[Experimental evidence of the existence of a parallel DNA double helix].
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Chromatography, High Pressure Liquid↗
Biomedical subjects
A A Chernyĭ
Publications and source records attributed to A A Chernyĭ.
[Inhibition of ADP-ribosylation by nerve growth factor in the pheochromocytoma PC-12 cell line].
The effect of nerve growth factor (NGF), purified to homogeneity from bovine seminal plasma using HPLC, on the level of endogenous ADP-ribosylation in pheochromocytoma PC-12 cell line was studied. NGF caused a 30% inhibition of ADP-ribosylation in the cellular homogenate, a 25% inhibition during serum-free cultivation, and a 50% inhibition in the presence of serum in the culture medium. NGF inhibited ADP-ribosylation of several proteins, including a protein with molecular weight of 40,000, probably of membrane origin. A possibility of the interrelation between NGF and cyclase system via receptor-dependent ADP-ribosylation of regulatory components of the adenylate cyclase was discussed.
Adenosine Diphosphate Ribose↗
[Structure of d(GT)n repeating sequences with parallel and antiparallel chains].
The ability of oligonucleotides 3'-d(GT)5pO(CH2)5Opd(GT)5-5' (anti[d(GT)]) and 3'-d(GT)5pO(CH2)6Opd(GT)5-3' (par[d(GT)]) to form hairpins and higher associates is studied. Optical methods of thermal denaturation and circular dichroism as well as the fluorescence of ethidium bromide and acridine orange bound to oligonucleotides were used. At room temperatures the formation of hairpin structure with parallel and antiparallel strands is possible. Thermodynamic parameters of par[d(GT)] and anti[d(GT)] are similar and equal to delta H = -15 kcal/mol, delta S = -50 cal/mol. deg. In the temperature range 3-10 degrees C par[d(GT)] and anti[d(GT)] form four-stranded structures with parallel chains, in which layers of four G-residues alternate with unpaired T-residues being bulged out easily. On comparison of occurrence of alternating (GT)n, (GC)n and (G)n sequences in genome it can be stated that (GT)n biological functions could be connected with conformational possibilities of the four-stranded parallel structures with unpaired T-residues.
Circular Dichroism↗
[Parallel DNA helices. Conformational analysis of regular poly(dG).poly(dC) helices with different variants of base binding].
We have performed a conformational analysis of DNA double helices with parallel directed backbone strands. The calculations were made for homopolymers poly(dG).poly(dC). All possible models of base binding were checked. By the potential energy optimization the dihedral angles and helices parameters of stable conformations of parallel double polynucleotides were calculated. The dependences of conformational energy on the base pair structure were studied. Possible structure of parallel helices with various nucleotide composition are discussed.
DNA↗
[System of distributed storage and analysis of genomic information].
A distributed computing system is developed to search and analyze genetic databases using parallel computing technologies. Queries are processed by a local network PC cluster. A universal task and data exchange format is developed for effective query processing. A multilevel hierarchic task batching procedure is elaborated to generate multiple subtasks and distribute them over cluster units under dynamic priority levels and with dynamic distribution of replicated source data subbases. Primary source data preparation and generation of annotation word indices are used to significantly reduce query processing time.
Databases, Genetic↗
[Parallel double DNA spiral. A conformational analysis of regular spirals of poly(dA).poly(dT) with different variations of joining bases].
We have performed a conformational analysis of DNA double helices poly(dA).poly(dT) with parallel directed backbone strands in heteronomic model frames. All possible models of base pairs and various mutual orientation of base pair and sugarphosphate backbones were checked. By the potential energy optimization the dihedral angles and helices parameters of stable conformations of parallel double polynucleotides were calculated. The dependences of conformational energy on the base pair structure were studied.
Base Composition↗
[Four-stranded DNA. Conformational analysis of regular spirals of poly(dT).poly(dA).poly(dA).poly(dT) with different base binding variations].
Conformational analysis of four stranded DNA helices poly(dT).poly(dA).poly(dA).poly(dT) with parallel arrangement of the identical sugar-phosphate chains connected by twofold symmetry has been performed. All possible models of symmetrical base binding were checked. By the potential energy optimization the dihedral angles and helices parameters of stable conformations of four stranded polynucleotides were calculated. The dependences of conformational energy on the base complex structure and mutual orientation of the poly(dA).and poly(dT) chains were studied. Possible biological functions of four stranded helices are discussed.
