Biomedical subjects

A A Krayevsky

Publications and source records attributed to A A Krayevsky.

At least 19 recordsLinked to original sources

PubMed2000

Stereochemical control of DNA biosynthesis.

Stereochemical control of DNA biosynthesis was studied using several DNA-synthesizing complexes containing, in each case, a single substitution of a 2'-deoxy-D-nucleotide residue by an enantiomeric L-nucleotide residue in a DNA chain (either in the primer or in the template) as well as 2'-deoxy-L-ribonucleoside 5'-triphosphates (L-dNTPs) as substrates. Three template-dependent DNA polymerases were tested, Escherichia coli DNA polymerase I Klenow fragment, Thermus aquaticus DNA polymerase and avian myeloblastosis virus reverse transcriptase, as well as template-independent calf-thymus terminal deoxynucleotidyl transferase. Very stringent control of stereoselectivity was demonstrated for template-dependent DNA polymerases, whereas terminal deoxynucleotidyl transferase was less selective. DNA polymerase I and reverse transcriptase catalyzed formation of dinucleoside 5',5'-tetraphosphates when L-dTTP was used as substrate. Comparison between models of template-primer complexes, modified or not by a single L-nucleotide residue, revealed striking differences in their geometry.

Base Sequence↗

PubMed2000

Terminal deoxynucleotidyl transferase catalyzes the reaction of DNA phosphorylation.

The reaction of phosphorylation and phosphonylation of an oligodeoxynucleotide 3'-terminal hydroxyl (oligodeoxynucleotidyl kinase activity) catalyzed by calf thymus terminal deoxynucleotidyl transferase (TDT) was found. Triphosphates modified at Palpha-, Palpha,gamma- or Palpha,beta,gamma-residues served as low-molecular weight substrates. The reaction was TDT specific; human DNA polymerasesalphaandbeta, as well as AMV reverse transcriptase did not catalyze it. The donor activity of modified triphosphates or triphosphonates depended on their structure and was increased with an increase in their hydrophobicity. The substrate activity of some modified triphosphates was up to one order of magnitude higher than that of ddTTP.

DNA↗

PubMed2000

Terminal deoxynucleotidyl transferase. catalysis of DNA (oligodeoxynucleotide) phosphorylation.

The phosphorylation and phosphonylation of the 3'-hydroxyl of oligodeoxynucleotide 3'-termini (oligodeoxynucleotidyl kinase activity) catalyzed by calf thymus terminal deoxynucleotidyl transferase (TDT) are discussed. Palpha and Palpha, Pgamma-substituted modified triphosphates serve as low-molecular weight substrates in this reaction to give oligodeoxynucleotides with a 3'-phosphorylated or phosphonylated hydroxyl. The reaction is specific for TDT, and it is not catalyzed by avian myeloblastosis virus reverse transcriptase. The phosphate or phosphonate donor activities of modified triphosphates depend on their structure and increase with hydrophobicity. Several modified triphosphates demonstrated very high substrate activity, in some cases, up to one order of magnitude higher than that for dTTP. It has also been shown that TDT catalyzes primer extension with dinucleoside 5',5'-tetraphosphates as substrates.

Animals↗

PubMed1998

2'-Deoxynucleoside 5'-triphosphates modified at alpha-, beta- and gamma-phosphates as substrates for DNA polymerases.

Replacement of alpha-, beta- and gamma-phosphate groups in 2'-deoxynucleoside 5'-triphosphates (dNTP) with phosphonate groups yields a new set of dNTP mimics with potential biological and therapeutic applications. Here, we describe the synthesis of 15 new dNTPs modified at alpha-, beta- and gamma-phosphates containing, in the case of dUTP, reporter and ligand groups at the C5 position of uracil. It was shown that gamma-substituted dNTPs were substrates for AMV reverse transcriptase despite of the large size of substituent at the gamma-phosphonate. On the other hand, these compounds were poorly utilized by DNA polymerase alpha. For dUTP analogues substituted at both gamma-phosphonate and C5 of uracil, the substrate affinity was 1-2 orders of magnitude lower than for their counterparts containing substituents either at gamma-phosphonate or C5 position. Meanwhile, C5-substituted beta, gamma-dibromomethylenediphosphonates demonstrated poor activity or were not active at all as substrates for AMV reverse transcriptase. Finally, 2'-deoxythymidine 5'-[beta, gamma-(methylphosphinyl)methylphosphonyl]-alpha-phosphate and its 3'-azido-3'-deoxy analog were substrates for AMV reverse transcriptase, but the substrate activity of these analogues was 50-100 times lower as compared with dTTP. HIV reverse transcriptase utilized these compounds 1 order of magnitude less efficiently than AMV reverse transcriptase; terminal deoxynucleotidyl transferase did not recognize them at all.

