied by a dramatic decrease in the flexibility of polynucleotide chains. However, it has a small effect (if any) on the flexibility of the poly(G) chain. The observed similarity of thermodynamic, optical and hydrodynamic++ properties of TVP complexes with single-stranded and double-stranded nucleic acids may reflect a similarity in the geometries of peptide complexes with nucleic acids. Electron microscopy studies show that peptide binding to poly(U) and dsDNA leads to compactization of the nucleic acids caused by interaction between the peptide tetramers bound to a nucleic acid. At the first stage of the compactization process the well-organized rod-like particles are formed, each consisting of one or more single-stranded polynucleotide fibers. Increasing the peptide concentration stimulates a side-by-side association and folding of the rods with the formation of macromolecular "leech-like" structures with the thickness of 20-50 nm.

Circular Dichroism↗
PubMedDate not supplied

[Synthetic DNA-bindings ligands containing reaction centers specific for AT- and GC-pairs in DNA].

In the present communication design, synthesis and DNA binding activities of three bis-netropsins and two netropsin analogs containing two N-propylpyrrolecarboxamide fragments linked covalently to peptides Gly-Gly-(analog I) and Val-Val-Val-Gly-Gly-(analog II) are reported. Each bis-netropsin consists of two netropsin-like fragments attached to peptides -Gly-Cys-Gly-NH2 (compound IIIa), H-Gly-Cys-Gly-Gly-Gly-(compound IV) or Gly-Cys-Sar-NH2 (compound IIIb) which are linked symmetrically via S-S bonds. Physico-chemical studies show that each bis-netropsin carries 6 AT-specific reaction centers and covers approximately 10 base pairs upon binding to poly(dA).poly(dT). This indicates that two netropsin-like fragments of the bis-netropsin molecule are implicated in specific interaction with DNA base pairs. The peptide fragments of bis-netropsins IIIa and IV form small beta-sheets containing two-GC-specific reaction centers. The DNase I cleavage patterns of bis-netropsin-DNA complexes visualized by high resolution gel electrophoresis show that the preferred binding sites for bis-netropsins IIIa and IV are identical and contain two runs of three or more AT pairs separated by two GC pairs. Specificity determinants of netropsin analog II binding in the beta-associated dimeric form are identical to those of bis-netropsin IIIa thereby indicating that there is a similarity in the structure of complexes formed by these ligands with DNA. In the monomeric form analog II exhibits binding specificity identical to that of analog I. Replacement of C-terminal glycine residues by sarcosines in the peptide fragments of bis-netropsin IIIa leads to a decrease in the affinity of ligand for DNA.

Base Composition↗
PubMedDate not supplied

[Structural organization of kinetoplast DNA and its compactization in a model system in vitro].

Studies on compactization and decompactization of the genome are of great importance for elucidation of structural mechanisms taking part in the regulation of gene activity. Kinetoplast DNA (kpDNA) is a convenient model for studies of compactization processes. KpDNA represents unique structure ("network"), consisting of catenated circular molecules of two types: minicircles (900 b.p.) and maxicircles (40 000 b.p.). The compactization process of kpDNA in vitro caused by interaction with synthetic peptide-dansylhydraside trivaline was studied. It was shown that at the initial stages the hairpins are observed on minicircles as if triple rings are being organized. The formation of hairpin is probably favoured by the presence in the minicircles of bent DNA, a specific nucleotide sequence causing rigid bending of the DNA helix. The hairpin does not make contact with the neighbouring DNA segment to form a triple ring, because the sizes of minicircles are too small. The minicircles compactization is finished with a complete collapse of the minicircles with the formation of rod-like structures. The catenation causes branching of rod-like structures. As a result of their intermolecular interaction, the branched rod-like structures become thicker. The process is completed with formation of the compact network, its diameter being 3-6 times smaller compared to the initial one.

Animals↗
PubMedDate not supplied

[Attachment of trivaline changes the specificity of binding of netropsin analogs with DNA].