Base Sequence↗
[Parallel DNA double helices. II. Conformational analysis of regular helices having a second order axis of symmetry].
Conformational analysis of double helices of DNA with parallel arranged sugar-phosphate chains connected by twofold symmetry has been performed. Homopolymers poly(dA).poly(dA), poly(dC).poly(dC), poly(dG).poly(dG) and poly(dT).poly(dT) were studied. For each of the homopolymers all variants of H-bond pairing were checked. The maps of closing of sugar-phosphate backbone were previously computed. By the optimization of potential energy the dihedral angles and helix parameters of relatively stable conformations of parallel stranded polynucleotides were calculated. The dependence of conformational energy on the nucleic base character and the base pair type were studied. Two main conformational regions for favourable "parallel" helix of polynucleotides were found. The former of these two regions coincide with the region of typical conformational parameters of B-DNA. On an average the conformational energy of "parallel" DNA is close to the energy of canonic "antiparallel" B-DNA.
DNA↗
[Parallel double helix and tertiary structure of nucleic acids].
The thermal denaturation of four oligonucleotides, viz. 3'-d(AT)5pO(CH2)6Opd(AT)5-3' (parAT), 3'-d(AT)5pO(CH2)5Opd(AT)5-5' (antiAT), 3'-d(A)10pO(CH2)6Op(T)10-3' (parA-T) and 3'd(A)10pOX X (CH2)6Opd(T)10-5' (antiA-T) in 0.01 M phosphate buffer at pH 7 in presence 0.1, 0.25, 0.5 and 1.0 M NaCl have been studied. It was shown that at lower temperature (0-20 degrees C) all oligomeres exist as complexes of two (canonic duplex) or four (eight) molecules of oligonucleotides, but at higher temperature (30-70 degrees C)- as hairpins with parallel (parAT and parA-T) of antiparallel (antiAT and antiA-T) orientation of chains. Thermodinamic parameters of separated strands-hairpins and hairpins--"low temperature complexes" transition were computated from the melting curves [A260 (T)] by nonlinear regression. AntiA-T was shown by ethidium bromide binding to exist at low strength (0.01 M phosphate buffer without NaCl) as four-stranded complex from two antiparallel double stranded helices parallely oriented and bonded by satisfy hydrogen-bond of groups not involved in WC-pairing. At higher ionic strength the two of such tetramers was conjugated by hydrophobic interaction into octamers. We speculate that four-stranded complexes serves to bring together, and zipper up two antiparallel double stranded helices at replication of DNA, cross-over of gomologues chromosomes and other biochemically important processes.
Anticodon↗
[Parallel double helical DNA. 1. Evidence for the existence of a spiral A-T-paired base].
The dependence of UV and CD spectra of oligonucleotide 3'-d(ApTpApTpApTpApTpApTp)-O(CH2)6O-5'-(pApTpApTpApTpApTp ApT) (eicosamer) in aqueous solution at pH 7 in the presence of 0.5 M NaCl on temperature and concentration was studied. It was shown that the eicosamer in concentrations below 5.10(-4) M forms a parallel stranded hairpin. From the thermal denaturation profile the thermodynamic parameters of parallel hairpin formation were determined. The values of delta H0, delta S0 and Tm were -90 +/- 8 kJ/mol, -300 +/- 20 J.mol-1.K-1 and 40.5 degrees C, respectively. The CD spectra of the parallel helix differ from those of B-form DNA by reduction of extreme magnitude at approximately 265 nm and appearance of a negative effect at approximately 285 nm.
Base Composition↗
[Ribosomal proteins interacting with Phe-tRNAPhe during enzymatic binding with translating ribosome before and after the release of the elongation factor EF-Tu].
Proteins, directly interacting with tRNA in R- and A-sites of E. coli ribosome were determined by means of ultraviolet-induced RNA-protein cross-links. It is shown, that tRNAPhe in the R-site (upon enzymatic binding of the ternary complex Phe-tRNAPhe. X Tu X GMPPCP to ribosome) directly interact with factor Tu and ribosomal proteins S4, S5, S8 and L6, while in the A-site (upon binding of Phe-tRNAPhe X Tu X GTP, GTP hydrolysis, Tu release and transpeptidation)--with proteins S5, S10, L6, L16 and S13/S14/L27.
Escherichia coli↗
[Use of continuous stacking hybridization in sequencing using modified oligonucleotide matrices].
