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M K Kukhanova

Publications and source records attributed to M K Kukhanova.

At least 19 recordsLinked to original sources
PubMed2005

Structural-functional relationships between terminal deoxynucleotidyltransferase and 5'-triphosphates of nucleoside analogs.

Substrate properties of nucleoside 5'-triphosphate (NTP) analogs, namely, 5'-triphosphates of L- and D-arabinonucleosides (D-FIAUTP, D-FMAUTP, and L-FMAUTP), D- and L-enantiomers of ddCTP analogs (D-ddCTP, L-ddCTP, D-FOddCTP, L-OddCTP, and L-SddCTP), and acyclic guanosine analogs (acyclovir and penciclovir) towards terminal deoxynucleotidyltransferase (TdT, EC 2.7.7.31) were studied. TdT can polymerize 5'-triphosphates of arabinonucleoside analogs (D-FIAUTP and D-FMAUTP). In contrast, L-FMAUTP is not recognized by TdT as a substrate. Kinetic parameters of D- and L-enantiomers of ddCTP analogs and 5'-triphosphates of acyclic nucleosides were evaluated. It is shown that stereospecificity of dNTP analogs and structure of the furanose residue play crucial roles in the interaction with TdT:L-enantiomers are much less potent as substrates compared to their D-counterparts. 5'-Triphosphates of acyclovir (ACVTP) and penciclovir (PCVTP) are about two orders of magnitude less effective as substrates than nucleosides bearing furanose residues, with PCVTP being a better substrate than ACVTP. It can be assumed that the hydroxyl group of PCVTP mimics the 3'-hydroxyl group of the ribose residue and plays an important role in the interaction with TdT.

Catalysis↗
PubMed1996

Modified substrates of DNA polymerases and design of antivirals.

The results obtained in our laboratory on investigating of substrate properties of a large number of compounds towards different DNA polymerases have been summarized. On the basis of systematic analysis a directed synthesis of nucleotides with antiviral properties was performed.

Antiviral Agents↗
PubMed1995

New modified substrates for discriminating between human DNA polymerases alpha and epsilon.

Two 2'-deoxynucleoside 5'-alpha-methylenephosphonyl-beta, gamma-diphosphates were synthesized. They were incorporated into the DNA chain by DNA polymerase alpha from human placenta. Meanwhile, they were not recognized by DNA polymerase epsilon and beta of the same origin as well as by reverse transcriptases from human immunodeficiency virus and avian myeloblastosis virus.

Avian Myeloblastosis Virus↗
PubMed1993

Modified nucleoside 5'-triphosphates containing 2',3'-fused three-membered rings as substrates for different DNA polymerases.

5'-Triphosphates of 1-(2',3'-epithio-2',3'-dideoxy-beta-D- lyxofuranosyl)thymine, 1-(2',3'-epithio-2',3'-dideoxy-beta-D-ribofuranosyl)thymine and 2',3'-lyxoanhydrothymidine have been shown to be termination substrates for human immunodeficiency virus (HIV) and avian myeloblastosis virus (AMV) reverse transcriptases as well as DNA polymerase I from E. coli and DNA polymerase beta from rat liver. At the same time they do not terminate DNA synthesis catalysed by DNA polymerase epsilon from human placenta. Km values of ltTTP, rtTTP and laTTP incorporation into the DNA chain during catalysis by AMV reverse transcriptase agree closely with each other being 1.5-2.5 times higher than Km value for dTTP. Furthermore, Vmax values for modified substrates are only 2-3 times lower than Vmax for dTTP. The evidence favours the hypothesis of high affinity of modified nucleotides with a flattened furanosyl ring for DNA polymerase active sites.

Animals↗
PubMed1992

3'-C-branched 2'-deoxy-5-methyluridines: synthesis, enzyme inhibition, and antiviral properties.

