The effect of ionic strength and temperature on the conformation of ribosomal RNA from E. coli.
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Escherichia coli↗
Biomedical subjects
E V Frisman
Publications and source records attributed to E V Frisman.
[DNA interaction with low molecular ligands of different structure. II. Complexes of DNA with actinomine and its analogs].
DNA-complexes with actinomine and its analogues containing omega-dialkylaminoalkyl groups at 1,9 positions of the phenoxazone moiety were studied by technique of spectrophotometry, viscometry and flow birefringence. In the process of spectrophotometry titration two groups of spectra corresponding to different DNA--ligand ratio in a complex were observed. According to the experimental data the investigated compounds are bounded to DNA by means of intercalation and external binding. There within a region of low degrees of binding the intercalation type of the ligand--DNA interaction prevails. In virtue of the spectrophotometry data the intercalation binding share was calculated. The intrinsic viscosity of a complex increases in the case of ligand intercalation and does not change as it joins to the DNA double-helix from outside. Optical anisotropy of DNA molecule increases linearly irrespective of the way of ligand binding. Data on the flow birefringence permits to conclude that under external binding the angle between the normal to the ligand chromophore plane and the axis of DNA double-helix is about zero. During ligand intercalation the equilibrium rigidity of DNA molecules increases.
Chemical Phenomena↗
[DNA interaction with low molecular weight ligands of different structure. III. DNA complexes with distactins].
The DNA complexes with distactins have been investigated by means of spectrophotometry, viscosimetry and flow birefringence methods. The distactins are actinocin's derivatives containing in the 1,9 positions of the phenoxazone moiety oligopyrrolcarboxamide groups (like those of distamycin A), which have from one to three fragments of 1-methyl-4-amino-2-pyrrolic acid. The mode of DNA-distactins binding in water solution depends on the quantity of the methylpyrrole rings in the oligopeptide groups. The ligand with oligopeptide groups containing three methylpyrrole rings joins the DNA double helix only from outside by means of oligopeptide groups. The compounds with one and two methylpyrrole rings form two kinds of complexes with DNA: external binding and intercalation. In the latter case both chromophore and methylpyrrole fragments, interact with DNA.
Animals↗
[Comparative study of DNA interactions with daunomycin and proflavine in a solution].
The comparative investigations of DNA complexes with daunomycin and proflavine were proceeded by the technique of spectrophotometry, viscometry and flow birefringence for two ionic strengths of environment (mu). According to the spectrophotometry data there is an unique type of ligand binding with DNA for mu = 0.1. The intrinsic viscosity and optical anisotropy of DNA-daunomycin complex increase nonlinearly together with its equilibrium rigidity as the amount of the binding ligand (r) rises, contrary to the behaviour of the same characteristics of DNA-proflavine complexes. The discussion of the experimental data within a scope of different models of binding reveals the best agreement with the intercalation model. Evaluation of the angels between the orientation planes of chromophore and aminoglucose residue of a daunomycin molecule and the axis of DNA double-helix was performed. Apart from intercalation there is a process of external binding of daunomycin with DNA in the low ionic strength (mu = 0.001) solutions which arises mainly at higher values of r. This type of binding weakens the long-range electrostatic interactions (and also to a certain extent the short-range ones) in DNA chain that determine the behaviour of the parameters under study.
Acridines↗
[Interactinos of DNA with low molecular weight ligands of various structures. I. Complexes of DNA with actinomycin and its simple analogs].
The DNA complexes with actinomycin D and its simple analogues have been investigated by means of spectrophotometry, viscometry and flow birefringence methods. The number of binding sites per base pair of ligand on DNA depends on the nature of substitute in 1.9 position of the phenoxasone chromophore. It has been shown that phenoxasone derivatives without aminogroup in 2 position complex with DNA as in the case of simple actinomycin analogues. The intrinsic viscosity and optical anisotropy of DNA-analogues complexes increase linerly with increasing quantity of bound ligand. This testifies that the binding of the compounds under investigation to DNA molecule is of intercalation type. The character of variation of hydrodynamical and optical parameters of DNA molecule by its binding with actinomycin differs qualitatively from that observed by the binding with analogues. The experimental data obtained for DNA-actinomycin complexes can be interpreted only by suggesting a specific secondary structure alteration of the DNA molecule. It has been shown that the simple actinomycin analogues can not be used as an appropriate model for investigation of DNA-actinomycin complexes structure.
Animals↗
[Calculation of the intrinsic viscosity of synthetic and biological polyelectrolytes of various rigidity].
