Biomedical subjects

Iu P Lysov

Publications and source records attributed to Iu P Lysov.

29 records · Page 2Linked to original sources

PubMedDate not supplied

[Conformation of dinucleoside phosphates: the conformation encoding hypothesis].

The temperature dependence of the spin-lattice relaxation rate of nucleic bases protones and HI' of ApA, ApC, CpA and CpC (D2O, pH 7) were measured. The possible closed conformers of these dinucleoside phosphates (DNP) were computed by atom-atom potential method. On the basis of conformational calculation and experimental data the composition of closed state was determined. Besides the right-handed "canonic" conformers, the "non-canonic" right- and left-handed conformers were shown to be present in the solution of all DNP studied. It is important to note that, "canonic" conformers of DNP studied being equally probable, the possibility of the realization of "non-canonic" conformers is determined by the nucleotide sequence. It may be expected that different nucleotide sequences have unique "non-canonic" conformations. That type of dependence of the spatial organization of polynucleotides on its nucleotide sequence we call "the conformational encoding".

Adenosine↗

PubMedDate not supplied

[Eight types of stacking interaction in dinucleotides. Conformational analysis of ApA, ApC, CpA, CpC, GpG].

On the basis of general stereochemical considerations the classification of the stacking state of dinucleoside phosphate (DNP) including eight types of stacks of nucleic bases has been suggested. With the use of the algorithm, which makes possible determination of the backbone conformation for the given nucleic bases arrangement, the stacking conformes of DNP were analysed by atom-atom potential method. For all compounds different types of stacking conformes were obtained with energy values lower than that for the unstacking state. It follows from the results of calculations that for description of the conformational situation of DNP in solution the "non-canonical" conformers should be born in mind. In particular the forms having different sugar conformations in Np- and in pN-parts of the dimers are of interest. The effect of choice of the atom-atom potential functions on optimal conformation of DNP is discussed. For single-stranded RNA several regular and non-regular structures are proposed.

Adenine Nucleotides↗

PubMedDate not supplied

[Study of the conformational situation in an aqueous solution of dinucleoside phosphates using proton spin lattice relaxation].

With the use of experimentally measured spin-lattice relaxation rates of H(5), H(6), H(2), H(8) and H(1') the analysis of the conformational situation in aqueous solution of CpC, CpA, ApC and ApA has been carried out. In all cases, the close state is shown to be described by the equilibrium of right- and left-handed forms. The right-handed forms are favourable for all DNP studied and are related to the "canonical" Pba type. On the contrary, the possibility of realization of one or the other noncanonical forms (these are mainly left-handed conformers) is determined strictly by nucleotide sequences. The noncanonical conformers for CpC and CpA are Mbb forms, in which both monomeric units are characterized by anti-conformation, and the base of the 3'-end is turned 180 degrees around the glycosidic bond as compared to the canonical form. The forms of Mab type are possible for ApC. In this case, the purine monomer exists in syn-, but the pyrimidine monomer--in anti-conformation. Both bases are turned to 180 degrees. Finally, in the case of ApA, the forms of Mba type with high-anti-conformation of both monomers are realized. The conformational behaviour of oligonucleotides and the possible biological role of noncanonical conformations are discussed taking into consideration the results obtained.

Chemical Phenomena↗

PubMedDate not supplied

[Oligonucleotides and their analogs. III. Circular dichroism and conformation of analogs cytidylyl-(3'--5')-adenosine].

The CD spectra of 11 analogues of CpA, containing modified carbohydrate residue, achiral hydroxyalkyl- and optically active hydroxymethylene substituents have been studied. On the basis of the dependence of the CD spectra on temperature, the constants of U in equilibrium S equilibria and thermodynamic parameters in the approximation of dilute solution was calculated. The calculation was carried out on a computer in the terms of a two-state model. The influence of the modifications of the carbohydrate on the stability of the S-conformation is discussed. The CD spectra of S-conformation was calculated and the assumption of the origin of oligonucleotides CD is considered. Possible mechanisms of how water participates in the stabilization of the S-conformation of dinucleoside phosphate are analyzed.

Adenosine↗

PubMedDate not supplied

[Conformational possibilities of the regular single-stranded polyribonucleotides].

It was shown that in case of C(3')-endo pucker of ribose two left and two right types of helices are possible from the energetical point of view. However, such helices with C(2')-endo conformation of ribose are extremely unfavourable due to the steric hindrance caused by 2'-OH group. In this case the low energy structures have bases outside and phosphate groups inside the helix. The right and the left poly(A) helices have similar energy values, the barrier of transition between them being rather small. Biregular structures, i.e. the helices on which dinucleotide serves as the repeating unit, were also considered. These forms proved to be energetically optimal in the case of poly(A-C).