A synthesis scheme for 3'-C-methyl-2'-deoxynucleosides and 3'-C-methylidene-2',3'-dideoxy-5-methyluridine has been proposed with 2-deoxyribose as the starting material. Methyl 5-O-benzoyl-2-deoxyribofuranose was oxidized and the mixture of the 3'-keto derivatives was separated into the alpha- and beta-anomers. The beta-keto derivative was converted by reaction with MeMgBr, and after reaction with thymine and subsequent deprotection 1-(3'-C-methyl-2'-alpha-deoxy-alpha-D-threo-pentofuranosyl)thymine and its beta-anomer were obtained. The same reactions with the alpha-keto sugar gave 1-(3'-C-methyl-2'-deoxy-alpha-D-erythro-pentofuranosyl)thymine and its beta-anomer. 1-(5-O-Benzoyl-3'-C-methyl-2'-deoxy-alpha-D-threo-pentofuranosyl)thymine was converted to a mixture of 3'-C-methylidene-2',3'-dideoxy-5-methyluridine and 3'-C-methyl-2',3'-dideoxy-2',3'-didehydro-5-methyluridine, which were separated. The stereoselectivity of the Grignard reagent's attachment to 2-deoxyfuranose 3-ulosides has been ruled by the substitute configuration at Cl. Also, the effect of the hydroxyl or OBz group configuration at C3 on the condensation stereoselectivity of 3-C-methyl-2-deoxyfuranosides with silylated thymine has been studied. The structure of the obtained compounds was proved by 1H NMR UV, 13C NMR, and CD spectroscopy, as well as elemental (C, H, N) analysis. The C2'-endo-C1'-exo conformation, the anti conformation of thymine in relation to the glycosidic bond, and the gauche+conformation in relation to the C4'-C5' bond are characteristic for the 3'-C-methyl-2'-deoxythymidine structure in the crystals. 3'-C-Methyl-2'-deoxythymidine 5'-triphosphate was synthesized and proved to be a competitive inhibitor, with respect to dTTP, of a number of DNA polymerases, including the reverse transcriptases of human immunodeficiency virus type 1 (HIV-1) and avian myeloblastosis virus (AMV). None of the DNA polymerases examined were able to incorporate this compound into the growing DNA chain. In contrast, 3'-C-methylidene-2',3'-dideoxy-5-methyluridine 5'-triphosphate was found to be incorporated at the 3'-end of the DNA chain by HIV-1 reverse transcriptase, albeit with very low efficiency. 3'-C-Methyl-2'-deoxy-5-methyluridine did not suppress HIV-1 replication in MT-4 cells at 500 microM while its 5'-phosphite derivative exhibited modest anti-HIV-1 activity.

Antiviral Agents↗
PubMed1992

Formation of phosphonester bonds catalyzed by DNA polymerase.

3'-Fluoro-2',3'-dideoxythymidine 5'-(alpha-methylphosphonyl)-beta,gamma- diphosphate and 2'-deoxythymidine-5'-(alpha-methylphosphonyl)-beta, gamma- diphosphate have been synthesized. Both compounds are incorporated into DNA chains during catalysis by reverse transcriptases of human immunodeficiency (HIV) and avian myeloblastosis (AMV) viruses, DNA polymerase beta from rat liver, terminal deoxynucleotidyl transferase from calf thymus and (at a very low rate) is by E. coli DNA polymerase I, Klenow fragment. The first compound is a termination substrate while the second is capable of multiple incorporation into the DNA chains. For instance, reverse transcriptase catalysis resulted in the appearance of 8 residues of second compound. DNA polymerases alpha and epsilon from human placenta incorporated none of the above compounds into DNA chains, although an inhibition of DNA synthesis by both compounds was observed with all enzymes mentioned. The 3'----5'-exonuclease activity of DNA polymerase I, Klenow fragment, hydrolyzed DNA fragments containing phosphonomethyl internucleoside groups, while such DNA fragments were resistant to the E. coli exonuclease III.

Avian Myeloblastosis Virus↗
PubMed1990

[Comparative inhibitory analysis of DNA biosynthesis catalyzed by retrovirus reverse transcriptase].