On the basis of the excluded-volume effect theory for nonionic polymer molecules developed by Alexandrowicz semi-empirical formulas for calculation of the intrinsic viscosity [eta] of polyelectrolytes of various rigidity are proposed. The expression for the second virial coefficient of gas consisting of cylindrical particles is used for the determination of explicit form of the effective excluded volume of the segment upsilon0. In addition the alteration of Flory's parameter phi (epsilon) by the expansion of a macromolecule, and the alteration of thermodynamic rigidity A of the polyelectrolyte molecule in the range of low ionic strengths mu have been taken into account. All that leads to good agreement between calculated and experimental values of [eta] of polyelectrolytes under consideration, i. e. native and denatured DNA and poly (acrylic acid), in a wide range of mu. The calculated dependence A = A (mu) providing the best agreement between the theoretical and experimental values of [eta], also describes reasonably the experimental dependence A = A (mu) obtained from the macromolecule's optical anisotropy measurements for native DNA or from unperturbed dimensions of the macromolecule, determined on the basis of the Stockmayer and Fixman equation for denatured DNA.
Biopolymers↗
[Influence of ionic strength on the thermodynamic rigidity of the native DNA molecule in aqueous and aqueous-organic solvents].
The analysis of experimental and theoretical data for the dependence of the thermodynamic rigidity of the native DNA molecule on the ionic strength of solution has been fulfilled. It has been shown that in aqueous-salt solutions of DNA the statistical segment length (A) of the DNA molecule remains constant over the range of intermediate ionic strengths (mu > 0.002) and considerably increases over the range of small mu < 0.002. On the basis of viscosimetry and flowbirefringence measurements of aqueous-organic solutions of native DNA it has been hypothesized that the macromolecule's thermodynamic rigidity does not depend on the dielectric properties of the medium. In this connection it has been concluded that nonshielded Coulomb interactions between the nearest phosphate groups exert a stronger influence on the thermodynamic rigidity of the macromolecule as compared with Debye--Hückel interactions. The consideration of the hydrodynamical and optical data for aqueous organic DNA solutions of difinite ionic strength shows that the value of [n]/[eta] for DNA and consequently the optical anisotropy of the macromolecule remains constant irrespective of the presence of nonelectrolyte. On this basis it has been concluded that no appreciable alteration of the microform anisotropy occurs in all the systems under consideration.
DNA↗
[Effect of solvent structure on amide reaction with native DNA molecules. I. Aqueous mixtures of N,N-dimethylformamide and urea].
The influence of N,N-dimethylformamid (DMF) and urea (U) on the conformation of the native DNA molecule has been studied by methods of flow birefringence and viscometry. The investigations have been performed over a wide range of amides and supporting electrolyte concentrations. An essentially different influence of small additions of DMF and U on the macromolecule's dimensions was observed. At urea concentrations Cu < 0.03 mol% the DNA intrinsic viscosity [eta] decreases monotonously and the larger, the lower is the ionic strength mu of the solution. At DMF concentration CDMF approximately 1.5 mol% a cooperative decrease in [eta] of DNA, which also depends on mu was revealed. In the range of intermediate and large nonelectrolyte concentrations the influence of DMF on hydrodynamical and optical behaviour of the native DNA molecule resembles that of alcohols. The observed changes of [eta] are conditioned by conformational transitions in the DNA molecule. The constancy of macromolecule's optical anisotropy over a nonelectrolyte concentration range under investigation permits to interpret these transitions as occuring at the level of the tertiary structure of the native DNA molecule. The polyelecrolyte volume effects are considered on the basis of Manning's condensation model, and the structure singularities of water-organic solvents are taken into account. It has been shown that the nonelectrolyte influence on the native DNA molecule conformation may be direct (by means of ion-dipole interactions) or indirect (as result of changes in dielectric properties of solution). It is noted that the solvent structure is a very important factor which determines the interactions between low molecular organic compounds and the native DNA molecule.
Chemical Phenomena↗
[Effect of solvent structure on amide reaction with native DNA molecules. II. Aqueous acetamide mixtures].
The influence of acetamide (AA) on the native DNA molecule conformation has been studied by methods of flow birefringence and viscometry. On one hand, it was shown that hydrodynamical and optical behaviour of the macromolecule at extremely low additions of AA is qualitatively the same as in the presence of nonelectrolytes which stabilize the water structure. On the other hand, the influence of intermediate and large AA concentrations on the native DNA molecule conformation is qualitatively the same as of corresponding urea concentrations, which is known to be a structure-breaker. The influence of AA on the thermostability of the native DNA molecule as well as on the stacking-association constant of adenosine has been studied by a spectrophotometric method. The obtained data confirm the hypothesis of the importance of ion-dipole interactions between nonelectrolytes and the phosphate groups of the DNA molecule.
