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I V Kutiavin

Publications and source records attributed to I V Kutiavin.

16 recordsLinked to original sources
PubMed1997

[Selective stabilization of AT-rich DNA duplexes by oligodeoxyribonucleotide conjugates with distamycin analogues].

Oligodeoxyribonucleotide conjugates with distamycin analogues containing up to five pyrrolecarboxamide moieties were synthesized. The stability of duplexes formed by these conjugates was shown to depend directly upon the number of pyrrolecarboxamide moieties in the ligand molecule. For the duplexes formed by octaadenylate and octathymidilate conjugates with the distamycin pentapyrrole analogue, stability was demonstrated to be achieved by either one or two ligand molecules; however, duplexes containing two ligand molecules are more stable.

DNA↗
PubMed1995

[Effect of the intercalating dyes ethidium and phenazine, covalently jointed to the 5'- or 3'-end of the pentanucleotide d(pGAAAG), on the thermodynamics of complementary and cooperative interaction].

Thermal stability was studied and thermodynamic parameters of complex formation were calculated for pentanucleotide complexes [formula: see text] and corresponding complexes of pentanucleotide derivatives carrying at their 5'- or 3'-ends covalently bound residues of intercalating dyes: N-(2-hydroxyethyl)-phenazine (Phn) or 2-N-(3-aminopropionyl)-ethidium. Pentanucleotide derivatives were shown to form more stable complementary complexes. The best stabilizing effect was observed when the dye was oriented towards the long single-stranded fragment of tetradecanucleotide, melting temperature of the complexes being by 22.5 (Phn) and 31.2 degrees C (Etd) greater than that of unmodified complexes in the case of 5'-derivatives and by 21.6 (Phn) and 27.2 degrees C (Etd) for 3'-derivatives. Cooperativity constant of pentanucleotide derivatives in "tandem" complexes IV-VII was higher than that of unmodified pentanucleotide. For complex IV at 37 degrees C the constant values were 33 (unmodified), 35 (5'Phn), 57 (3'Phn), 190 (5'Etd), 100 (3'Etd). With n = 3 in complex VII cooperativity constants approached 1 in any case.

Base Sequence↗
PubMed1992

[Site-directed chemical restriction of a single-stranded DNA fragment by an alkylating derivative of the tetranucleotide d(pApGpCpA) in the presence of tetranucleotide effectors].

Alkylation of a single-stranded DNA 302-mer by a 5'-O-phosphoryl-[4-(N-2-chloroethyl-N-methylamino)benzyl]amide derivative of the tetradeoxyribonucleotide d(pApGpCpA) in the presence of 3',5'-di-N-(2-hydroxyethyl) phenazinium derivatives of tetranucleotides as effectors led to specific chemical cleavage of the target at the guanosine residues of the sites ... pTpGppT. The reagent can be selectively addressed to one of three alkylation sites with the aid of a pair of tetranucleotide effectors flanking the chemically reactive tetranucleotide in the complex with the target DNA. The yield of the cleavage depends on the concentration of both the reagent and effectors, and can be enhanced, if a chain of two or more effectors from each side of the reagent is used. In this case, 3',5'-di-Phn-tetranucleotide effectors are to immediately flank the reagent.

Alkylation↗
PubMed1990

[Study of the spatial structure of the duplex d(pTGTTTGGC) d(pCCAAAC)A in aqueous solution by methods of uni- and two-dimensional (1)H-NMR spectroscopy and organic molecular mechanics].

Structure of the complementary complex d(pTGTTTGGC) d(pCCAAAC)A in the aqueous solution has been investigated by one- and two-dimensional 1H NMR spectroscopy. The resonances of nonexchangeable protons of bases as well as methyl and deoxyribose 1', 2'a, 2'b, 3' and 4' protons have been assigned by means of two-dimensional J-correlated spectroscopy (COSY) and two-dimensional nuclear Overhauser enhancement spectroscopy (NOESY). Using one-dimensional NOE measurements, 62 interproton distances (intranucleotide: (H6/H8)i--(H1')t, (H6/H8)i--(H2'a)i, (H1')i--(H2'a)i, (H1')i--(H2'b)i; internucleotide: (H6/H8)i--(H1')i-1, (H6/H8)i--(H2'a)i-1, (H6/H8)i--(H2'b)i-1, (H5/CH3)i--(H6/H8)i-1, (H5/CH3)i--(H2'a/H2'b)i-1) have been determined for nearest-neighbour protons. Spin-coupling constant values for some sugar protons have been obtained from COSY spectra. The restrained molecular mechanics calculations have yielded the possible solution structures of duplex fitting the experimental set of interproton distances and coupling constants.

