Interaction specificity of benzimidazol group compounds with AT-containing polynucleotides.

The interaction between polynucleotides: poly(dA)-poly(dT), poly(dA-dT), poly(am2dA-dT), and the AT-specific compounds of benzimidazol group has been studied. It is been shown that these compounds bind to poly(dA)-poly(dT) and poly(dA-dT) at low and high salt concentration in solution. Poly(am2dA-dT) interacts with AT-specific compounds only at low salt, where this polynucleotide is in a B-form, but not at high salt, when the polynucleotide converts to another conformation. Thus, the interaction specificity of the groove-binding ligands is influenced not only by the minor groove substituents, but the peculiarities of the secondary structure of polynucleotides.

["External chromophores" and intensive bands in circular dichroism spectra of liquid-crystalline microphases of nucleic acids]. / "Vneshnie khromofory" i intensivnye polosy v spektrakh krugovogo dikhroizma zhidkokristallicheskikh mikrofaz nukleinovykh kislot.

From the analysis of CD-spectra of liquid crystalline microphases formed from DNA molecules in complexes with "external chromophores" requirements are formulated for the compounds to be used in revealing peculiarities of spatial structure of nucleic acids liquid crystalline microphases. These requirements satisfied it is possible to record the CD-spectra having intensive bands in the regions of chromophores absorption. These bands prove the helical pattern of the spatial structure of nucleic acid liquid crystalline microphase.

[Optical properties of DNA complexes with antitumor compounds of bivalent platinum]. / Opticheskie svoistva kompleksov DNK s protivoopukholevymi soedineniiami dvukhvalentnoi platiny.

The optical properties of the DNA complexes with the compounds of bivalent platinum were studied. The compounds differed by the nature of the anionic and neutral ligands and their spatial arrangement about the platinum atom. It was shown that the same as cis-[Pt (NH3)2Cl2] the platinum compounds with the biological activity, i.e. [Pt (en) Cl2], cis-[PtNH3 (Bz) Cl2] and cis-[Pt (NH3)2NO2Cl] induced at low values of r (a ratio of the number of the platinum moles added to the number of the DNA nucleotide moles in the solution) an increase in the amplitude of the positive band in the spectrum of the circular dichroism (CD) of the linear DNA and a marked decrease in the amplitude of the negative band in the spectrum of the CD of the liquid crystalline microphase of DNA formed in the presence of polyethyleneglycol. By the character of the action on the CD spectrum of the linear and condensed DNA [Pt (tetrameen)Cl2] which had no selective antimitotic effect might be referred to the above platinum compounds. Trans-[Pt (NH3)2NO2Cl], [PtNH3PyCl2], cis-[Pt (NH3)2(NO2)2] and [Pt (NH3)3Cl]Cl having no biological activity either induced only a decrease in the amplitude of the positive band in the CD spectrum of the linear DNA or had no effect on the CD spectrum. The effect of these compounds on the CD spectrum of the liquid crystalline microphase of DNA was slightly pronounced or not observed.

[Effect of biologically active compounds of divalent platinum on the properties of the liquid crystal "microphase" of DNA]. / Vliianie nekotorykh biologicheski aktivnykh soedinenii dvukhvalentnoi platiny na svoistva zhidkokristallicheskoi "mikrofazy" DNK.

The optical properties of the "microphases" modeling the state of the DNA molecule in the cell and formed of both the low molecular DNA and the DNA complexes with cis- and trans-isomers of dichlorodiamine platininum (II) were studied. It was shown that the intensive band characteristic of the circular dichroism spectrum of the initial DNA "microphase" was decreasing with binding of DNA to cis-Pt (II) or trans-Pt (II). The effect of cis-Pt (II) on the "microphase" optical properties was more significant than that of trans-Pt (II). The effect correlated with the biological activity of the cis- and trans-compounds of platinum. Possible causes of the decrease in the optical activity of the DNA "microphase" are discussed.

A compact from of methylated DNA is solutions containing poly (ethylene glycol).

Some peculiarities of compactization of double-stranded DNA molecules containing methylated nitrogen bases have been studied in water-salt solutions of PEG. It is shown that the methylation of N7-atoms of guanyl residues in original DNA molecules does not prevent the formation of DNA compact particles, but results in a decrease of the amplitude of the negative band in the CD spectrum of compact particles. The influence of N7-guanine methylation on the shape of the CD spectrum being the greater, the lower is the concentration of PEG. The dependence of the negative band amplitude in the CD spectrum on the content of methylated guanyl residues is practically the same for low-molecular weight DNA's from different sources. The observed decrease in the negative band amplitude is interpreted as a result of alterration of guanyl residue orientation relative to the helix axis which leads to diminished optical activity of the "microcrystalline" domains of compact particles. The evidence obtained suggests that changes in the secondary structure of DNA lead to considerable difference between CD spectra of compact particles of methlated DNA and psi-form of DNA. (The changes in the CD spectrum of the DNA compact particles occur also as a result of methylation of C5-atoms of cytosine residues). It is suggested that the negative band in the CD spectrum can be used a criterion for detection of negligible alterations in the DNA secondary structure.

