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S G Kamzolova

Publications and source records attributed to S G Kamzolova.

At least 19 recordsLinked to original sources
PubMed2005

Electrostatic potentials of E.coli genome DNA.

Distribution of electrostatic potential of the complete sequence of E. coli genome was calculated. Comparative analysis of electrostatic patterns for 359 promoter and nonpromoter nucleotide sequences was carried out. It is found that nonpromoter regions are characterized by more homogeneous distribution of electrostatic potential with no common specific elements. Electrostatic patterns of promoter DNAs can be specified due to the presence of some distinctive motifs which may be involved as promoter signal elements in RNA-polymerase-promoter recognition.

Base Sequence↗
PubMed2000

RNA polymerase--promoter recognition. Specific features of electrostatic potential of "early" T4 phage DNA promoters.

Comparative analysis of electrostatic potential distribution for "early" T4 phage promoters was undertaken, along with calculation of topography of electrostatic potential around the native and ADP-ribosylated C-terminal domain of RNA polymerase alpha-subunit. The data obtained indicate that there is specific difference in the patterns of electrostatic potential distribution in far upstream regions of T4 promoters differing by their response to ADP-ribosylation of RNA polymerase. A specific change in profiles of electrostatic potential distribution for the native and ADP-ribosylated forms of RNA polymerase alpha-subunit was observed suggesting that this factor may be responsible for modulating T4 promoter activities in response to the enzyme modification.

Adenosine Diphosphate Ribose↗
PubMed1999

Electrostatic potentials of DNA. Comparative analysis of promoter and nonpromoter nucleotide sequences.

Distribution of electrostatic potential of DNA fragments was evaluated. A method for calculation of electrostatic potential distribution based on Coulomb's law is proposed for long DNA fragments (approximately 1000 nucleotide pairs). For short DNA sequences, this technique provides a good correlation with the results obtained using Poisson-Boltzmann equation thus justifying its application in comparative studies for long DNA fragments. Calculation was performed for several DNA fragments from E. coli and bacteriophage T7 genomes containing promoter and nonpromoter regions. The results obtained indicate that coding regions are characterized by more homogeneous distribution of electrostatic potential whereas local inhomogeneity of DNA electrostatic profile is typical for promoter regions. The possible role of electrostatic interactions in RNA polymerase-promoter recognition is discussed.

Anion Transport Proteins↗
PubMed1996

[Regulatory properties of RNA polymerase from rifampicin-resistant E. coli strain rpoB403].

Activities of RNA polymerases from wild type B/r strain of E. coli and its pleiotropic rpoB403 rif-r mutant were studied using five various DNA matrices and various groups of early region promotors of T4 and T7 phage DNA. The mutation differentially affects RNA polymerase-catalyzed RNA synthesis depending on the promotor used. Relative efficiency of A3 promotor of T7 phage DNA is enhanced in case of the mutant enzyme. rpoB403 mutation can be used for the classification analysis of promotors differing in their interaction with the enzyme.

Antibiotics, Antitubercular↗
PubMed1995

[Interaction of Escherichia coli RNA polymerase with promoters. The need for a classified approach in studying the code of promoter-polymerase recognition].

The data on E. coli RNA polymerase (E sigma 70) interaction with its numerous promoters are reviewed. Two different approaches to the problem of promoter-polymerase recognition code are analyzed. One approach is consistent with the idea of a universal code on the basis of a consensus promoter. According to this approach, the unique active center in the enzyme is involved in interaction with all promoters. The second approach is based on the original concept suggesting the existence of several active centers in RNA polymerase, each of them interacting with its own group of promoters. This approach is based on the idea that promoter-polymerase recognition is coded by different programs for different groups of promoters; therefore, the problem should be contemplated from the standpoint of a classification analysis of promoters. Supporting evidence in favour of this concept is presented.

DNA-Directed RNA Polymerases↗
PubMed1993

Interaction of bacterial RNA-polymerase with two different promoters of phage T7 DNA. Conformational analysis.

Using a rifampicin-resistant RNA polymerase with altered specificity to different promoters, the D promoter of T7 phage DNA with increased affinity to the mutant enzyme was chosen. This promoter and the T7 A1 promoter with unchanged affinity as well as some nonpromoter DNA fragments were used to compare temperature-induced conformational transitions of RNA polymerase in the course of complex formation. Conformational alterations of RNA polymerase were monitored by the fluorescent label method. It was shown that RNA polymerase undergoes a set of conformational transitions during complex formation with each promoter, some of which were similar by the character of change to spectral parameters of the label (reflecting RPi and, probably, RPo formation). The local structure of complexes formed above 33 degrees C differs for A1 and D. The conformational analysis reveals at least one temperature-dependent stage upon nonspecific interaction of the enzyme with nonpromoter DNA at 13-16 degrees C. Models of functional organization of the enzyme recognizing center and some features of the structure of the promoters which may be essential for their recognition are discussed.