In the present communication, synthesis and DNA binding activities of three analogs of the antibiotic netropsin are reported. Each analog contains two N-propylpyrrolecarboxamide units linked covalently to either Dns-Gly-Val-Val-Val-Gly-Gly- (I), Val-Val-Val-Gly-Gly (II) or Gly-Gly (III). It is shown that analogs I and II can self-associate in aqueous solution and methanol as revealed from the fact that UV absorbance and circular dichroism spectra obtained for these analogs are concentration-dependent. By contrast, analogs III exists as a monomer, even at concentration levels of the order of 1.10(-3) M. Determination of the apparent sizes of intramolecular aggregates by gel-filtration shows that analog I in aqueous solution at concentration levels of the order of 1.10(-3) M forms a series of aggregates containing from 2 to 12 monomers. Analog II exhibits a lower tendency to form intermolecular aggregates as compared with that of analog I. Dimerization constants are determined for analogs I and II in aqueous solution and methanol. The binding of N-propylpyrrolecarboxamide units and peptide fragments of analog I to DNA can be independently monitored by circular dichroism and fluorescence methods. If self-associated species of analog I (or II) are present in solution, the ligand exhibits a markedly different order of base pair sequence preferencies as compared with that of analog III. The results obtained are consistent with the inference that analogs I and II in a beta-associated form recognizes base pair sequences containing two runs of 3 AT pairs separated by two GC pairs.

Base Sequence↗
PubMedDate not supplied

[Interaction of synthetic pentapeptide with DNA: specificity of binding and compactness of DNA].

Binding of synthetic pentapeptide Val-Thr-Thr-Val-Val-N2H2Dns (where Dns is a residue of 5-dimethylamino naphthyl-1-sulfonic acid) is studied by circular dichroism, electron microscopy and fluorescence methods. It is found that this peptide can self-associate in aqueous solution as revealed from the concentration-dependent changes in the UV absorbance and fluorescence spectra. At high peptide concentration (3.10(-4) M) massive peptide aggregates are formed in solution and can be visualized by electron microscopy. It is shown that pentapeptide binds to DNA predominantly in a self-associated form and exhibits preferences for certain nucleotide sequences. It binds more strongly to poly(dG).poly(dC) and poly[d(A-C)].poly[d(G-T)] than to poly(dA).poly(dT). The complex with poly(dA).poly(dT) dissociates in the presence of 0.05 M NaCl, whereas the complex with poly(dG).poly(dC) is stable even in the presence of 0.2 M NaCl. The binding is a cooperative process which is accompanied by compaction of DNA at peptide/DNA base pair ratios greater than 2. At the initial stage of the compaction process the coalescence of DNA segments covered by bound peptide molecules results in the formation of DNA loops stabilized by interaction between bound peptide molecules. Increasing peptide/DNA ratio leads to the formation of rod-like particles as revealed from electron microscopy studies. Further increase in the peptide concentration leads to folding of fibrillar macromolecular complexes into globula each containing a single DNA molecule.

Amino Acid Sequence↗
PubMedDate not supplied

[Study of the structure of tRNA by the energy migration method using fluorescent labels covalently bound to specific tRNA loci].

Optical and fluorescent characteristics of fluorescein covalently attached to 3'-end of tRNAFhe and X-nucleotide in the extra arm of several species of tRNA from E. coli have been studied. The probe is shown to be a sensitive factor indicating the conformational change of tRNA induced by Mg2+ and Na+ ions. By measuring the extent of energy transfer the distances between the fluorescent probe attached to 3'-terminus and X-nucleotide of tRNA and specific binding site of ethidium bromide on tRNA were determined to be 40.5 A and 32.5 A, respectively. The distances measured are in good agreement with the NMR spectroscopy data showing that the specific binding site for ethidium bromide on tRNA is localised near the sixth base pair of the acceptor stem.

Amino Acyl-tRNA Synthetases↗
PubMedDate not supplied

[Addition of the fluorescent label to the 3'-OH end of DNA and the 3'-OH end of nascent RNA].

3'(2')-O-acyl derivatives of the uridine triphosphate were synthesized. Acyl residues contained fluorescent dye; fluoresceine or rodamine C. Optical properties and stability of UTP analogues were studied. Their ability to serve as the substrates for calf thymus terminal deoxyribonucleotidyl transferase and E. coli RNA polymerase was also examined. It was shown that both enzymes were able to use tested analogues as substrates. Incorporation of the analogues into nascent RNA and DNA chains inhibited the synthetic reaction because of primer inactivation. The rate of the incorporation of the analogues showed an exponential time dependence

Animals↗