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O F Borisova

Publications and source records attributed to O F Borisova.

53 records · Page 3Linked to original sources
PubMedDate not supplied

[Parallel double helix and tertiary structure of nucleic acids].

The thermal denaturation of four oligonucleotides, viz. 3'-d(AT)5pO(CH2)6Opd(AT)5-3' (parAT), 3'-d(AT)5pO(CH2)5Opd(AT)5-5' (antiAT), 3'-d(A)10pO(CH2)6Op(T)10-3' (parA-T) and 3'd(A)10pOX X (CH2)6Opd(T)10-5' (antiA-T) in 0.01 M phosphate buffer at pH 7 in presence 0.1, 0.25, 0.5 and 1.0 M NaCl have been studied. It was shown that at lower temperature (0-20 degrees C) all oligomeres exist as complexes of two (canonic duplex) or four (eight) molecules of oligonucleotides, but at higher temperature (30-70 degrees C)- as hairpins with parallel (parAT and parA-T) of antiparallel (antiAT and antiA-T) orientation of chains. Thermodinamic parameters of separated strands-hairpins and hairpins--"low temperature complexes" transition were computated from the melting curves [A260 (T)] by nonlinear regression. AntiA-T was shown by ethidium bromide binding to exist at low strength (0.01 M phosphate buffer without NaCl) as four-stranded complex from two antiparallel double stranded helices parallely oriented and bonded by satisfy hydrogen-bond of groups not involved in WC-pairing. At higher ionic strength the two of such tetramers was conjugated by hydrophobic interaction into octamers. We speculate that four-stranded complexes serves to bring together, and zipper up two antiparallel double stranded helices at replication of DNA, cross-over of gomologues chromosomes and other biochemically important processes.

Anticodon↗
PubMedDate not supplied

[Temperature-dependent structural changes in complexes of tRNA(adenine-1)-methyltransferase from Thermus thermophilus HB8 and tRNA studied by optical and electron microscope methods].

The complexation of tRNA (adenine-1-)-methyltransferase from Thermus thermophilus HB8 (E.C.2.1.1.36) with Escherichia coli tRNA(Phe) and yeast tRNA1(Val) was investigated in a temperature range from 20 to 90 degrees C. The quantity of methylase subunits bounded with tRNA and the association constant (Ka) were determined by means of fluorescence quenching of the enzyme tryptophane residues by tRNA molecules. The number of enzyme subunits bounded with one tRNA molecule at temperatures 20-70 degrees C is equal to 8 +/- 2. The Ka values increase from (2 divided by 3).10(7) at 20 degrees C up to 8.5.10(7) M-1 at 70 degrees C. The temperature increase from 70 to 90 degrees C causes a decrease in the enzyme specific activity and in Ka values. In the temperature range from 75 to 90 degrees C a cooperative transition of methylase macromolecules into associates was observed. This association is accompanied by an increase of UV-light scattering and of fluorescence polarization coefficient of methylase tryptophane residues. In the absence of tRNA the size of enzyme associates (d) is evaluated to be more than 320 nm (d greater than or equal to lambda-320 nm), in the presence of tRNA-less than 320 nm (d much less than lambda-320 nm). An electron microscopic investigation of methylase and its complexes with tRNA at 20 degrees C revealed disk-like particles with a diameter and height of 8-11 nm and 4-5 nm, respectively. These disk-like methylase preparations dialized against distilled water form flexible polymeric rods with a diameter of 10-12 nm and the length of about several hundreds nm. During complexation of methylase with tRNA, in the same conditions as the dializes was carried out, large associates were not revealed.

Escherichia coli↗
PubMedDate not supplied

[A study of tRNA(adenine-1-)-methyltransferase from Thermus thermophilus HB8 with tRNA using enzymatic and spectral methods].

The contact sites of yeast tRNA1Val with tRNA(adenine-1-)-methyltransferase (EC 2.1.1.36) were studied by comparing the partial digests of free and enzyme bound tRNA. The RNAases Sa, V1, S1 and A were used for this purpose. Phosphodiester bonds on the proximal end of the acceptor stem and adjacent D- and T psi-stems, forming a continuous area, are protected by the methylase from the action of RNAases. On the contrary an enhancement of phosphodiester bond splitting of the D- and T psi-loops and of the anticodon stem is observed in the presence of methylase, which is interpreted as tertiary structure relaxation of tRNA owing to complex formation. The isotherm of ethidium bromide adsorption on free and methylase bound tRNA has shown that in enzyme shields approximately 50% of tRNA double stranded regions.

Binding Sites↗
PubMedDate not supplied

[Comparison of the conformation of RNA from phage MS2 and 16S rRNA. Interaction with dyes specific for the secondary structure of native RNA and RNA subjected to hydrolysis by nuclease S1].