Base Sequence↗
PubMed1990

[Effective selective modification of a single-stranded fragment of DNA with alkylating derivatives of short oligodeoxyribonucleotides in the presence of reaction effectors N-(2-hydroxyethyl)phenazine derivatives of oligodeoxyribonucleotides].

Tri-, tetra-, penta- and hexanucleotides bearing a reactive 4-(N-methylamino-N-2-chloroethyl)benzylamide group can effectively and selectively modify a single-stranded DNA fragment (302 nucleotides) in the presence of effectors, N-(2-hydroxyethyl)phenazinium derivatives of oligonucleotides complementary to DNA sequences adjacent to the binding site of the reagent. The reagents investigated modify not only single-stranded but also secondary-structured DNA regions. The modification extent depends on the length of oligonucleotide parts of the reagent and effector. A gap between the two stretches associated with the target DNA prevents the effector from functioning. The substitution of an octanucleotide effector by two tetranucleotide ones only slightly reduces the modification extent with a hexanucleotide reagent. A very efficient and specific modification can be achieved by using two effectors flanking the reactive oligonucleotide derivative. The approach leads to the modification extent of up to 89% with a hexanucleotide reagent.

Alkylating Agents↗
PubMed1990

[Photomodification of nucleic acids by N-(2-hydroxyethyl)phenazine derivatives of oligonucleotides].

Photomodification of a 302-membered single-stranded DNA fragment by 5'-mono- and 3',5'-di-N-(2-oxyethyl)phenazine (Phn) derivatives of oligonucleotides has been investigated. Under strong laser irradiation (lambda 532 nm; power density 2,5 GV/cm2, irradiation dose 30 J) the DNA fragment in the presence of Phn-reagents was significantly destructed (up to 70-95%). The level of complementary addressed modification (24-51%) is a direct function of the length of oligonucleotide address of the photoreagent and the amount of Phn residues, stabilizing the complementary complex. The character of the nonaddressed modification is close to the statistic one, although for a number of photoreagents a rather efficient nonspecific modification of 5'-terminal sequence of target DNA has been detected. Of interest also is an unusually broad positional direction of the DNA fragment photomodification in the area of perfect complementary coupling of 5'-Phn-reagents.

Base Sequence↗
PubMed1987

[Modification of nucleic acids in stabilized complementary complexes. II. Effectiveness and direction of alkylation of dodecadeoxyribonucleotide d(pA-A-C-C-T-G-T-T-T-G-G-C) with 4-(N-2-chloroethyl-N-methylamino)benzylidene derivative of the complementary heptanucleotide d(pC-C-A-A-A-C)-A containing a N-(2-hydroxyethyl)phenazinium residue at the 5'-end].

Modification of dodecadeoxyribonucleotide d(pA-A-C-C-T-G-T-T-T-G-G-C) (I) with a heptanucleotide 4-(N-2-chloroethyl-N-methylamino)benzylidene (RCI) derivative d(pC-C-A-A-A-C) ARCI (II) and with similar reagent (III) bearing an additional 5'-terminal N-(2-hydroxyethyl)phenazinium residue (Phn) has been unvestigated. Both reagents (II) and (III) alkylated dodecanucleotide (I) mainly at the 5'-terminal phosphate, Phn residue not affecting specificity of the alkylation. Stabilization of the complementary complex target oligonucleotide-oligonucleotide derivative by the Phn group resulted in substantial increase of efficiency and rate of the intracomplex alkylation of the dodecanucleotide.

Alkylation↗
PubMed1987

[Effectiveness of the modification of a single-stranded DNA fragment by alkylating derivatives of oligonucleotides].