The opportunity of DNA sequencing by hybridization with oligonucleotide matrix (SHOM) with simultaneously use continuous stacking hybridization and gapped-matrices is considered. The analysis of reconstruction efficiency for various combinations matrices and l-oligonucleotides libraries were made. In most cases combine use of continuous stacking hybridization and gapped matrices permits to decrease the number of additional stacking hybridization twice without lost of efficiency.
Nucleic Acid Hybridization↗
[Effectiveness of sequencing using stacking hybridization on oligonucleotide matrices with varying length of immobilized oligonucleotides].
The opportunity of enhancing the sequencing efficiency by applying continuous stacking hybridization is considered. The approach is based on the increase of duplex length by continuous stacking hybridization of oligonucleotides added to solution (l-oligonucleotides) to oligonucleotides immobilized on matrix (L-oligonucleotides). An analysis of reconstruction efficiency for sequenced fragments up to length of 30000 nucleotides was made. Various combinations of L- and l-oligonucleotide length were considered. The results obtained enable one to evaluate the potentialities of the proposed method for various nucleotide matrices and the complexity of experiment. Use of continuous stacking hybridization permits a considerable increase of the length of sequenced DNA fragments. We offer the approach for resolving ambiguities in branching points, which occur because of long repeats. It is based on continuous stacking hybridization of several l-oligonucleotides which form a "chain" stabilized by mutual stacking interaction.
DNA↗
[Measurement of distances between DNA segments for increasing the effectiveness of sequencing using hybridization on an oligonucleotide matrix].
DNA sequencing by hybridization on oligonucleotide matrix (SHOM) makes use of a matrix of immobilized oligonucleotides. Yet the method is not directly applicable for sequencing of fragments with long monotonous repeats. Measurement of the distances between certain segments within the DNA fragment analyzed provide additional information for sequencing. This information can be obtained by digesting DNA with a set of restriction endonucleases, or by PCR with primers complementary to certain DNA regions, with subsequent measurement of the length of the resulting fragments in gel electrophoresis. Use of this additional information increases the reconstruction efficiency and in many cases solves the problem of repeating and monotonous segments within analyzed DNA fragment. The current work presents the use of this information and the estimated efficiency of its usage.
Algorithms↗
[A compressed form for presenting data to banks on the primary and spatial structure of biopolymers. Means for accessing compressed data banks].
Description of open CAN format (Compressed Amino acids and Nucleotides) is presented for storing genetic information in compressed form in data banks (DB). Data compression principles are demonstrated in detail on examples of EMBL DB (sequences of nucleotides), SWISSPROT DB (sequences of amino acids) and PDB DB (3D structures). A unified compressed data format provides a possibility to integrate EMBL, SWISSPROT, and PDB DB in one data bank. We are going to use this approach for integration of GENBANK and other similar DBs. One of the outcomes of the research is a library of data retrieval procedures for access to DB, providing developers of the application software packages with a uniform interface to DBs with biologically related data. The proposed scheme for data representation was recommended by the Expert Commission of the Informatics Section of the RSSIP "Human Genome" as a standard for distribution of data banks in Russia.
Amino Acid Sequence↗
[Reconstruction of a sequenced sequence using results of stacked hybridization with an oligonucleotide matrix].
The efficiency of additional rounds of continuous stacking hybridization in DNA sequence reconstruction by hybridization with oligonucleotide matrix (SHOM) is considered. At first, DNA is hybridized with a matrix of oligonucleotides of the length L. The overlapping of the tuples which have formed perfect duplexes with the DNA, on the one hand, has enabled us to reconstruct unambiguously a part of the sequence, and on the other hand, suggested a modified scheme for reconstructing the remaining part. Then the additional hybridizations should be carried out in the presence of shorter oligonucleotides of the length l, that are able to form perfect duplexes of the length L + l in continuous hybridization closely to matrix tuples. In this case the stability of a duplex consisting of l-tuples and long DNA is enhanced due to stacking interaction. The information obtained about the succession of L + l sites considerably increases the efficiency of reconstruction, which can eventually reach the efficiency of a matrix consisting of (L + l)-tuples. We propose here an algorithm for compiling such a set of l-tuples to be added that the number of additional hybridizations can be appreciably diminished. For an octanucleotide matrix and different sets of pentanucleotides to be used for continuous stacking hybridization, the length of unambiguously sequenced DNA undergoes a rise from 200 to some thousands bp.
Base Sequence↗