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S M Zhenodarova

Publications and source records attributed to S M Zhenodarova.

At least 19 recordsLinked to original sources
PubMed1994

Trivaline molecular complexes with trinucleotides form in solution the extended, about 1000 A in length structures.

The fluorescence, flow linear dichroism and electron microscopy (EM) have shown the trivaline ability to interact in solution with certain molecules of trinucleotides. This interaction results in formation of extended structures up to several thousand angstroms in length. Such structures were observed for trivaline complexes with homopurine, homopyrimidine or random sequences of deoxyribo- and ribonucleotides, independently of the presence or absence of the terminal 5'-phosphate residue. A model of such a structural organization is proposed. An elementary structural unit consists of a trivaline beta-dimer and adsorbed trinucleotide. So, "dimeric" complex is formed. Two such "dimeric" complexes combine with each other by means of peptide-peptide contacts (as with beta-sandwich). So, "tetrameric" complex is formed. It has a dyad axis. Two such structural units combine with each other by means of Hoogsteen's hydrogen bonds. So, "octameric" complex is formed. It has three mutually perpendicular dyad axes. The "octameric" complexes appear to be able to combine with each other by means of stacking interactions, and to form the regular organized aggregates consisting of many dozens of elementary units. So, "stacking" structure is formed. The "octameric" complex is the symmetry translational unit of such a structure. The spatial position of the bases in all these structures is additionally fixed by the nucleo-peptide interactions. These aggregates have the appearance of extended structures on electron micrographs.

Microscopy, Electron↗
PubMed1992

[The use of nucleolytic enzymes (ribonucleases, polynucleotide phosphorylases and endonuclease from Serratia marcescens) for producing initial blocks of synthetic endoribonucleases].

The simplest variant of synthetic substrate-ribozyme complex has been proposed. The schemes of potential ribozyme "subunits" synthesis have been worked out: R1--GCUUGAAACAAA; R2--AAAAACUGAUGAAAGC. The macroscale synthesis of dinucleoside monophosphate ApU, GpC, CpU catalyzed by immobilized ribonucleases of different specificity and preparation of oligoadenylates by hydrolysis of poly-A in the presence of endonuclease Serratia marcescens, as well the synthesis of conservative sequences of potential ribozyme such as ApUpG, CpUpG, GpApU, ApApApG and others have been described.

Base Sequence↗
PubMed1990

[Stepwise synthesis of oligonucleotides. XXXV. Native and immobilized polynucleotide phosphorylase from Thermus thermophilus in oligoribonucleotide synthesis].

A polynucleotide phosphorylase was isolated from the Thermus thermophilus protein fractions, obtained at different steps of purification of elongation factors, and immobilized on agarose activated with cyanogen bromide and macroporous glass modified with (3,3-diethoxypropyl)triethoxysilane. The preparations of the native and immobilized enzyme catalyzed rather efficiently the addition of adenylyl and guanylyl residues to oligonucleotide primers, in contrast to the E. coli and M. luteus polynucleotide phosphorylases. Tri-, tetra- and pentanucleotides with 3'-terminal guanosine and adenosine were obtained including structural analogues of the anticodon fragment 34-37 of yeast tRNA(Phe).

Catalysis↗
PubMed1989

[Substrate specificity of T4 RNA-ligase. The effect of the nucleotide composition of substrates and the size of phosphate donor on the effectiveness of intermolecular ligation].

Nucleoside 2' (3'),5'-diphosphates, dinucleotides pApA, pApC, pApU, pGpC, pCpC, pUpU (phosphate donors), and trinucleoside diphosphates, such as NpCpC, NpCpU, NpUpC, NpUpU and GpApN (N = U, C, A or G; phosphate acceptors) were used to study the substrate specificity of T4 RNA ligase. Relative efficiency of the mono- and dinucleotide donors depends on the 5'-terminal nucleoside moiety of the dinucleotide: upon ligation with the minimal phosphate acceptor GpUpC, dinucleotides pApA, pApC, and pApU are more effective than nucleotide diphosphate pAp; pGpC is more effective than pGp; efficiencies of pCpC and pCp are almost identical, and efficiency of pUpU is slightly lower than that of pUp. In relative efficiency, dinucleotide donors, varying only in 5'-terminal unit, do not correspond to mononucleotides: pApC greater than pCpC greater than pGpC and pCp greater than pUp approximately pAp much greater than pGp. The effects observed for homooligomeric substrates cannot be extra-polated on heterooligomers.

Chromatography, DEAE-Cellulose↗
PubMed1987

[Stepwise synthesis of oligonucleotides. XXXIV. Preparative synthesis of trinucleoside diphosphates and longer oligoribonucleotides using immobilized ribonucleases].