Comparative study of DNA biosynthesis inhibition, catalyzed by avian myeloblastose virus (AMV) reverse transcriptase (RT), human immunodeficiency virus (HIV) recombinant and native RT, has been performed. 3'-Azido-2',3'-dideoxythymidine 5'-triphosphate (AzTTP); 3'-azido-2',3'-dideoxythymidine 5'-methylenephosphonate-diphosphate: 3'-azido-2',3'-dideoxythymidine 5'-phosphate-phosponoacetate; 3'-azido-2',3'-dideoxythymidine 5'-phosphate-dibromomethylenephosphonate; 2',3'-O-isopropylidenecytidine 5'-methylenephosphonate-diphosphate (rC-IP-MPDP) were used as inhibitors. AzTTP proved to by the most active inhibitor (its activity against HIV RT is higher than against AMV RT), although not selective as the phosphonates; only rC-iP-MPDP has low selectivity.

Avian Myeloblastosis Virus↗
PubMed1987

[Ability of 3'-substituted nucleoside phosphothioates to terminate DNA synthesis catalyzed by various DNA-polymerases].

Ability of some new substrates containing the 5'-alpha-thiotriphosphate residue to terminate the DNA synthesis catalyzed by several DNA polymerases has been investigated. The cell-free test system contained the M13mp10 phage single-stranded DNA and a synthetic oligonucleotide primer. Reverse transcriptase from avian myeloblastosis virus catalyzed termination of DNA synthesis by 3'-azido-3'-fluoro- and 3'-amino-2',3'-dideoxythymidine-5'-(alpha-thio)triphosphates, whereas rat liver DNA polymerase beta and E. coli DNA polymerase I (Klenow's fragment) utilized only the second and the third compounds, and calf thymus DNA polymerase alpha failed to utilize any of the substrates. Low specificity of reverse transcriptase to different moieties of the substrate molecules is discussed.

Animals↗
PubMed1987

Some aspects of DNA polymerase functioning.

The group of DNA polymerases was studied using some new nucleoside 5'-triphosphate analogs with termination substrate properties. Among DNA polymerases tested the least specific appeared reverse transcriptases of retroviruses and the most specific were DNA polymerases alpha type from high eucaryotes including mammalians.

Animals↗
PubMed1987

[A new terminator of DNA biosynthesis--possible conformation analog of the substrate in a DNA-synthesizing complex].

2',3'-Dideoxy-2',3'-dehydrothymidine 5'-triphosphate (dddTTP) reveals the termination substrate properties in the DNA synthesis catalyzed by E. coli polymerase I (Klenow fragment), rat liver DNA polymerase beta, calf thymus terminal deoxynucleotidyl transferase, and reverse transcriptase of avian myeloblastosis virus but does not affect calf thymus DNA polymerase alpha. For DNA polymerase I, dddTTP by an order of magnitude is more effective than any known termination substrate. It is supposed that dddTTP models the conformational state of the substrate's carbohydrate moiety in the complex DNA polymerase + template-primer.

Catalysis↗
PubMed1987

[Incorporation, into the DNA, chain of a fluorescent derivative of 2-deoxyuridylic acid during catalysis of synthesis by DNA-polymerase A].

A 2'-deoxyuridine 5'-triphosphate analogue with a dansyl (5-dimethylaminonaphtalene 1-sulphonyl) residue in the 5-position of uracyl has been synthesised. This compound substitutes dTTP in the DNA synthesis catalyzed by Klenow's fragment of E. coli DNA polymerase I on the M13mp10 phage DNA as template with synthetic 14-member primer. When the synthesis is terminated by four termination substrates, structure of the synthesised DNA chain can be read. It demonstrates in principle possibility of determination of DNA sequence by means of fluorescence.

Base Sequence↗
PubMed1986

Nucleoside 5'-triphosphates modified at sugar residues as substrates for calf thymus terminal deoxynucleotidyl transferase and for AMV reverse transcriptase.

Terminal deoxynucleotidyl transferase from calf thymus and RNA-directed DNA polymerase (reverse transcriptase) from the avian myeloblastosis virus catalyze the incorporation of 3'-amino-2',3'-dideoxynucleoside 5'-triphosphates, as well as some of their 3'-derivatives, 3'-amino-3'-deoxyarabinonucleoside 5'-triphosphates and some other nucleoside 5'-triphosphates modified at sugar residues. After incorporation of the appropriate 5'-mononucleotide residue into the DNA, further chain elongation is blocked. This finding opens up a possibility for selective inhibition of DNA synthesis catalyzed by a certain enzyme.