Acetamides↗
[Study of DNA complexes with a synthetic fragment of histone H4 and polypeptide (Gly-Orn-Gly)n].
Complexes of DNA with synthetic N-terminal peptide of histone H4 (A-13) and with poly(Gly-Orn-Gly) in 0.015 M NaCl solution have been studied by means of viscometry, light scattering and circular dichroism. The process of intramolecular compactization begins to occur at a low content of poly(Gly-Orn-Gly) in complexes, while in the case of A-13 compactization takes place only when the content of A-13 in complexes attains 13--14%. Intermolecular aggregation of both complexes takes place with the increase of peptide content in the complexes. Intramolecular compactization and aggregation do not influence the local conformation of DNA as revealed by CD spectra. The possible mechanism of these peptide-DNA interactions suggested.
Chemical Phenomena↗
[Effect of xanthobin on the degree of damage to DNA molecules by gamma-irradiation].
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Caffeine↗
[Study of the interaction of a DNA molecule with coordination compounds of divalent platinum. I. Effect of cis-diaminodichloroplatinum on molecular parameters of DNA in solution].
DNA interaction with cis-diaminodichloroplatinum (cis-DDP in solutions of different ionic strength was studied by flow birefringence, viscometry, circular dichroism. Though cis-DDP is not an electrolyte, electrostatic interactions are important for binding of cis-DDP with DNA probably for transporting cis-DDP to a macromolecule. The charges aqua-complex is formed by cis-DDP. The complexation being dependent on the platinum/DNA ratio in solution. Along with the increase of platinum concentration, it forms first the complexes with phosphate groups, then with bases without destruction of the DNA secondary structure. The next type of complex formation is accompanied by the local destruction of the hydrogen bonds and stacking interactions. And when the Pt/DNA ratio grows high enough, DNA is denatured. It is suggested that the stability of the complex is provided by nitrogen groups of the bases incorporated in the platinum first coordination sphere. The phosphate DNA groups play the role of counterions in the external coordination sphere.
Circular Dichroism↗
[Interaction of DNA molecules with divalent platinum coordination complexes. II. Effect of the nature and location of ligands in the first platinum coordination sphere].
The interaction of DNA molecule with some coordination compounds of the divalent platinum: cis-DDP, trans-DDP, [(NH3)4Pt]Cl2 and K2PtCl4 was studied. It was shown that the transition of the cis-DDP, trans-DDP, and [PtCl4]2- to aquo-complexes is necessary for their binding with DNA in solution. It was shown that the labile chloride groups are responsible for the formation of the energetically strong binding. The distance between chloride groups in cis-DDP is optimal for incorporation of two groups of DNA bases into the first coordination sphere of platinum. The complexes are also stabilized with phosphate in the external coordination sphere of platinum. The sterical non-conformity between the DNA structure and positions of chloride groups and the orientation of the amino groups in trans-DDP are the main obstructions for the formation of bidentate DNA-trans-DDP complexes. The existence of more than two vacant positions for binding with DNA in [PtCl4]2- does not stabilise the complex. The compound [(NH3)4Pt]Cl2 cannot produce coordination bonds with DNA, because its first coordination sphere is completed with amino groups; it interacts with DNA, forming principally different complexes.
Circular Dichroism↗
[The role of ethanol during gamma-irradiation of water-salt DNA solutions].
In this work we had assumed to clarify the role of the water structure in the process of the radiation damage of DNA. It is known that the aliphatic alcohols stabilize the water structure until the critical concentration. In this connection we have analyzed the changes of the long- and short-distance interactions in the DNA irradiated in the water-ethanol solutions with various concentration of the ethanol and ions of metal. It was shown that as the water structure becomes more stable the conformational damages in the DNA are decreasing and finally at the some concentration of the alcohol in the irradiated solution the damages disappear. By the achieving of the alcohol concentration which lead to the destruction of the water structure the radiation results in the same changes of the considered parameters as in the case of the DNA irradiated in the water-salt solution with ethanol. The analyses of the experimental data allow us to conclude that the radiation destroys the structure of the water and thus helps the positive ions from the solution to come nearer to the DNA, to say, the radiation reduce intramolecular electrostatic interactions. This concept allows us to explain the observed changes of intrinsic viscosity and the difference in the polarizabilities of the DNA in the process of the radiation damage.
Animals↗
[Interaction of DNA molecules with coordination complexes of divalent platinum. III. Platinum compounds with two pyrimidine ligands].
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Cisplatin↗