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M G Brevnov

Publications and source records attributed to M G Brevnov.

7 recordsLinked to original sources
PubMed2000

Parallel self-associated structures formed by T,C-rich sequences at acidic pH.

Oligonucleotides of nonregular heteropyrimidine sequences incorporating or not incorporating purine residues 5'-d(ACTCCCTTCTCCTCTCTA), 5'-d(ACTCCCTGGTCCTCTCTA), 5'-d(TCTCTCCTGGTCCCTCC), and 5'-d(TCTCTCCTCTTCCCTCC) can form self-associated parallel-stranded (ps) structures at pH 4-5.5. The ps structures were identified by studying at neutral and acidic pH UV melting transitions, FTIR spectra, and fluorescence of pyrene-labeled oligonucleotides as well as by chemical joining of 5'-phosphorylated oligonucleotides. A gel electrophoresis run for oligonucleotides 5'-d(TCTCTCCTCTTCCCTCC) and 5'-d(ACTCCCTTCTCCTCTCTA) has shown the formation of homoduplexes at low DNA strand concentrations. Ps structures are held by C-C(+) base pairs and have N- and S-types of sugar puckering as detected by FTIR spectroscopy in the millimolar concentration range. Guanine inserts as well as thymine and purine inserts into an oligomeric cytosine sequence make the formation of the tetraplex i-motif unfavorable. MvaI restriction endonuclease, which recognizes the CCT/AGG sequence in DNA, does not cleave parallel pseudosubstrates.

Acids↗
PubMed1998

The Ecl18kI restriction-modification system: cloning, expression, properties of the purified enzymes.

Ecl18kI is a type II restriction-modification system isolated from Enterobacter cloaceae 18kI strain. Genes encoding Ecl18kI methyltransferase (M.Ecl18kI) and Ecl18kI restriction endonuclease (R.Ecl18kI) have been cloned and expressed in Escherichia coli. These enzymes recognize the 5'.../CCNGG...3' sequence in DNA; M.Ecl18kI methylates the C5 carbon atom of the inner dC residue and R.Ecl18kI cuts DNA as shown by the arrow. The restriction endonuclease and the methyltransferase were purified from E. coli B834 [p18Ap1] cells to near homogeneity. The restriction endonuclease is present in the solution as a tetramer, while the methyltransferase is a monomer. The interactions of M.Ecl18kI and R.Ecl18kI with 1,2-dideoxy-D-ribofuranose containing DNA duplexes were investigated. The target base flipping-out mechanism is applicable in the case of M.Ecl18kI. Correct cleavage of the abasic substrates by R.Ecl18kI is accompanied by non-canonical hydrolysis of the modified strand.

Base Sequence↗
PubMed1997

DNA duplexes with reactive dialdehyde groups as novel reagents for cross-linking to restriction- modification enzymes.

To create new, effective reagents for affinity modification of restriction-modification (R-M) enzymes, a regioselective method for reactive dialdehyde group incorporation into oligonucleotides, based on insertion of a 1-beta-D-galactopyranosylthymine residue, has been developed. We synthesized DNA duplex analogs of the substrates of the Eco RII and Mva I R-M enzymes that contained a galactose or periodate-oxidized galactose residue as single substituents either in the center of the Eco RII (Mva I) recognition site or in the flanking nucleotide sequence. The dependence of binding, cleavage and methylation of these substrate analogs on the modified sugar location in the duplex was determined. Cross-linking of the reagents to the enzymes under different conditions was examined. M. Eco RII covalent attachment to periodate-oxidized substrate analogs proceeded in a specific way and to a large extent depended on the location of the reactive dialdehyde group in the substrate. The yield of covalent attachment to a DNA duplex with a dialdehyde group in the flanking sequence with Eco RII or Mva I methylases was 9-20% and did not exceed 4% for R. Eco RII.

Aldehydes↗
PubMed1996

[Kinetic modeling of the mechanism of allosteric interactions of restriction endonuclease EcoRII with two DNA segments].

The effect of correlations between kinetic parameters of two inducible substrates on allosteric activation of EcoRII endonuclease hydrolysis of one substrate was studied. The pairs of DNA duplexes were constructed that were the substrates of EcoRII restriction endonuclease or their analogs and had different kinetic constants of interaction with the enzyme; the effects of their concentrations on mutual hydrolysis induction were studied. A kinetic mechanism is suggested considering the allosteric effects of two DNA recognition sites on dimeric molecule of EcoRII. Mathematic modeling was used to analyze the kinetic mechanism and evaluate optimal characteristics of the inductor. Thus, activation increases when (i) substrate concentration decreases, (ii) enzyme binding of two inductor or substrate molecules decreases, (iii) binding of one substrate molecule increases versus binding of one inductor molecule, and (iv) kcat of the enzyme-substrate complex including on substrate and one inductor increases.

Allosteric Regulation↗
PubMed1995

Interaction of the MvaI and SsoII methyltransferases with DNAs altered at the central base pair of the recognition sequence.

The interaction of the MvaI and SsoII DNA methyltransferases (MTases; M.MVaI and M.SsoII, respectively) with a set of synthetic DNA duplexes, containing a M.MvaI and M.SsoII recognition site (CCWGG), was investigated. In these DNA duplexes dA or dT of the recognition site was replaced by nucleoside analogs with modified sugar moieties and heterocyclic bases (2'-deoxy-2'-fluorouridine (flU), 1-(beta-D-2'-deoxy-threo-pentofuranosyl)thymine (xT), 1-(beta-D-3'-deoxy-threo-pentofuranosyl)uracil (tU)), or by 1,3-propanediol (Prd). A new approach for monitoring methylation of each strand of DNA duplexes by MTases was developed. It allowed the determination of the influence of the modification in one DNA strand on the methylation of the other. In most cases, for both M.MvaI and M.SsoII, sugar analog-containing duplexes showed inhibition of methylation of only the modified strand. Prd-containing DNA duplexes were not substrates for M.MvaI. M.SsoII did not methylate DNA duplexes in which the dT residue was replaced by Prd.

Amino Acid Sequence↗
PubMed1995

Modified substrates as probes for studying uracil-DNA glycosylase.

In order to study the mechanism of action of uracil-DNA glycosylase (UDG) from human placenta, single-stranded (ss) and double-stranded (ds) oligodeoxyribonucleotides (oligos), containing deoxyuridine (dU) and a wide variety of their analogs were used. It was shown that UDG has a twofold preference for ss oligos over ds oligos and a twofold preference for intermolecular duplexes over similar hairpin-like duplexes. The replacement of dU with 1-(beta-D-2'-deoxy-threo-pentofuranosil)uracil (xU) or 1-(beta-D-3'-deoxy-threo-pentofuranosil)uracil (tU), which results in a change in sugar hydroxyl configuration, has no influence on UDG binding to such substrates, but inhibits uracil removal. A oligo containing 2'-deoxy-2'-fluorouridine (flU), with a 3'-endo conformation of modified sugar is recognized by UDG 100-200-fold less efficiently than the natural ones. F or Br atoms or a methyl group were introduced at position 5 of a dU residue in an oligo. It was shown that the nature of a substituent at this position is essential for UDG function.

Base Sequence↗