The interaction of ethidium bromide (EtBr) with double-stranded (ds), and acridine orange (AO) with single-stranded (ss) fragments of 16S rRNA Escherichia coli in a wide range of ionic strength, at various pH, Zn2+ ion concentrations and partial hydrolysis by nuclease S1 was investigated. It was shown that about 90% of the RNA molecule is accessible to both dyes, when the ionic strength is near of 0.01 (pH 7). Approximately half of the RNA becomes inaccessible to dyes, when the ionic strength was increased up to 0.08-0.24 (pH 4.7-7), independent on the presence of Zn2+ ions (10(-3) M). About a half of the ds-, and a quarter of the ss-segments of the RNA, deduced from the secondary structure model were protected from the interaction with EtBr and AO. The hydrolysis of about a half of ss-segments upon addition of the Zn2+ (10(-3) M) ions did not affect the RNA tertiary structure. The experimental data obtained confirm the idea of the existence of some "nucleus" (or "nuclei") within the 16S rRNA molecule. The "nucleus" seems to be inaccessible to the dyes and is very stable to heat denaturation. It was supposed that this structure is organized by means of interaction of some of the parallelly oriented ds-segments, as it was suggested earlier for the phage MS2 RNA structure.

Acridine Orange↗
PubMedDate not supplied

[Nuclear ribonucleoproteins containing pro-mRNA. XIV. Structural study using ethidium and fluorescamine].

Nuclear 30S RNP particles were studied by means of fluorescence techniques. It's shown that fluorescamin interacts with NH2-groups of protein molecule. As a result, covalent fluorescent label is formed. Quantum yield (rho), fluorescence spectra, lifetime of excited state (tau) and polarization of fluorescamin complexes with 30S particles were studied. Excitation spectra have their maximum at 395 nm, and fluorescence spectrum at 480 nm. These figures correspond to spectra of fluorescamin complexes with NH2-groups of lysine. Mean quantum yield (rho = 0.27) and lifetime of excited state of fluorescence (tau = 7.8 nsec) were measured. It's shown that fluorescamin forms two types of fluorescent complexes in 30S particles. These complexes differ only by their rho(rho1 = 0.11, rho2 = 0.30) and rho(rho1 = 3.6 nsec, rho2 = 10.0 nsec) by 2.7 times. Migration radius between fluorescamin bound to protein and ethydium bromide adsorbed on double-stranded regions of pre-mRNA in RNP-particles was measured. It's equal to 32 A. Adsorbtion isotherms of ethydium bromide were measured by fluorescence in 0.1 and 0.4 M NaCl. Data obtained showed that 6% of pre-mRNA in 30S particles bound the dye as a strong complex, i. e. this part of pre-mRNA is double-stranded. RNase treatment of RNP had no effect on this value. But the increase of NaCl concentration up to 0.4 M caused the dissociation of protein subunits to some extent followed by appearance of up to 40% free NH2-groups interacting with fluorescamin. Measuring of energy migration from fluorescamin to ethydium bromide showed that double-stranded pre-mRNA regions strictly bound to protein sticked out from RNP particle at a distance of about 27 A. The increase of NaCl concentration up to 0.4 M leads to disruption of this strict bond of double-stranded regions with protein. As a result, these regions of pre-mRNA become labile and move away from the RNP particle at more than 30 A. According to theoretical calculations, there is about 1--2 pre-mRNA hairpins (18--9 base pairs respectively) per one 30S particle.

Ethidium↗
PubMedDate not supplied

[Study of the secondary and tertiary structure of phage MS2 RNA using nucleases and fluorescent dyes specific for secondary structure].

The binding of ethidium bromide (EtBr) and acridine orange (AO) to RNA in native state or after hydrolysis by S1 and SV nucleases that specifically split single-stranded and double-stranded segments was studied. Nuclease S1 hydrolysis of RNA does not increase the number of EtBr strong binding sites, Tm and hyperchromic effect being also unchanged. Hydrolysis by double-stranded segments accessible to EtBr is followed by the diminishing of Tm and hyperchromism. A supposition is put forward that the main role in stabilization of the RNA tertiary structure is played by double-stranded segments arranged so that some of them are hidden and do not interact with dyes. One of the possible models may be parallel oriented intramolecular "hair-pins" forming compact "rod-like" structures.

Coliphages↗
PubMedDate not supplied

[Study of 2.5S RNA of 1,4-alpha-glucan branching enzyme by fluorescent methods using ethidium bromide].

