Biomedical subjects

B I Sukhorukov

Publications and source records attributed to B I Sukhorukov.

At least 19 recordsLinked to original sources

PubMed2002

Structural and thermodynamic features of complexes formed by DNA and synthetic polynucleotides with dodecylamine and dodecyltrimethylammonium bromide.

Complex formation of native and denatured DNA, single-stranded polyribonucleotides poly(A) and poly(U), as well as double-stranded poly(A).poly(U) with dodecylamine (DDA) and dodecyltrimethylammonium bromide (DTAB) has been studied by UV-, CD-, IR-spectroscopy and fluorescence analysis of hydrophobic probe pyrene. DDA and DTAB were shown to bind cooperatively with DNA and polyribonucleotides, resulting in the formation of complexes containing hydrophobic micelle-like clusters. Critical aggregation concentration (CAC) of DDA and DTAB shifts sharply to lower values (30-50 times) in the presence of DNA and polynucleotides as compared to critical micelle concentration (CMC) of free DDA and DTAB in solution. The analysis of binding isotherms within the frame of the model of cooperative binding of low-molecular ligands to linear polymers allowed us to determine the thermodynamic parameters of complex formation and estimate the contribution of electrostatic interaction of positively charged heads of amphiphiles with negatively charged phosphate groups of DNA and polyribonucleotides, and hydrophobic interaction of aliphatic chains to complex stability. Electrostatic interaction was shown to make the main contribution to the stability of DNA complexes with DDA, while preferential contribution of hydrophobic interactions is characteristic of DTAB complexes with DNA. The opposite effect of DDA and DTAB on the thermal stability of DNA double helix was demonstrated from UV-melting of DNA-while DTAB stabilizes the DNA helix, DDA, to the contrary, destabilizes it. The destabilizing effect of DDA seems to originate from the displacement of intramolecular hydrogen bonds in complementary Watson-Crick A.T and G.C base pairs with intermolecular H-bonds between unsubstituted DDA amino groups and proton-accepting sites of nucleic bases.

Amines↗

PubMed2000

Inhibitory effect of polyelectrolytes on oligomeric enzymes.

The effect of polyelectrolytes on the stability and catalytic characteristics of oligomeric enzymes--pig muscle lactate dehydrogenase (LDH) and bovine liver glutamate dehydrogenase (GDH)--was studied by fluorescent spectroscopic and steady state kinetic methods. It was shown that the binding of negatively charged polyelectrolytes--polystyrene sulfonate, polymethacrylate, and polyphosphate--destroys the tertiary and partially the secondary structure of LDH and GDH, resulting in their complete inactivation at pH < 7. The concentrations of polyelectrolytes needed for inhibition of the enzymes were in this case by two or more orders of magnitude lower than the corresponding concentrations for monomers--toluene sulfonate, methacrylate, and phosphate. The affinity of the substrate (pyruvate) for LDH did not vary in the presence of the polyelectrolytes, but the inhibition was removed by excess of substrate. We propose that the oligomeric state of enzymes causes polyelectrolytes to act on them in a special manner, this special effect differing significantly from the effect of polyelectrolytes on monomeric enzymes. The effect consists in that polyelectrolytes cleave the oligomeric structure of the enzymes, this "cleaving" effect being higher the greater the hydrophobicity of the polyelectrolyte chain.

Animals↗

PubMed1996

Multilayer films containing immobilized nucleic acids. Their structure and possibilities in biosensor applications.

Langmuir-Blodgett (LB) and film technologies based on electrostatic attraction self-assembly (SA) are shown to be useful for immobilization of nucleic acids (DNA, polynucleotides) onto solid supports in sensor devices. The nucleic acids were immobilized in complexes with cationic surfactants (for LB) and polycations (for SA). Infrared spectral studies showed that DNA unfolds in multilayer LB films with octadecylamine and conserves its double helical structure in the LB films with dioctadecyldimethylammonium and in the SA films with polyallylamine, polyethylenimine and poly-L-lysine. Atomic groups and the types of interactions determining the complex formation of these films have been identified. The hydration of LB and SA films was studied to find out binding sites of water molecules and to evaluate the flexibility of nucleic acid compounds in the multilayer films. The possibilities of biosensor applications of these LB and SA films were monitored on binding of specific reagents for DNA by DNA-containing films and mononucleotides by a complementary single-stranded polynucleotide immobilized on a positively charged solid support.

Biosensing Techniques↗

PubMed1990

Infrared and X-ray diffraction study of the effect of protonation of DNA on its B-to-A transition.

The influence of H+ on the secondary structure of DNA and on its B-to-A transition has been studied by employing X-ray diffraction and infrared spectroscopy. Helical parameters for DNA molecules with different degrees of protonation were determined. It was shown that H+ binding stabilizes the B-form of DNA in fibers over a wide range of water and inorganic salt content. Only 0.03 H+ bound per nucleotide is sufficient to prevent the B-to-A transition caused by decreasing relative humidity in DNA fibers containing 4% NaCl. The effectiveness of B-form stabilization by H+ is explained by changes in DNA-solvent molecule interactions, especially in the major groove of double helices.