[Compact form of DNA in solution. X. Peculiarities of circular dichroism spectra of DNA compact particles forming polyethylene glycol-containing water-salt solutions]. / Kompaktnaia forma DNK v rastvore. X. Osobennosti spektrov krugovogo dikhroizma kompaktnykh chastits DNK sformirovannykh v vodno-solevykh rastvorakh, Soderzhashchikh polietilenglikol'.

The experimental data indicating that the amplitude of the negative band in CD spectra of DNA compact particles forming in PEG-containing water-salt solutions intensifies with the decrease of DNA molecular weight are presented. This effect is not explained by the light scattering on the compact particles. The presence of the negative band in CD spectrum of DNA compact particles is interpreted as result of formation of dichrographic-active "microcrystalline" region ("domains") (if DNA compact particles are formed from double-stranded molecules with unaltered secondary structure); it is also supposed that the number of these regions in the particle and their dichrographic activity doesn't depend on the particles size. This interpretation is in agreement with experimental data on the increase of the number of compact particles with the decrease of DNA molecular weight. Proportionality coefficient in the linear dependence of the amplitude of negative band on the size of DNA compact particles in solution depends apparently on dichrographic activity of "microcrystalline" regions, and this activity is connected with structural peculiarities of initial DNA molecules.

[DNA compact form. 8. X-ray diffraction study of DNA compact particles, formed in solutions containing polyethylene glycol]. / Kompakthaia forma DNK v rastvore. VIII. Rentgenografiueskoe issledovanie kompaktnykh chastits DNK, obrazuiushchikhsia v vodno-solevyx rastvorax, soderzhashchikh poliztilenglikol'.

A comparative X-ray study of DNA compact particles, formed in PEG-containing solution from native DNA and from DNA molecules with altered secondary structure was carried out. Low-angle reflections, present in X-ray patterns of compact particles (in powder form) from native DNA, correspond to spacings of 84, 42 and 35 A, while wide-angle reflections correspond to spacings of 12.8; 8.4, 6.0, 4.5, 3.4 A. Low-angle reflections at 84 and 42 A are present also in X-ray patterns of compact particles, formed from DNA molecules with altered secondary structures. These two reflections are believed to be the results of an ordering of DNA molecules within the compact particles. The main features of this ordering appear in the first approximation to be independent on DNA secondary structure. The CD spectra of all types of compact particles, mentioned above, were also studied. It has been shown that the intense negative band (lambda approximately 270 nm) in a CD spectrum appeared only in the case of compact particles, formed from native DNA molecules. The nature of the revealed correlation between the 35 A reflection and the CD negative band is discussed. Data presented in the paper allow one to suppose that the 35 A reflection in X-ray patterns and the CD negative band result from specific interactions between double-stranded DNA fragments spatially brought together in compact particles. Such type of interaction is believed to be characteristic only of native DNA molecules.

A comparative X-ray diffraction and circular dichroism study of DNA compact particles formed in water-salt solutions, containing poly(ethylene glycol).

Comparative CD and X-ray diffraction studies of DNA compact particules which were obtained in PEG-containing water-salt solutions, have been carried out. Compact particles, formed from native DNA, produce a psi CD spectrum (characterized by a negative band at lambda-270 nm) and a small-angle X-ray diffraction pattern, which shows two reflections: I at 34-40 A and II at 80-90 A (together with its second-order reflection). Compact particules, formed from DNA molecules with partially disordered secondary structure, do not produce the psi CD spectrum and the reflection I, while the reflection II remains unchanged. It is suggested that the spacing of 34-40 A is associated with a side-by-side packing of DNA fragments in "microcrystallization' regions in compact particules and that such "microcrystallization' accounts for the generation of the psi CD spectrum.

[DNA compact form in solution. VII. Transforming activity of precompact forms of DNA]. / Kompaktnaia forma DNK v rastvore. VII. Transformiruiushchaia sposobnost' predkompaktnoi i kompaktnoi form DNK.

