PubMed Health⌕ Search

Biomedical subjects

A N Siniakov

Publications and source records attributed to A N Siniakov.

32 records · Page 2Linked to original sources
PubMed1987

[Current approaches to the synthesis and reconstruction of genetic material].

Advanced approaches to the synthesis and reconstruction of genetic material developed in the Institutes of Molecular Biology and Genetics during the past years are summarized. The evolution of methods for oligonucleotide synthesis and scopes for their use in gene production are discussed. The principles of localised mutagenesis methods developed in the Institute are described, such as: a) mutagenesis directed to the regulatory gene regions; b) segment-localized mutagenesis; c) mutagenesis directed by phosphotriester analogues of oligonucleotides. Examples of employing these methods for induction of regulatory mutants of phage lambda, production of fused genes, mutant interferon genes, construction of new DNA vectors, construction of hybrid H1-H3 subtype haemagglutinine gene of influenza virus etc. are presented. The approach to in vivo site-directed mutagenesis is experimentally substantiated.

Genes, Synthetic↗
PubMed1986

[Synthesis and cloning of a DNA fragment containing a probable site for eukaryotic mRNA binding to ribosome].

A series of oligonucleotides, including two polynucleotides of 33 bases long, were synthesized by a solid-phase phosphotriester method. Potassium salt of 3-nitro-1,2,4-triazole in the presence of 18-crown-6 ether was used as nucleophilic catalyst. The partly complementary polynucleotides were elongated by DNA-polymerase I (Klenow fragment) to the full duplex, which was digested with SalGI and was inserted into a plasmid pUR222. Phe synthesized DNA fragment precedes the gene of human gamma-interferon in the chromosome and contains the site for mRNA binding to ribosome.

Base Sequence↗
PubMed1984

[Synthesis of a 33-member polynucleotide containing the "core" att site of phage lambda DNA and its cloning].

Two polynucleotides containing 33 monomeric units were synthesized by a solid-phase phosphotriester method. These polynucleotides form a duplex with protruding 5'-ends, which allows to clone the duplex in EcoRI site of a cloning vehicle. Each polynucleotide was purified by electrophoresis in polyacrylamide gel, and the duplex obtained was cloned in EcoRI site of pUR 222 plasmid DNA. The structure of the cloned duplex containing the "core" att site of phage lambda was confirmed by sequencing.

Bacteriophage lambda↗
PubMedDate not supplied

[Stabilization of DNA triple helix using conjugates of oligonucleotides and synthetic ligands].

Possibility of stabilization of DNA triple helix is discussed using a covalent conjugation to the third strand (through its terminal phosphate) of ligands that have affinity to double and triple helices. Two types of stabilizers are considered: minor groove binders based on oligopyrroles and triplex-specific interacalators. As a target, a synthetic 29-mer duplex containing a natural polypurinic sequence of the human immunodeficiency provirus was employed. The stabilization with minor groove binders requires several conditions to be respected: a sufficiently long linker capable of reaching out the minor groove from the major one, a specific double-stranded structure of the oligopyrrole fragment and its in-phase fitness to the target sequence. The best stabilizers of a triplex turned out to be novel conjugates in which two parallel molecules containing six pyrrole units each are linked to the same 5'-phosphate of a 16-mer triplex-forming oligonucleotide. The stabilizing properties of these derivatives were comparable with those of benzoindoloquinoline (BIQ) intercalators attached to the terminal phosphate of triple-helix forming oligonucleotides.

DNA↗
PubMedDate not supplied

[Functionalization of oligonucleotides containing internucleotide phosphoamide bonds].

A new method for functionalization of oligonucleotides by addition of aminoalkyl derivatives to the intermolecular phosphorus atom of the oligonucleotide N3'-P5' phosphoramidate bond in the presence of triphenylphosphine, 4-dimethylaminopyridine, and 2,2'-dipyridyl disulfide was suggested. The reaction proceeded with both low-molecular alkylamines (1,6-diaminohexane or N,N-dimethyl-1,3-diaminopropane) and a ligand in minor groove containing a aminoalkyl group.

Amides↗
PubMedDate not supplied

[A rapid and effective solid-phase synthesis of DNA-sequence binding polyamides].

A rapid and effective variant of solid-phase synthesis of DNA-sequence-specific polyamides on the basis of 4-amino-1-methylpyrrole-2-carboxylic acid, 4-amino-1-methylimidazole-2-carboxylic acid, beta-alanine, and gamma-aminobutyric acid was suggested. It is based on the use of di- and trimeric oligocarboxamide building blocks, which help reduce the time of synthesis, increase its yield and purity of products, and efficiently use manual synthesis for the synthesis of long oligocarboxamides. The yields of hairpin ligands with up to 10 units are 35-50% and the synthesis takes no more than 6 h.

Alanine↗
PubMedDate not supplied

[Stabilization of G x C-containing DNA duplexes by polyamides with parallel orientation in the minor groove].

The polyamides based on 4-amino-1-methylpyrrol-2-carboxylic acid, 4-amino-1-methylimidazole-2-carboxylic acid, and beta-alanine that stabilize oligonucleotide duplexes consisting of G x C pairs through parallel packing in the minor groove were studied. The initial duplex TTGCGCp x GCGCAA melts at 28 degrees C; the TTGCGCp[NH(CH2)3COPyIm betaImNH(CH2)3NH(CH3)2][NH(CH2)3COIm betaImPyNH(CH2)3N(CH3)2] x GCGCAA duplex (bisphosphoramidate with parallel orientation of ligands, where Py, Im, and beta are the residues of 1-methyl-4-aminopyrrol-2-carboxylic and 1-methyl-4-aminoimidazole-2-carboxylic acids and beta-alanine, respectively), at 48 degrees C; and the TTGCGCp[NH(CH2)3COIm betaImPyNH(CH2)3COIm betaImPyNH(CH2)3N(CH3)2] x GCGCAA duplex (a hairpin structure with antiparallel orientation), at 56 degrees C. The English version of the paper: Russian Journal of Bioorganic Chemistry, 2004, vol. 30, no. 5; see also http: // www.maik.ru.

