[Evaluation of cytotocicity and efficiency of antioxidant protection of hydrophilic derivatives of 2,4,6-trialkylphenols in Escherichia coli cells]

The effects of five new derivatives of 2,6-dialkyl-4-propylphenole containing in para-radical different ionogenic groups (-SO3Na, -S-SO3Na, -S-(NH2)2Cl) in the presence and in the absence of hydrogen peroxide on the survival of E. coli AB1157 cells and its isogenic strain defective in repair enzyme genes were studied. Cell survival treated with hydrogen peroxide was remarkably increased in the presence of (3-(3,5-dimethyl-4-hydroxyphenyl)propyl)-1-sulphonate of sodium (Cl). Replacement of methyl ortho-radicals in the structure of Cl for tret-buthyl or cyclohexyl groups led to a decrease of the compounds ability to protect the cells from exogenic hydrogen peroxide. Between derivatives of 2,6-di-tret-buthylphenol the compound with thiosulphonate group demonstrated properties comparable with those for its sulphonate analog, then a chloride of isotiurone at concentration 3 mM completely suppressed the growth of cells in presence and in the absence of H2O2. Compound Cl may be considered as most perspective for detail analysis as antioxidant.

[The dependence of cytotoxicity and antioxidant activity of ammonii derivatives of alkylphenols upon percularities of their structure]

Effect of seven structurally similar N, N-dimethyl-(4-hydroxyaryl)alkylammonium chlorides in the presence and in the absence of hydrogen peroxide on the survival of E. coli cells AB1157 and its isogenic strain BH910 defective in genes of repair enzymes has been analyzed. Among the studied compounds only chloride of N,N-dimethyl-(3,5-dimethyl-4-hydroxybenzyl)ammonium (C1) has no cytotoxic properties and increases the survive of the cells of both strains in the presence of H2O2 better than trolox (water soluble analog of alpha-tocopherol). C1 analogs: 3-methyl-(5-di(tert-butyl)-4-hydroxybenzyl) and 3-(3,5-di(tert-butyl)-4-hydroxyphenyl)propyl)amines derivatives effectively protected from H2O2 only mutant cells BH910. Among the structural analogs of C1 cytotoxicity increases at substitution of methyl groups in aromatic cycle by tert-butyl and cyclohexyl groups. Only C1 among the seven new compounds is the most promising antioxidant for the subsequent more detailed analysis.

[Antioxidative activity of thiophane [bis(3-(3,5-di-tert-butyl-4-hydroxyphenyl)propyl)sulfide]

The antioxidant activity, mutagenicity, and genotoxicity of bis(3-(3,5-di-tert-butyl-4-hydroxyphenyl)propyl)sulfide (thiophane) were studied using bacterial tests. The results of both an Ames test and SOS chromotest, as well as those studying the survival of E. coli cells deficient in enzymes responsible for the repair of DNA oxidative damage, testify to the fact that thiophane is not mutagenic and genotoxic, and it protects Salmonella typhimurium cells better than the well-known antioxidant trolox.

[The mechanism of supercoiled DNA recognition by eukaryotic type I topoisomerases. II. A comparison of the enzyme interaction with specific and nonspecific oligonucleotides]

Data on the interaction of DNA type I topoisomerases from the murine and human placenta cells with specific and nonspecific oligonucleotides of various structures and lengths are summarized. The relative contributions of various contacts between the enzymes and DNA that have previously been detected by X-ray analysis to the total affinity of the topoisomerases for DNA substrates are estimated. Factors that determine the differences in the enzyme interactions with specific and nonspecific single- and double-stranded DNAs are revealed. The results of the X-ray analysis of human DNA topoisomerase I are interpreted taking into account data on the comprehensive thermodynamic and kinetic analysis of the enzyme interaction with the specific and nonspecific DNAs.

[The mechanism of the supercoiled DNA recognition by eukaryotic type I topoisomerases. I. The enzyme interaction with nonspecific oligonucleotides]

Interaction of the DNA type I topoisomerases from the murine and human placenta cells with nonspecific oligonucleotides was analyzed. The contributions of strong and week nonspecific electrostatic, van der Waals's, and hydrophobic interactions, and hydrogen bonding of the enzymes to the complex formation with the single- and double-stranded DNAs were determined. The factors that determine the top-priority recognition of the topologically stressed DNA were revealed. The results were interpreted in comparison with the X-ray analysis data for human DNA topoisomerase I.