Avian Myeloblastosis Virus↗

PubMed1998

Substrates of DNA polymerases with planar conformation of sugar: model of substrate transition state?

Several years ago, we published an hypothesis concerning conformation of the glycone moiety of different substrates in active centers of several DNA metabolizing enzymes (Nucleosides & Nucleotides 1993, 12, 649-670). This hypothesis prompted us to further study the subtle conformational changes on substrates of DNA polymerases. Data collected in our, as well as other laboratories, have been analyzed, and models of active centers of different DNA polymerases are discussed below. Based on the model of substrate requirements, we now can divide DNA polymerases into two distinguished classes.

Animals↗

PubMed1997

Effect of triphosphate modifications in 2'-deoxynucleoside 5'-triphosphates on their specificity towards various DNA polymerases.

Some natural and glycon-modified dNTPs with beta,gamma-pyrophosphate substitution at the triphosphate residue were synthesized and studied to evaluate the effect of these modifications on substrate properties of dNTPs in DNA synthesis catalyzed by human placental DNA polymerases alpha and beta, avian myeloblastosis virus reverse transcriptase, and calf thymus terminal deoxynucleotidyl transferase. Reverse transcriptase proved to be the enzyme least specific to such modifications; the substrate activity of beta,gamma-methylenediphosphonate substituted dTTP and 3'-azido-3'-deoxy-dTTP decreased in the following order: CF2 = CHF > CBr2 > CFMe >> CH2. This order is individual for each DNA polymerase. It is interesting to mention that beta,gamma-CBr2 substituted dTTP is neither a substrate nor an inhibitor of DNA polymerase beta. This specificity distinguishes DNA polymerase beta from other DNA polymerases studied.

Animals↗

PubMed1997

Stereoisomers of deoxynucleoside 5'-triphosphates as substrates for template-dependent and -independent DNA polymerases.

All four possible stereoisomers of dNTP with regard to deoxyribofuranose C-1' and C-4' carbon atoms were studied as substrates for several template-dependent DNA polymerases and template-independent terminal deoxynucleotidyl transferase. It was shown that DNA polymerases alpha, beta, and epsilon from human placenta and reverse transcriptases of human immunodeficiency virus and avian myeloblastosis virus incorporate into the DNA chain only natural beta-D-dNTPs, whereas calf thymus terminal deoxynucleotidyl transferase incorporates two nucleotide residues of alpha-D-dNTP and extends the resulting oligonucleotide in the presence of beta-D-dNTPs. The latter enzyme also extended alpha-anomeric D-oligodeoxynucleotide primers in the presence of beta-D-dNTPs. None of the studied enzymes utilized L-dNTPs. These data indicate that template-dependent DNA polymerases are highly stereospecific with regard to dNTPs, whereas template-independent terminal deoxynucleotidyl transferase shows less stereodifferentiation. It is likely that the active center of the latter enzyme forms no specific contacts with the nucleic bases of both nucleotide substrate and oligonucleotide primer.

DNA Primers↗

PubMed1996

Conserved nucleotides of 23 S rRNA located at the ribosomal peptidyltransferase center.

Two nucleotides of the 23 S rRNA gene were mutated; the nucleotides correspond to the first two positions of the universally conserved sequence PsiGG2582 at the peptidyltransferase ring of 23 S rRNA. The ribosomes containing the altered 23 S rRNA were analyzed. Previously, it was shown that ribosomal assembly was indistinguishable from that in wild-type cells, that the flow of the corresponding 50 S subunit into the polysome fraction was not restricted, but that the ribosomes were strongly impaired in poly(Phe) synthesis (C. M. T. Spahn, J. Remme, M. A. Schäfer, and K. H. Nierhaus (1996) J. Biol. Chem. 271, 32849-32856). Here we apply assay systems exclusively testing the puromycin reaction of ribosomes carrying plasmid-born rRNA, a dipeptide assay using the minimal P site donor pA(fMet) and a translocation system not depending on the puromycin reaction. The mutations in helix 90 exclusively abolish or severely impair the ribosome capability to catalyze AcPhe-puromycin formation. A possible explanation of these observations is that G2581 and Psi2580 (and possibly also G2582) are part of the binding site of C75 of peptidyl-tRNA in the P site. The results suggest that in this case, however, such an interaction would disobey canonical base pairing.