Data on transforming activity of DNA in water-salt (0.3 M NaCl) solutions containing polyethylene glycol (PEG) are presented. Bacillus subtilis deficient mutant lys 42 and prototrophic strain SHgw were used as recipient and donor, respectively, for transformation experiments. It has been shown that when PEG concentrations were increased the relative experiments. It has been shown that when PEG concentrations were increased the relative transforming activity (RTA) at first (at PEG concentrations approximately 30-40 mg/ml) increased to the value of 200-250%, then began to decrease. At PEG concentrations approximately 100-125 mg/ml, when DNA molecules form compact particles, the RTA does not exceed 10%. The observed changes in RTA are interpreted as a result of conformational changes of double-stranded DNA molecules. The increase in the RTA at low PEG concentrations may be explained as an increase in transforming activity of the precompact form of DNA, while the decrease in RTA at PEG concentrations exceeding 60-70 mg/ml was believed to be connected with the fact that compact particles of DNA could not penetrate through the walls of bacterial cells.

[DNA compact form. VI. Changes of DNA secondary structure under conditions preceding its compaction in a solution]. / Kompaktnaia forma DNK v rastvore. VI. Izmenenie struktury dvukhtsepochechnoi DNK v usloviiakh, predshestvuiushchikh ee kompaktizatsii.

Optical and thermochemical properties of E. coli DNA molecules are compared in solutions containing poly(ethyleneglycol) (PEG) in concentrations at which compactization is not yet observed. It is shown that under conditions preceding DNA compactization (CPEG less than 60 mg/ml) changes in CD spectra occur which suggest that the secondary structure of some DNA fragments is altered. These changes of the secondary structure result from dehydration of DNA molecules in PEG-containing solutions. Electron micrographs of DNA molecules obtained under conditions preceding compactization suggest that under these conditions linear DNA molecules may form "four-stranded" fragments as well as double-stranded "loops".

[The compact form of DNA in solution. V. The heat effect preceding compactization of double-chained DNA in PEG containing water-salt solutions]. / Kompaktnaia forma DNK v rastvore. V. Teplovoi éffekt, predshestvuiushchii kompaktizatsii dvukhtsepochechnoi DNK v soderzhashchikh PEG vodno-solevykh rastvorakh

DNA-dependent heat effects accompanying mixing of water-salt (0.3 M NaCl) solutions of PEG and DNA within the range of PEG 10-50 mg/ml at 25 degrees C were determined by the method of difference microcalorimetry. It was found that, unlike optical and hydrodynamical methods, microcalorimetry makes it possible to detect some changes of the DNA-PEG system preceding formation of compact particles of DNA. In the studied range of DNA concentrations (up to 50 X 10(-3) MG/ML) the specific DNA-dependent heat effect is essentially independent of DNA concentration. It is negative and its absolute value increases from 0 to 5 cal/g of DNA in the PEG concentration range from 0 to 35-40 mg/ml after that the rate of its increase raises greatly and at PEG concentration of 50 mg/ml it is equal to 35 cal/g of DNA. It is suggested that the studied DNA dependent heat effects at low concentrations of PEG (less than 40 mg/ml) are caused by dehydration of DNA preceding its compactization.

[The compact form of DNA in solution. IV. The effect of secondary structure defectiveness on the arrangement of double-chained DNA molecules into compact particles]. / Kompaktnaia forma DNK v rastvore. IV. Vliianie defektnosti vtorichnoi struktury na ukladku dvukhtsepochechnykh molekul DNK v kompaktnykh chastitsakh

Influence of pH on absorbance and CD-spectra of DNA in PEG-containing water-salt solutions has been studied. The changes in the spectra appeared due to disturbance of the DNA secondary structure upon acidification of the medium proir to or after DNA compactization. If acidification preceeds DNA compactization an intense negative band in the CD spectrum inherent to the compact particles is observed at pH values 7-4. The intensity of the band decreases with an increase of the acidity. The size of the compact particles as evaluated from the dependence of the apparent optical density on the wavelength value remains unchanged (about 1200 A). If the solution is strongly acidified (pH 4.0-2.8) and a considerable disturbance in the DNA secondary structure takes place a negative band in the CD spectrum completely disappears. If one acidifies a solution containing preformed DNA compact particles a decrease of the intensity of the CD negative band starts at lower pH values (less than 2.8). This process is accompanied by an increase of the size of the particles. Acidic "denaturation" of DNA within the compact particles (pH approximately 2.5) is followed by a dissappearance of the CD negative band and a considerable increase of the particle size. The data obtained indicate that the specific arrangement of DNA strands manifested in a CD negative band depends on the defects in the DNA secondary structure.