Models, Molecular↗

PubMedDate not supplied

[Nuclear magnetic resonance study of the conformational situation in an aqueous solution of dinucleoside phosphates].

The strategy of quantitative study of conformational situation in aqueous solutions of dinucleoside phosphates (DNP) has been proposed. It includes the following steps: (1) conformational calculation of stacking conformers (SC) of DNP; (2) measurement of thermodynamic parameters of conformational equililbrium; (3) determination of extensive parameters of stacking state (SS) on the basis of experimental data and thermodynamic parameters; (4) computation of extensive parameters of SC on the basis of the calculated geometry of SC and theoretical concepts of experimental method; (5) comparison of experimental parameters of SS with the calculated ones of SC to establish the SC participating in the equilibrium as well as its relative weights. This strategy was exemplified by ApA, ApC, CpA and CpC. The chemical shifts, spin-spin coupling constants and spin-lattice relaxation rates of DNP protons were used. The predominant SC was found to be related to Pba type with a large twirl angle (45-54 degrees) and almost parallel base planes. For all DNP the presence in equilibrium of left-handed forms was typical. These were Mab forms for ApA, Mbb forms for CpC and CpA, Mbb and Mab forms for ApC. About 10% of SS of ApA and CpA were presented by SC with trans-conformation of C(4')-C(5') bond of oN-part. The SC with C(3')-endo, C(3')-endo combination of ribose conformations were basic for ApA, ApC and CpA, and the only possible for CpC. In case of ApA, ApC and CpA the conformers with C(3')-endo, C(2')-endo sugar combination were presented.

Chemical Phenomena↗

PubMedDate not supplied

[Circular dichroism study of the conformational situation in an aqueous solution of adenylyl-(3'--5')-adenosine and its conformationally mobile analogs].

The temperature dependence of CD spectra of ApA, its (2'--5')-isomer, and a number of free conformational analogues, in which the ribose ring was replaced by acyclic hydroxyalkyl substituents, has been studied. The thermodynamic parameters of conformational equilibrium were determined. The role of separate functional groups and parts of DNP molecules in the organization and stabilization of the close state as well as the role of water in the stabilization of the one stranded helix of RNA is discussed.

Adenosine Monophosphate↗

PubMedDate not supplied

[Design of de novo specific DNA-binding peptides, using the motif beta-chain-turn-beta-chain for recognizing a nucleotide sequence in DNA].

De novo design and synthesis by a solid phase technique of linear and cyclic 26-residues peptides are reported. The peptides use beta-strand-turn-beta -strand motif for sequence recognition on DNA. Amino acid sequences in the two peptides are identical, but the structure of the cyclic peptide is constrained by S-S bridge between two cysteine residues. A 28-residue peptide containing at the N-terminus a copper-chelating peptide Gly-Gly-His is also synthesized which can be used as a potential DNA-cleaving reagent. Binding of these peptides to various natural and synthetic DNAs and DNA fragment with a known base pair sequence has been studied by CD spectroscopy, fluorescence methods and DNAse I footprinting technique. By means of CD spectroscopy it is shown that 26-residue linear and cyclic peptides are partially in disordered and beta-conformations in aqueous solution in absence and in presence of 20% trifluoroethanol (TFE), but assume partially an alpha-helix conformation in the presence of 50% TFE. It is shown that linear and cyclic peptides bind to DNA. The binding approaches saturation level when one peptide molecule is bound approximately per three or four DNA base pairs. We found that antibiotic distamycin A, binding in the minor DNA groove, competes effectively with the 26-residue linear and cyclic peptides for binding to poly(dA).poly (dT). According to the CD spectroscopy data the linear and cyclic peptides undergo conformation changes upon binding to DNA, whereas the DNA structure is not markedly altered. Difference CD spectra obtained by subtracting the spectrum of the free DNA from the spectrum of the peptide-DNA mixture differ from the spectrum of the free peptide. The shapes of difference CD spectra are consistent with a conformation transition from a disordered conformation into a beta-like conformation upon binding of peptide to DNA. DNAase I footprinting diagrams show that there is a specific protection by linear and cyclic peptides of the nucleotide sequences on two ends of operators OR1, OR2 and OR3 and pseudooperators within the cro gene of 434 phage.

Amino Acid Sequence↗

PubMedDate not supplied

[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↗

PubMedDate not supplied

[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↗

PubMedDate not supplied

[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↗