Immobilized guanyl-specific ribonucleases from Aspergillus clavatus (C2), A. oryzae (T1), and Bacillus intermedius 7P (Bi) have been used for preparative synthesis of ten trinucleoside diphosphates, three tetra- and one pentanucleotide having the only guanylic acid residue at the 5'-end. The nucleotide sequence of the oligonucleotide synthesised determined the choice of the ribonuclease.

Chemical Phenomena↗
PubMed1987

[Model substrates of enzymes modifying ribonucleic acids. Synthesis of deca- and undecanucleotid-fragments of 21-member oligoribonucleotide simulating T psi C-branch of yeast valine tRNA].

Decanucleotide (Ap)6GpTpUpC and undecanucleotide GpApUpCpCp (Up)5U have been synthesised. They constitute 5'- and 3'-parts of a 21-mer which imitates T psi C-arm of yeast tRNA(Val1) and is a potential substrate for m1A-methylases and pseudouridine synthetase. The oligonucleotide blocks, synthesised enzymatically by means of ribonucleases of various substrate specificity and polynucleotide phosphorylases (TpUpC, ApUpCpC, pGpTpUpC, GpApUpCpC) or obtained by hydrolysis of poly(U) and poly(A) with Serratia marcescens endonuclease (hexauridilate and hexaadenilate), were joined by T4 RNA ligase.

Intramolecular Transferases↗
PubMed1987

[Enzymatic incorporation into oligonucleotides of modified nucleosides].

Behaviour of modified nucleosides, tRNA components, and their analogues has been studied in the internucleotide bond formation catalysed by ribonucleases of various substrate specificity, polynucleotide phosphorylases, and T4 RNA ligase and the results are summarised in this paper. Pseudouridine, dihydrouridine, ribothymidine, 5-methylcytidine, inosine, and 6-methyladenosine can participate in the reaction of internucleotide bond formation the presence of most ribonucleases used, viz. Pb2, Pcl2, Pb1, Pch1, C2, T1, pancreatic RNase. 3-Methylcytidine and 4-acetylcytidine form internucleotide bond (as phosphate acceptors) usually by means of guanyl-specific ribonucleases, whereas 1-methylandenosine is incorporated with ribonuclease Pel2. 7-Methylguanosine and 1-methylguynosine 2',3'-cyclophosphates can be used as phosphate donors in the presence of ribonuclease Pb2; in the similar enzymatic reaction 6-isopentenyladenosine is an uneffective acceptor.

Base Composition↗
PubMed1983

[Enzymatic synthesis of oligonucleotides corresponding to the 3'-terminus of influenza virus RNA].

Dodecanucleotide CpCpUpGpCpUpUpUpUpGpCpU corresponding to 3'-terminus of influenza virus RNA has been synthesized. The initial blocks CpCpU, GpCpU, pGpCpU and pGpCpUp were prepared enzymatically in the presence of ribonucleases of different substrate specificity and polynucleotide phosphorylase M. luteus. pUpUpU was obtained by enzymatic degradation of polyuridilic acid. The initial blocks were joined by T4 RNA-ligase.

Base Sequence↗
PubMedDate not supplied

[RNA with polynucleotide kinase properties, isolated by in vitro selection].

Data on isolation from a large pool of RNAs of a fragment characterized by high-affinity ATP binding are reviewed. This ATP-binding domain flanking the regions of randomly sequenced nucleotide residues was used for preparation of an RNA pool, from which ribozymes displaying a polynucleotide kinase activity were isolated. The isolated ribozymes catalyzed the transfer of gamma-thiophosphate from ATP-gamma S to the 5' hydroxyl or to internal 2'-hydroxyls of their own chains. ATP was also used as a donor of phosphate; however, in this case the reaction rate was 55-300 times lower. Similarly to a true enzyme, one of these ribozymes shortened by 40 nucleotide residues at the 5' end repeatedly catalyzed the transfer of thiophosphate or phosphate to the 5' hydroxyl of an exogenous oligonucleotide.

Adenosine Triphosphate↗
PubMedDate not supplied

[ Fungal extracellular ribonucleases (Review)].

Results of studies of certain fungal extracellular ribonucleases mainly isolated from representatives of the genera Aspergillus and Penicillium are summarized. The isolation of these enzymes in highly purified states in the 1970-1980s strongly stimulated further studies of their structure, functions, and mechanisms of action. This also promoted the use of ribonucleases as catalysts in oligoribonucleotide syntheses and as objects of comparative and evolutionary biochemistry and other research works. Results of studies of the primary, secondary, and spatial structures of guanyl-specific fungal ribonucleases are reviewed. These studies revealed a high homology within the subfamilies of fungal, bacterial, and actinomycete RNases. Characteristics of the nonspecific Pb2 RNase are considered.

Aspergillus↗