The fluorescence yield and lifetime of ethidium bromide complexes with 1,4-alpha-glucan branching enzyme and its free nucleic acid component 2.5S RNA were measured. Both fluorescence parameters showed a 10-fold increase in comparison with those characteristics for the free dye. This increase allows to suggest the existence of double-stranded regions in 2.5S RNA both in the free as well as in the protein bound state. The coefficients of fluorescence polarization were also determined for ethidium bromide complexed with free and protein bound 2.5S RNA. They proved to be 13 and 18% respectively. No concentration depolarization was observed in both types of ethidium bromide and ethidium bromide--enzyme--RNA complexes. This proves that the double-stranded regions are rather short and that two ethidium bromide molecules can't be bound to each of them. The binding isotherms were measured for ethidium bromide absorbed on 2.5S RNA and on the holoenzyme. Their parameters napp and rmax are identical in the cases of free and protein bound 2,5S RNA (rmax = 0.046 +/- 0.001). However the binding constants of ethidium bromide complexes with free and protein bound 2.5S RNA differ significantly (Kapp = 2.2 X 10(6) M-1 for free 2.5S RNA and Kapp = 1.6 X 10(6) M-1 for the holoenzyme). The quantity of nucleotides involved in the two double-stranded regions accessible for ethidium binding is estimated to be about 28%. Increasing of Mg2+ ion concentration up to 10(-3) results in a decrease of ethidium bromide binding with double stranded regions. It may be due to a more compact tertiary structure of 2.5S RNA in the presence of Mg2+ in the free as well as in protein bound state.

1,4-alpha-Glucan Branching Enzyme↗
PubMedDate not supplied

[Study of the structural organization of RNA from phage MS2 using fluorescent dyes].

The spatial organization of phage MS2 RNA by binding to ethidium bromide (EtBr) and acridine orange (AO) to RNA was studied. The analyses of dye interaction by spectrophotometric and fluorometric methods have demonstrated that only about a half of 65-70% nucleotides of double-stranded segments can interact with AO and EtBr. On the other hand all the single-stranded segments appear to be accessible to AO binding. These interactions did not practically change when ionic strength (0.01-0.3), Mg2+ and Zn2+ concentrations (10(-3) M) or pH (4.7-7.4) varied. The data permit to suppose that phage MS2 RNA has a very stable tertiary structure which makes part of double-stranded segments unaccessible to inter calating dyes. Taking these and other facts into consideration we suppose that double-stranded segments play an important role in stabilization of the RNA tertiary structure. One of the most possible structure is a compact "rod-like" intramolecular aggregate of double-stranded hairpin-like segments of RNA with parallel orientation.

Coliphages↗
PubMedDate not supplied

[Nuclear ribonucleoproteins containing messenger RNA. 12. Fluorescence studies of the secondary structure of pre-mRNA in nuclear RNP-particles].

Secondary structure of pre-mRNA in nuclear ribonucleoprotein particles (30S-particles) was examined using fluorescent dyes: acridine orange, acriflavine and ethidium bromide. Comparison of ethidium bromide and acriflavine adsorption isotherms for RNP-particles and free RNA and a study of acridine orange dimerization on binding to RNP revealed that 70% of pre-mRNA in 30S-particles is accessible for the dye binding. Dye molecules were adsorbed on double-stranded sequences (11--12% of the total amount of RNA in 30S-particles) and on the single-stranded parts of RNA (58--59% of 30S-particles), the rest part of RNA was unaccessible for the dye binding. A method involving measurements of acriflavine fluorescence quantum yields was used for the determination of nucleotide composition of double-stranded parts of RNA in the 30S-particles. AU-nucleotide content thus obtained was approximately 50%, as was established also for free pre-mRNA. Na+ ions weaken the interaction between the protein and pre-mRNA in 30S particles and increase mobility of double-stranded parts of this nucleic acid.

Animals↗
PubMedDate not supplied

[Conformational transitions in tRNA fMet from E. coli induced by monovalent and divalent ions].

Conformational transitions in tRNAfMet E. coli the initiator tRNA in bacterial systems and in some other individual tRNAs have been studied as a function of monovalent and divalent ion concentrations. By measuring the extent of energy transfer between dye molecules adsorbed on tRNAs and by study of adsorption isotherms of dyes on tRNAs conclusion has been drawn about the similarity of conformational state of all tRNAs studied at low ionic strength (mu 0.01). A conformational change in tRNA, produced by an addition of Mg2+ and Na+ ions results in more than two fold decrease of the strong binding sites for dyes. A marked difference in the adsorption properties of tRNAfMet in comparison with other investigated tRNAs were found. The tRNAfMet was the only tRNA species that did not form the strong type of complexes with dyes at high ionic strength

Coloring Agents↗