Modification of a single-stranded DNA fragment 303 nucleotides long with addressed reagents d(pTGACCCTCTTCCC) A greater than CHRCl (I), d(pACCCTCTTCCC) A greater than CHRCl (II), d(CCTCTTCCC) A greater than CHRCl (III) and d(TCTTCCC) A greater than CHRCl (IV) complementary to the sequence 261-274 has been studied. It was shown that not only G258 residue, located near to the above sequence, but also G179 residue is modified. The latter can be explained by the vicinity of G179 and the alkylating group in the three-dimensional structure of the complex. Some modification of fragment 19-24 was observed due to non-complementary binding of the reagent. Association constants of the reagents (I)-(IV) with 261-274 sequence of the fragment were calculated using the dependence of the modification extent of G258 and G179 on the reagent concentration. The constants at 25 and 35 degrees C were found to be 260 and 31 (I), 0,5 and 2 (II), 0,46 and 0,13 (III), 0,0020 and 0,0023 (IV) microM-1.

Alkylating Agents↗
PubMed1986

Complementary addressed modification and cleavage of a single stranded DNA fragment with alkylating oligonucleotide derivatives.

A single stranded DNA fragment was modified with alkylating derivatives of oligonucleotides complementary to a certain nucleotide sequences in the fragment. The derivatives carried aromatic 2-chloroethylamino groups at their 3'- or 5'-terminal nucleotide residues. Some of the derivatives carried both alkylating group and intercalating phenazine group which stabilized complementary complexes. It was found that these oligonucleotide derivatives modify the DNA fragment in a specific way near the target complementary nucleotide sequences, and the DNA fragment can be cleaved at the alkylated nucleotides positions. Alkylating derivatives carrying phenazine groups were found to be the most efficient in reaction with the DNA fragment.

Alkylation↗
PubMed1986

[Affinity modification of E. coli RNA-polymerase in a complex with the promoter by phosphorylating derivatives of primer oligonucleotides].

Oligonucleotides 2 to 7 nucleotide residues long, complementary to the codogenic strand of T7 promoter A2, have been synthesized; all of them contained a ribo-unit at the 3'-end. They were converted into 5'-(N-methyl)phosphoimidazolides, and the affinity reagents obtained were allowed to bind covalently to RNA polymerase in the presence of a promoter. Some of the nucleotide residues covalently attached occupied proper positions relative to the active centre of the phosphodiester bond synthesis and on addition of [alpha-32P]UTP were elongated, so that highly selective affinity labelling occurred. With oligonucleotides of various lengths, different distribution of the label between beta, beta' and sigma subunits of RNA polymerase took place. Most efficient was labelling of beta-subunit by the residue--pCpGpCpU, and of sigma-subunit by the residue--pApApApTp-CpGpCpU (p--radioactive phosphorus atom). In both cases, the amino acid residues labelled were histidines.

Binding Sites↗
PubMedDate not supplied

[Interaction of alkylating oligonucleotide derivatives with mammalian cells. A study of the uptake mechanism of derivative cells].

Interaction of alkylating deoxyribooligonucleotide derivatives, bearing 4-[(N-2-chloroethyl-N-methyl)amino]benzylamine residues at their 5'-terminal phosphates, with mouse fibroblasts L929 and with ascite carcinoma cells Krebs 2 has been investigated. It was found, that the derivatives are taken up by the cells according to the endocytosis mechanism. At high concentration of the oligonucleotide derivatives in the cultivation medium (greater than 10 microM), the fluid phase endocytosis is the major pathway of uptake; binding of the derivatives by the cells is partially reversible and their intracellular mean concentration approaches 1/20 of their extracellular concentration. At low concentration of the oligonucleotide derivatives, the predominant mechanism is the more efficient adsorption endocytosis; at concentration of the derivatives less than 0.5 microM, their mean intracellular concentration exceeds that in the culture medium. Stability of the oligonucleotide derivatives in cells depends on their nucleotide composition. Their nucleolytic degradation rate is low enough to allow them to react with cellular biopolymers.

Alkylating Agents↗
PubMedDate not supplied

[Selective alkylation of G24 residue in tRNAPhe].

Alkylation of E. coli tRNAPhe with 4-(N-2-chloroethyl-N-methylamino) benzyl-5'-phosphamide of oligonucleotide d(pAACCA) was studied. G24 residue located near the sequence C17GGDA21 partially complementary to the oligonucleotide moiety of the reagent was shown to be alkylated. Oligonucleotide d(pAACCA) inhibited the alkylation. Association constant of oligonucleotide derivative with tRNAPhe (10(3) M-1) was evaluated from the dependence of the extent of tRNA modification on the concentration of the reagent. The reported method for selective alkylation of tRNA may be used for preparing photoaffinity derivatives of tRNA bearing an arylazidogroups in desired position.

Alkylation↗