Thermodynamic, kinetic, and structural basis for recognition and repair of 8-oxoguanine in DNA by Fpg protein from Escherichia coli

X-ray analysis does not provide quantitative estimates of the relative importance of the molecular contacts it reveals or of the relative contributions of specific and nonspecific interactions to the total affinity of specific DNA to enzymes. Stepwise increase of DNA ligand complexity has been used to estimate the relative contributions of virtually every nucleotide unit of 8-oxoguanine-containing DNA to its total affinity for Escherichia coli 8-oxoguanine DNA glycosylase (Fpg protein). Fpg protein can interact with up to 13 nucleotide units or base pairs of single- and double-stranded ribo- and deoxyribo-oligonucleotides of different lengths and sequences through weak additive contacts with their internucleotide phosphate groups. Bindings of both single-stranded and double-stranded oligonucleotides follow similar algorithms, with additive contributions to the free energy of binding of the structural components (phosphate, sugar, and base). Thermodynamic models are provided for both specific and nonspecific DNA sequences with Fpg protein. Fpg protein interacts nonspecifically with virtually all of the base-pair units within its DNA-binding cleft: this provides approximately 7 orders of magnitude of affinity (Delta G degrees approximately equal to -9.8 kcal/mol) for DNA. In contrast, the relative contribution of the 8-oxoguanine unit of the substrate (Delta G degrees approximately equal to -0.90 kcal/mol) together with other specific interactions is <2 orders of magnitude (Delta G degrees approximately equal to -2.8 kcal/mol). Michaelis complex formation of Fpg protein with DNA containing 8-oxoguanine cannot of itself provide the major part of the enzyme specificity, which lies in the k(cat) term; the rate is increased by 6-8 orders of magnitude on going from nonspecific to specific oligodeoxynucleotides.

[Study of the DNA primary structure effect on induction of mutations by alkylating agents]

Analysis and comparison of mutation spectra is one of the major tasks of molecular biology, since mutation spectra often reveal important properties of various mutagens and proteins involved in the repair/replication systems. Mutability is known to vary significantly along the nucleotide sequence. Mutations are abundant at certain positions (mutation hotspots). In this work, we applied regression analysis based on the basic logic patterns to understand the role of the nucleotide sequence context in mutation induction. The spectra of mutations induced by various alkylating agents were studied. The nucleotide bases at positions -2, -1, +1 and +2 were shown to have the most significant effect in G:C-->A:T replacements.

Formation of the D-loop structure complexes between DNA and oligonucleotides and affinity modification of DNA by chemically reactive derivatives of oligonucleotides lead to the recombination

INTRODUCTION

Affinity modification of DNA by chemically reactive derivatives of complementary oligonucleotides (ODNs) and antisense ODNs has shown an application for the inhibition of gene expression and the growth of viruses and parasites in high organisms. Unfortunately, the rapid advancement of antisense therapeutic approaches is not parallel to the investigation of possible consequences of antisense and gene-directed ODNs on genetic material of the cells being treated. Here we tried for the first time to estimate a possible genetic impact of antisense ODNs and their chemically reactive derivatives on the cells using bacteria and the plasmid DNA.

MATERIAL AND METHODS

Recombination of direct repeats, induced by the formation of reversible complexes of plasmid DNA with complementary ODNs and after covalent binding of the alkylating derivative of the ODNs with DNA, has been investigated. For this purpose, a polylinker sequence flanked by 165 bp direct repeats was inserted within the tet gene of pBR 327. This plasmid was used to construct DNA containing AT- and GC-rich sequences placed in the central region of the polylinker.

RESULTS

Transformation of E. coli cells with the plasmids (and with mixtures of the plasmids with d(pN)17 complementary to the AT- and GC-rich sequences) did not produce deletions. After modification of plasmids with alkylating derivatives of d(pN)17, the deletion of the polylinker DNA region (recombination) revealed the restoration of the tet gene function. The same effect was found at the cell transformations with the D-loop complex of the plasmids with ODNs, but the frequency of the transformants was about 1.5-2 times lower. The data obtained demonstrate that the complexes of DNA with complementary ODNs and the modification of the plasmids by reactive ODN derivatives result in induction of the recombination process and in loss of genetic material.

Repair of uracil residues closely spaced on the opposite strands of plasmid DNA results in double-strand break and deletion formation

The role of closely spaced lesions on both DNA strands in the induction of double-strand breaks and formation of deletions was studied. For this purpose a polylinker sequence flanked by 165 bp direct repeats was inserted within the tet gene of pBR327. This plasmid was used to construct DNA containing one or two uracil residues which replaced cytosine residues in the KpnI restriction site of the polylinker. Incubation of the plasmid DNA construct with Escherichia coli cell-free extracts showed that double-strand breaks occurred as a result of excision repair of the opposing uracil residues by uracil-DNA glycosylase (in extracts from ung+ but not in extracts from ung- E. coli strains). Recombination of direct repeats, induced by double-strand breakage of plasmid DNA, can lead to the deletion of the polylinker and of one of the direct repeats, thus restoring the tet+ gene function which can be detected by the appearance of tetracycline-resistant colonies of transformants. Transformation of E. coli cells with single or double uracil-containing DNAs demonstrated that DNA containing two closely spaced uracil residues was tenfold more effective in the induction of deletions than DNA containing only a single uracil residue. The frequency of deletions is increased tenfold in an ung+ E. coli strain in comparison with an ung- strain, suggesting that deletions are induced by double-strand breakage of plasmid DNA which occurs in vivo as a result of the excision of opposing uracil residues.

The molecular basis of the origin of complete and mosaic mutants

To study the molecular basis of the origin of complete and mosaic mutants, pBR322 plasmids with damage to one or both DNA strands were constructed by limited chemical modification of plasmid DNA. Damage to one strand of DNA resulted in the induction of predominantly mosaic mutants. Data were obtained indicating that complete mutations arise as a result of damage to both strands in the region of the mutated gene.