[Kinetics of cyclization, coupled with ligated oligonucleotide modules, as a means of studying DNA bends]. / Kinetika tsiklizatsii, sopriazhennoi s ligirovaniem oligonukleotidnykh blokov, kak sredstvo issledovaniia izgibov DNK.

A theoretical study of cyclization accompanying multimerization of oligonucleotide blocks is presented. The primary binding due to the cohesive ends of the blocks is subject to subsequent enzyme-catalyzed covalent fixation. Conditions were found for determining the thermodynamic probabilities of circular DNA conformations from the experimentally measurable rates of cyclization. An exact analytical description for the dynamics of multimerization without cyclization and an approximate description for cyclization accompanying multimerization are given.

[The effect of temperature and ionic strength on the electrophoretic motility of synthetic DNA fragments]. / Vliianie temperatury i ionnoi sily na élektroforeticheskuiu podvizhnost' sinteticheskikh fragmentov DNK.

The following DNA fragments were studied: T5A5, U5G5, C5G5, RI (CCGAATTCGG), and RV (CCGATATCGG). The ligated decamers were run on 8% polyacrylamide gel. The PAGE anomaly was measured by the R-factor. Under standard conditions R is maximum for A5G5 and U5A5 (R = 1.9-2.0); R has intermediate values for RI and T5A5 (R200 = 1.05-1.10). T5A5 exhibits unusual non-monotonous temperature dependence of the R-factor, which reaches its maximum at 35 degrees C. Based on this fact we make two conclusions: (i) PAGE anomaly is highly sensitive to the DNA winding angle tau, (ii) tau = 36 degrees for T5A5 under these conditions. For A5G5, RI and RV the temperature dependence of the R-factor is conventional: R monotonously decreases. Conceivably tau less than 36 degrees for these sequences. In the presence of 10 mM of MgCl2 the anomaly increase for all fragments, except for T5A5; e.g. for C5G5R150 R200 = 1.2. This testifies to the moderate curvature of C5G5. The results of the measurements were interpreted on the basis of the wedge AA and junction An/B models. To get a better agreement with the experiment these models should be supplemented with the bends in the YR dimers (TA, CG, CA) directed into the major groove and with the bends in AT directed into the minor groove.

[Localization of melted regions in supercoiled DNA by means of chemical modification]. / Lokalizatsiia rasplavlennykh uchastkov v sverkhspiral'noi DNK pri pomoshchi khimicheskoi modifikatsii.

Diethyl pyrocarbonate was used as a probe in mapping early melting stages in supercoiled DNA. It was shown that in the process of early melting of pAO3 DNA two denatured regions (about 15 b.p.) arouse near the left and right boundaries of the cruciform structure. In course of further melting denatured regions appeared within AT-rich stretches and the cruciform structure itself disappeared.

[Comparative analysis of the structure of double-stranded RNA from killer strains of Saccharomyces cerevisiae]. / Sravnitel'nyi analiz stroeniia dvuspiral'nykh RNK killernykh shtammov Saccharomyces cerevisiae.

Double-stranded RNAs (M and L molecules) of two strains of the killer system Saccharomyces cerevisiae M437 (wild type) and ski-5 (superkiller mutant) were studied by means of electron microscopy and high resolution thermal melting. The M molecules of the ski-5 mutant were by 100 b.p. shorter than those of M437. L molecules were of the same length for both strains. Analysis of the differential melting curves of L molecules showed that L molecules differ significantly in their nucleotide sequences, whereas M molecules were practically identical. It was found that M molecules contained a long AU region: that of M molecules of M 437 was 170-180 b.p. long and contained almost no GC pairs, whereas the AU region of M molecules of the ski-5 mutant was three times shorter and contained GC pairs.

[Melting of short DNA fragments. Relation between the nucleation constant of a spiral region and the ionic strength]. / Plavlenie korotkikh fragmentov DNK. Opredelenie zavisimosti konstanty nukleatsii spiral'nogo uchastka ot ionnoi sily.

Melting of two DNA duplexes of known nucleotide sequences containing 14 and 36 base pairs has been investigated within the range of ionic strength from 0.2 to 0.02 M [Na+]. The values of melting enthalpy of base pair delta H were measured for the duplex of 14 base pairs in the solutions of varying ionic strength. The values of delta H were obtained from slopes of linear plots of reciprocal melting temperature versus logarithm of oligonucleotide chains concentration. In the aforementioned range the decrease of the ionic strength causes a 5% decrease of delta H. By fitting the theoretical profiles to the experimental ones the ionic strength dependence of the nucleation constant beta was measured for DNA fragments of various lengths. With the decrease of the ionic strength the value of beta drops 2 times for the short duplex and 8 times for the long one.

[Electron microscope maps of SA7 DNA melting]. / Elektronno-mikroskopicheskie karty plavleniia DNK SA7.

Electron microscopic denaturation maps corresponding to the first peaks of the differential melting curve of SA7 DNA were constructed by fixation of partly denatured molecules with glyoxal at temperatures within the melting range. These maps were oriented with respect to the functional map of the virus genome. The localization and the size of the most AT-rich SA7 DNA regions were determined.

[Formation of cruciform structures in pAO3 plasmid DNA on increasing superhelical density]. / Obrazovanie krestoobraznykh struktur v DNK plazmidy pAO3 pri uvelichenii sverkhspiral'noi plotnosti.

The dependence of the crusiciform structure formation on superhelical density was studied by means of high resolution gel-electrophoresis. A short pAO3 DNA plasmid (1683 b. p.) which is a quarter of the ColE1 DNA plasmid and contains the main palindrome of ColE1 DNA was used. The excellent resolution of all topoisomers of pAO3 DNA in gel-electrophoresis made it possible to observe a sharp abruption in the pattern of pAO3 DNA topoisomers separation. The two-dimensional gel-electrophoresis data showed that observed abruption is caused by a sharp decrease of writhing in the molecules with superhelical density--sigma approximately equal to 0,05. An analysis of S1-nuclease digestion products of DNA with different superhelical density was accomplished and these data showed that a sharp structural transition in supercoiled DNA pAO3 is caused by formation of a cruciform structure in the main palindrome.

[Reaction of endonuclease EcoRI with DNA of the plasmid ColEI]. / Reaktsiia vzaimodeistviia restriktazy EcoRI s DNK plazmidy ColEI.

Interaction of restrictase EcoRI with supercoiled and open forms of ColEI DNA is studied in the range 0-55 degrees. At temperatures 25-37 degrees superhelical ColEI DNA is converted to linear form, the most complete cleavage of supercoiled molecules were observed at 25 degrees. This reaction is not followed by accumulation of intermediate open circular DNA forms. At 45-55 degrees open circular DNA forms with nicks at the restriction site are formed along with linear molecules. Similar effects were observed at 10 degrees, whereas at 0 degree only open circular DNA molecules are formed.