Animals↗

PubMed1986

Probing of mRNA binding sites involved in interactions with rat liver ribosomes using poly(U) spin labeled at the ribose moiety.

The interaction of rat liver ribosomes with poly(U), spin labeled (SL) at the 2'OH groups of ribose residues by N-(2,2,5,5-tetramethyl-3-carbonylpyrroline-1-oxyl)-imidazole, has been studied by electron spin resonance (ESR) spectroscopy. The ESR spectra demonstrate that SL-poly(U) with a modification of 1 spin label per 20 ribose residues binds to 80S ribosomes as well as to 40S subunits in a 1:1 stoichiometry at 12 mM MgCl2. The same result is found with highly modified poly(U) bearing 1 SL per 4 ribose residues. Addition of excessive amounts of unmodified poly(U) displaces bound SL-poly(U) from the ribosome which points to a competition for the same binding site at the ribosome. The biological activity of SL-poly(U) was tested with regard to trigger 80S ribosomes for binding of Phe-tRNAPhe and for poly(Phe) synthesis. SL-poly(U) bearing 1 SL group per 20 ribose residues directs the binding of only 50% of the amount of Phe-tRNAPhe bound to ribosomes in the presence of unmodified poly(U). When SL-poly(U) bearing 1 SL group per 4 ribose residues is used, this value drops to 25%. Poly(Phe) synthesis is even more impaired: In the presence of poly(U) bearing 1 SL-group per 20 ribose residues only about 30% of the amount of poly(Phe) coded by unmodified poly(U) are synthesized and in the presence of SL-poly(U) bearing 1 SL group per 4 ribose residues poly(Phe) synthesis is completely abolished. The results suggest that modification of the ribose moiety has only a relatively small influence on the binding of mRNA to ribosomes but causes substantial impairment of the mRNA function, whereas, as shown earlier (Ebert et al., Acta Biol. Med. Germ. 41, 431, 1982), modification of the base moiety of poly(U) (in a proportion of 1 SL per 30 bases) does not influence coding efficiency for poly(Phe) synthesis.

Animals↗

PubMed1986

[Irreversible changes in phage DNA after its protonation in solution and inside the virion detected by the transfection method].

The dependence of irreversible structural changes in phage lambda DNA on the degree of its protonation in a solution and inside the virion has been found by measuring the transfection activity of bacteriophage. The different effect of ionic strength on pH-dependence of the irreversible changes in the structure of DNA upon its protonation in a solution or in situ has been registered and explained. The insignificant shift of pH from neutral region value in 0.1 M NaCl has resulted in a damaging effect of H+ ions on compact DNA in situ as compared to the DNA in a solution. The effect of H+ ions on compact DNA in situ is mainly based on the formation of noncovalent intermolecular DNA-protein and DNA-DNA linkages.

Bacteriophage lambda↗

PubMed1982

Fluorescence quenching and spin label electron spin resonance studies of stacking self-association in aqueous solutions of 2-aminopurine riboside and its 5'-mono- and -diphosphate.

The autoassociation of 2-aminopurine riboside (rn2Pur) and its 5'-mono- (P-rn2Pur) and 5'-diphosphate (PP-rn2Pur) in neutral aqueous solutions was investigated using fluorescence quenching and ESR spin-label methods within the range 276-358 K. Respective equilibrium constants and thermodynamic functions were derived therefrom assuming two models of infinite autoassociation: (i) an isodesmic one (K2 = K3 = ... Kp), and (ii) one in which K2 no equal to K2 = K4 ... Kp. Comparative analysis of these data and that of the parent 2-aminopurine, obtained previously, allowed us to formulate the following conclusions: (1) the mechanism of autoassociation of rn2Pur varies with temperature in such a way that a T = 318 K the isodesmic model is fulfilled (K2 = Kp); at high temperatures Kp/K2 greater than 1, i.e. the process is cooperative, while at lower temperatures it becomes anticooperative (Kp/K2 greater less than 1); (2) at 298 K the tendency to autoassociation decreases in the order; rn2Pur greater than P-rn2Pur greater than PP-rn2Pur; (3) rn2Pur forms highly packed complexes with the bases stacked and the ribofuranose residues interacting via hydrogen bonds or water bridges; (4) autoassociation of P-rn2Pur and PP-rn2Pur is mainly governed by stacking of the bases, while the ribose phosphate residues attain a trans configuration corresponding to the lowest electrostatic repulsion between charged phosphate groups; even at high ionic strength (I = 0.8), a positive electrostatic contribution to the free enthalpy of autoassociation is observed; (5) the two methods employed gave similar results for P-rn2Pur, but somewhat different ones for rn2Pur because the presence of the spin label (nitroxide stable radical) at the 2'(3')-OH group of the ribose residues prevents its interaction via hydrogen bonding with an unlabeled one of an adjacent nucleoside.