Animals↗
PubMed1986

Nucleoside 5'-triphosphates with modified sugars as substrates for DNA polymerases.

A number of nucleoside 5'-triphosphate analogs were tested with Escherichia coli DNA polymerase I and Klenow fragment of the enzyme, bacteriophage T4 DNA polymerase and calf thymus DNA polymerase alpha. It was shown that 3'-amino-2',3'-dideoxynucleoside 5'-triphosphates as well as a number of 3'-derivatives of dTTP(3'NH2) are able to terminate DNA synthesis catalyzed by each enzyme if the reaction is performed in the absence of natural substrates. ddNTP and dNTP(3'F) were found to be inactive with DNA polymerase alpha only, but araNTP(3'NH2) was inactive with E. coli DNA polymerase I. dTTP(3'N3), dGTP(3'N'3), dCTP(3'N3), araNTP(3'N3) and (alpha-thio)dTTP(3'F) were unable to inhibit any of the above-mentioned DNA polymerases, in contrast to reverse transcriptase, accessible to the most nucleotide analogs tested.

DNA↗
PubMed1985

[DNA polymerase beta from the rat liver. Isolation, properties and inhibitory analysis of a homogeneous preparation].

A simple and reproducible purification procedure of homogeneous DNA polymerase beta from rat liver is developed, including sedimentation and saline extraction of rat liver chromatin, chromatography of the extract on DEAE-cellulose, phosphocellulose, Gel Blue A, and DNA sepharose. The purified enzyme isolated with the 8.4% yield proved to be a homogeneous protein with m.w. 38-40 kDa, specific activity 31 units/g, pI 8.6-8.9. Incorporation of [3H]TTP into activated DNA catalysed by DNA polymerase beta was strongly inhibited by dNTP (3'NH2), ddTTP, dNTP (3'F) and slightly inhibited by aCTP and aNTP (3'NH2).

Animals↗
PubMed1984

2',3'-Dideoxy-3' aminonucleoside 5'-triphosphates are the terminators of DNA synthesis catalyzed by DNA polymerases.

It is shown that 2',3'-dideoxy-3'-aminonucleoside 5'-triphosphates with adenine, guanine, cytosine and thymine bases are effective inhibitors of DNA polymerase I, calf thymus DNA polymerase alpha and rat liver DNA polymerase beta. The effect of the above-mentioned compounds is markedly higher than corresponding action of the well-known DNA synthesis inhibitors arabinonucleoside 5'-triphosphates and 2',3'-dideoxynucleoside 5'-triphosphates. 2',3'-dideoxy-3'-aminonucleoside 5'-monophosphate residues incorporate into the 3'-terminus of the primer and terminate the DNA chain elongation. The possibility of using 2',3'-dideoxy-3'-aminonucleoside 5'-triphosphates as terminators for DNA sequencing by the polymerization method is demonstrated.

Animals↗
PubMed1983

Cooperative effects in the peptidyltransferase center of Escherichia coli ribosomes.

We have measured the binding isotherms of C--A--C--C--A(3'NH)-[14C]Phe to the 70S ribosomes and 50S subunits of Escherichia coli and proposed a theoretical model for adsorption when cooperative interaction occurs between ligands that are adsorbed on ribosomes. Analysis of the experimental binding isotherms leads to the following conclusions. A ribosome (or subunit) binds two C--A--C--C--A(3'NH)-Phe molecules. The binding of C--A--C--C--A(3'NH)-Phe to a ribosome (or subunit) is a cooperative process, characterized by a cooperativity coefficient tau = 40 +/- 5 or more. The binding of C--A--C--C--A(3'NH)-AcPhe at the donor site of the peptidyltransferase center (association binding constant 1.5 X 10(6) M-1) and the binding of puromycin at the acceptor site also occur cooperatively with a coefficient of 10-25, the association binding constant of puromycin at the acceptor site being (1-2) X 10(4) M-1. The puromycin association binding constant at the donor site multiplied by the cooperativity coefficient of two interacting puromycin molecules absorbed on a ribosome equals 100-200 M-1.

Acyltransferases↗