Base Sequence↗
PubMed1991

Specific modification of Escherichia coli RNA polymerase with monomercury derivative of fluorescein acetate.

The method of specific modification of RNA polymerase with a monomercuric fluorescein derivative, fluorescein-monomercuriacetate (FMMA), is proposed. Under an appropriate condition of modification, FMMA is capable of mercaptid bonding with one of the alpha-subunits. It is shown that covalent modification with FMMA does not affect the kinetic parameters (KB and k2) of RNA synthesis nor does it lead to the inhibition of the overall RNA synthesis. The spectral characteristics of FMMA covalently bound to RNA polymerase were found to be sensitive to some temperature-induced conformational alterations of RNA polymerase, indicating that the labeled enzyme allows study of conformational behaviour of RNA polymerase during its functioning.

Binding Sites↗
PubMed1987

[Specific chemical modification of cytidine in T4 DNA by a spin label].

A procedure for selective modification of DNA from T4 phage non-glucosylated mutant by the spin label--N(2,2',5,5') tetramethyl-3-carboxypyrrolidine-1-oxyl)-imidazole was developed. The spin label was shown to interact with hydroxyl groups of 5-hydroxymethyl-2 deoxycytidines. The modification does not affect the secondary structure of DNA, its conformation or template properties in a cell-free system of RNA synthesis.

Cytidine↗
PubMed1986

Physico-chemical study of complex formation of DNA with wild-type and mutant E. coli RNA polymerases. Recognition properties of beta-subunit.

Complex formation of T7 DNA with RNA polymerase from E. coli B/r WU-36-10-11-12 (E. coli W12) and its rifampicin-resistant mutant rpoB409 was studied. The rpoB409 mutant possesses a highly pleiotropic effect due to alteration in the RNA polymerase beta-subunit structure. The two RNA polymerases have been previously shown to differ in gene selection during RNA synthesis on T7 DNA. In this study it was found that the change in selective properties of the mutant RNA polymerase occurs during its interaction with DNA, the general ability of the enzyme to melt DNA being unaffected.

Carbon Radioisotopes↗
PubMed1982

An RNA polymerase with reduced fidelity of RNA synthesis from an E. coli mutant suggests the existence of a correction system of non-complementary nucleotide incorporation during transcription.

An RNA polymerase mutant of E. coli B/r-rpoB402, with a pleiotropic effect on stability of the phenotype has recently been obtained (8-11). The present study is concerned with the fidelity of in vitro RNA synthesis carried out by highly purified RNA polymerase from the wild type strain and rpoB402 mutant. The data indicate that mutational alteration of RNA polymerase reduced the accuracy of the enzyme to a value lower than that required for the cell. The results suggest the existence of some correcting system during transcription.

DNA-Directed RNA Polymerases↗
PubMed1981

[Role of RNA polymerase in ensuring fidelity in copying the template during transcription in E. coli].

The heterogeneity of cell size of E. coli WU-36-10-11-12 and its four RNA-polymerase (rif-r) mutants with pleiotropic effect -- rpoB401, rpoB402, rpoB403 and rpoB409 was investigated for the purposeful choice of E. coli mutant with an altered fidelity of transcription. The stability of the phenotype of E. coli strains was shown to depend on the structural state of RNA polymerase. In vitro RNA-polymerase of the morphologically most unstable mutant rpoB402 incorporates non-complementary GMP or CMP on the poly [d(AT).d(AT)] template more frequently than the enzyme from the wild-type strain. The data obtained suggest that the beta-subunit of RNA-polymerase determines the fidelity of transcription and the selection of complementary nucleotides.

DNA-Directed RNA Polymerases↗
PubMed1977

[T2 DNA, modified by 2,2,6,6-tetramethyl-4-bromoacetooxypiperidine-i-oxyl as a template for RNA polymerase from E. coli B].

T2-DNA was modified by 2,2,6,6-tetramethyl-4-bromoacetooxypiperidine-1-oxyl (I) at different NaCl concentrations (10(-1) M NaCl--10(-4) M NaCl). Modified DNA were investigated as templates for the RNA-polymerase from E. coli B. It was shown that T2-DNA modified I in 0,1 M NaCl completely preserves the native secondary structure, has a low degree modification (1 molecule I per 1000-2000 nucleotide pairs), but is a noneffective template for the RNA-polymerase from E. coli B (20%-40% as compared with unmodified T2-DNA). Under these conditions the modification occurs probably at the "weakest" (readily melting) sites of DNA. The role of these "weak" sites on DNA as promotors is discussed. The modification of T2-DNA by reagnet I has a stronger inhibitory effect on the total RNA synthesis than on the RNA-synthesis stable to rifampicin. Possible existence of two kinds of "early" promotors on T2-DNA is assumed.

Coliphages↗