Alanine↗
PubMedDate not supplied

[Effect of structural factors on the stability of duplexes formed by oligonucleotide conjugates with minor groove ligands].

The effect of structural factors on the stability of duplexes formed by DNA minor groove binders conjugated with oligonucleotide mono- or diphosphoramidates of the general formula Oligo-MGBm (where Oligo is an oligonucleotide; m = 1 or 2; MGB is -L(Py)2R, L(Py)4R, -L(Im)4R, or -L(Py)4NH(CH2)3CO(Py)4R; Py is a 4-aminopyrrol-2-carboxylic acid residue, L is a gamma-aminobutyric acid or an epsilon-aminocaproic acid residue, R = OEt, NH(CH2)6NEt2, or NH(CH2)6N+Me3) was studied by the method of thermal denaturation. The mode of binder interaction with minor groove depends on the conjugate structure; it may be of the parallel head to head type for bisphosphoramidates and of the antiparallel head to tail type for monophosphoramidates of a hair-pin structure. The effects of the duplexes with parallel orientation (bisphosphoramidates, MGB is L(Py)4R, m = 2) and those of the hairpin structure with the antiparallel orientation (monophosphoramidates, MGB is L(Py)4(CH2)3CO(Py)4R, m = 1) on Tm values were close. The influence of the linker (L) and substituent (R) structures upon Tm was more pronounced for monophosphoramidate (MGB is L(Py)nR, m = 1) than for bisphosphoramidate (MGB is L(Py)nR, m = 2). No more than two oligopyrrolcarboxamide residues (either in parallel or antiparallel orientations) can be incorporated into the duplex minor groove. Moreover, it was shown by the example of monophosphoramidates (Oligo-L(Py)4R and Oligo-L(Py)4NH(CH2)3CO(Py)4R) that the addition of a second ligand capable of incorporation into the minor groove increased Tm of the corresponding duplex in comparison with the duplex formed by the starting monophosphoramidate. At the same time, the introduction of the ligand incapable of incorporating decreased the Tm value. The mode of interaction of the conjugated ligand with the oligonucleotide duplex is determined by its structure. For example, dipyrrolcarboxamide containing an ethoxy group at the ligand C-end stabilizes the duplex due to the stacking interaction with the terminal A*T pair, whereas tetrapyrrolcarboxamides stabilize the duplex by incorporation into the minor groove.

Amides↗
PubMedDate not supplied

[Interaction of HIV-1 reverse transcriptase with new minor groove ligands and their conjugates with oligonucleotides].

The influence of new non-natural regular minor groove binders (MGB), containing 2-4 imidazole, pyrrole or thiazole residues, and their conjugates with oligonucleotides, on the polymerization reaction catalyzed by HIV-1 reverse transcriptase was analyzed. Various model template-primer complexes: poly(A)-oligo(U), poly(A)-oligo(dT), poly(dA)-oligo(U), poly(dA)-oligo(dT) and activated DNA were used. The concentration of oligopeptides, giving 50% inhibition (I50) of the RT-dependent polymerization reaction, was shown to depend strongly on the structure of template-primer complexes, number and type of the heterocycle rings in the MGBs analyzed. The range of I50 for the most of the compounds studied is 7.7 x 10(-3)-1.0 x 10(-5) M. The affinity of MGB is minimal for poly(A)-oligo(U). However, some of imidazole and pyrrole-containing MGBs demonstrated unusually high affinity (I50 = 3 x 10(-9)-4 x 10(-8) M) to the above template-primer in complex with RT. The affinity of conjugates of thiazolecarboxamides with oligonucleotides complementary or partially complementary to the template, is 1-4 orders higher compared to free thiazolecarboxamides. The possible reasons of the dependence of I50 values upon the structure of the template-primer complexes, the structure of MGB, and their conjugates with oligonucleotides are discussed.

HIV Reverse Transcriptase↗
PubMedDate not supplied

[Preparation of hybrid proteins consisting of human interleukin-2 and the cytotoxic A-subunit of Shigella toxin].

Recombinant plasmids providing the synthesis of chimeric proteins consisting of amino acid sequences of human interleukin-2 (IL-2) and Shiga toxin cytotoxic A-subunit (ILA and AIL chimeric toxins) were constructed. The ILA and AIL chimeric toxins were shown to inhibit protein synthesis in the rabbit reticulocytes cell-free system. These chimeric toxins displayed two opposite activities of the constituent parts of their molecules on T-lymphocytes from the peripheral blood of healthy volunteers. Hybrid protein AIL (approximately 10(-6) g/ml) has caused the most significant depression of T-lymphoblast proliferation.

Bacterial Toxins↗
PubMedDate not supplied

[Effective expression of genes for interleukin-2 and its mutant analogs in E. coli cells].

Recombinant plasmids were constructed for the efficient expression in E. coli cells of the human interleukin-2 (HIL-2) gene and two its mutant analogues obtained by of chemical-enzymic synthesis and polymerase chain reaction (deletion of 14 C-terminal amino acids and a change of the codon for Trp121 to Phe). The recombinant HIL-2 but not the mutant analogues were shown to be biologically active. Both analogues obtained were weak antagonists to HIL-2.

Base Sequence↗