Electron Spin Resonance Spectroscopy↗

PubMed1981

Calorimetric study of the complexes between polyuridylic acid and adenylic nucleotides.

Soluble complexes of poly (U) and adenylic nucleotides in NaCl solutions were studied by scanning microcalorimetry. The melting enthalpies, delta Hm, of poly (U) complexes with adenosine, 2',3' -cAMP, 2'(3')-AMP, 5-AMP, ADP, ATP in 1 M NaCl are 50.5; 45.0; 42.9; 28.6; 26.1 and 25.6 kJ/mole triplets, respectively. Delta Hm is independent of the complex melting temperature, Tm. The calorimetric enthalpies are considerably lower than the apparent delta Hv.H. obtained from Tm dependence on free monomer concentration. The enthalpy of complex formation in 1 M NaCl depends neither ob the number nor on the degree of ionization of the phosphate groups but is essentially determined by their 5' - or 2'(3')-position. In contrast to 2'(3')- AMP. 2 poly (U), delta Hm of 5'AMP. 2 poly (U) increases considerably at lowering Na+ concentration. The enthalpy of poly (U) double helix melting in 1 M NaCl is 8.8 kJ/mole pairs which is 2.5 times lower than that in MgCl2 solutions.

Adenine Nucleotides↗

PubMed1980

Spin-labeled polyribonucleotides.

Poly (U), poly (C) and poly (A) were spin labeled with N-(2,2,5,5-tetramethyl-3-carbonylpyrroline-1-oxyl)-imidazole. This spin label interacts selectively with 2' OH ribose groups of polynucleotides and does not modify the nucleic acid bases. The extent of spin labeling is not dependent upon the nature of the base and is entirely determined by rigidity of the secondary structure of the polynucleotide. The extent of modification for poly (U), poly (C) and poly (A) was 4.2, 1.7 and 1.5 per cent, respectively, the secondary structure of the polynucleotides being practically unchanged. Some physico-chemical properties of the spin-labeled polynucleotides were investigated by ESR spectroscopy. Rotational correlation times of the spin label and activation energy of its motion were calculated.

Cyclic N-Oxides↗

PubMed1980

IR study of base stacking interactions.

For D2O solutions of 1,3-dimethyluracil, cytidine, caffeine, inosine and 2'-deoxyadenosine the concentration dependence of IR spectra (1800-1400 cm-1) have been found which reflects stacking association of these compounds. A method is proposed to use this data to obtain thermodynamic parameters of association and the molecular spectra in the monomer and associated forms. The homoassociation constant for 1,3-dimethyluracil was estimated as k=0.65. Stacking is shown to change radically the spectra, inducing a high-frequency shift of carbonyl vibrations and a decrease in the intensity of skeletal stretching vibration bands. This allows one to distinguish between the stacking interactions and hydrogen bonding. A conclusion is made about the considerable contribution of stacking interactions into the change of IR spectra of DNA and other polynucleotides following conformational transitions.

Caffeine↗

PubMed1977

[Interaction of a membrane preparation of Na+, K+-ATPase with a spin-labeled analog of ATP].

Interaction of membrane Na+, K+-ATPase preparation from brain gray matter with spin-labelled ATP analogue, in which free iminoxyl radical is joined as a result of 2'(3')-OH ribose groups acylation, is studied. The rotatory mobility of spin-labelled ATP analogue in Na+,K+-ATPase preparation is found to change in non-linear manner during temperature variation (the break-point on the curve being at 20-23degrees C). It correlates with temperature dependence of Na+,K+-ATPase and temperature dependence of lipid viscosity in the membranes, determined by means of hydrophobic spin probes. Substitution of Mg2+ ions with paramagnetic Mn2+ ions resulted in an intense magnetic dipole-dipole interaction between a spin label and Mn2+ ion, which indicated the formation of triple complex enzyme--spin-labelled ATP--Mn2+.

Adenosine Triphosphatases↗

PubMed1976

[Effect of salts, stabilizing and destabilizing the structure of water, on the stacking association of adenosine].

A spectrophotometric study, based on the concentration relationship of electron absorption spectra, of the effects of salts which stabilize and destabilize the water structure on the constant (K) of adenosine: stacking association has been carried out. A significant decrease of K was observed in NaClO4 which embodied strong destabilizing effect. Opposite effect was observed on other salts studied. According to K value the stacking-interaction of adenosine in the range of salt concentration 0 divided by 3M for different anions and cations are arranged in rows: SO4--greater than Cl- greater than ClO4-; Na+ greater than Li+greater than K+. The data obtained suggest that the effect of salts on thermostability of various oligo- and polynucleotides and on B leads to C DNA transition may be essentially concerned with the effect of both cations and anions of salts on the stacking-interaction of bases.

Adenosine↗

PubMed1975