Base Sequence↗

PubMed1996

Proliferating cell nuclear antigen promotes misincorporation catalyzed by calf thymus DNA polymerase delta.

A proliferating cell nuclear antigen (PCNA)-dependent complex, detectable after nondenaturing polyacrylamide gel electrophoresis, is formed between calf thymus DNA polymerase delta (pol delta) and synthetic oligonucleotide template-primers containing a mispaired nucleotide at the 3'-terminal position of the primer. This complex is indistinguishable in composition from that formed with a fully base paired template-primer. Extension of a mispaired primer terminus is a component of DNA polymerase fidelity. The fidelity of pol delta on synthetic oligonucleotide template-primers was compared with and without its specific processivity factor, PCNA. In the absence of PCNA, pol delta misincorporates less than one nucleotide for every 100,000 nucleotides incorporated correctly. Addition of PCNA to reactions reduces fidelity by at least 27-fold. PCNA also confers upon pol delta, the ability to incorporate (and/or not excise) the dTTP analog, 2'-deoxythymidine-5'-O-(alpha-phosphonomethyl)-beta, gamma-diphosphate. A model is proposed whereby the increased stability (decreased off-rate) of the pol delta.template-primer complex in the presence of PCNA facilitates unfavorable events catalyzed by pol delta. This model suggests an explicit mechanistic requirement for the intrinsic 3'-5'-exonuclease of pol delta.

Animals↗

PubMed1996

Modified nucleotides as substrates and inhibitors of adenylate kinase from different sources.

The substrate and inhibitory properties of modified nucleotides with respect to adenylate kinase from rabbit muscles, human placenta and Escherichia coli were studied. A number of 5'-hydrogenphosphonates and 5'-fluorophosphates of modified nucleotides were shown to inhibit the phosphorylation reaction catalyzed by these enzymes. A clear difference between phosphonates of 3'-deoxyribonucleotides and the corresponding ribo- and 2',3'-dideoxyribonucleotides was found. 3'-Azido-2',3'-dideoxythymidine and its phosphorus derivatives did not inhibit the adenylate kinase reaction.

Adenylate Kinase↗

PubMed1996

Gamma-phosphate-substituted 2'-deoxynucleoside 5'-triphosphates as substrates for DNA polymerases.

Several 2'-deoxythymidine 5'-triphosphate and 3'-azido-2', 3'-dideoxythymidine 5'-triphosphate analogs containing a hydrophobic phosphonate group instead of the gamma-phosphate were synthesized and evaluated as substrates for human immunodeficiency virus (HIV) and avian myeloblastosis virus reverse transcriptases, human placental DNA polymerases alpha and beta, and calf thymus terminal deoxynucleotidyl transferase. They were efficiently incorporated into the DNA chain by the retroviral enzymes but were not utilized by the mammalian ones. Also, some gamma-ester and gamma-amide derivatives of dTTP and 3'-azido-2',3'-dideoxythymidine 5'-triphosphate (AZTTP) were synthesized and studied. They proved to be substrates for both the retroviral and mammalian enzymes under study. The Km values for incorporation of the dTTP derivatives into the DNA chain were close to those for dTTP and AZTTP. The Km for the AZTTP derivatives were one order of magnitude greater than those for dTTP and AZTTP. The results obtained indicate that HIV and avian myeloblastosis virus reverse transcriptases have no sterical obstacles for binding the triphosphate fragment bearing a bulky substituent at the gamma-position. Modification of the gamma-phosphate in AZTTP increased the selectivity of HIV reverse transcriptase inhibition versus DNA polymerase alpha. gamma-Methylphosphonate and gamma-phenylphosphonate were dephosphorylated in human serum much less rapidly than AZTTP. Besides, they were shown to be markedly more hydrophobic than AZTTP. Thus, replacement of the gamma-phosphate in AZTTP with gamma-phosphonate markedly alters its substrate properties toward some cellular DNA polymerases and blood dephosphorylating enzymes but does not change its substrate activity with respect to HIV reverse transcriptase.

Animals↗

PubMed1996

Reverse transcriptase inhibitors suppress telomerase function and induce senescence-like processes in cultured mouse fibroblasts.

Spontaneous transformation of mouse embryonic fibroblasts in the presence of the reverse transcriptase inhibitors azidothymidine and carbovir led to the formation of telomerase-free clones. After prolonged cultivation of fibroblasts in the presence of carbovir, resistant cells with a very high level of telomerase activity were obtained. Azidothymidine and carbovir, but not dideoxycytidine, induced senescence-like processes in cultures of immortal mouse fibroblasts. After long-term incubation, cell proliferation gradually decreased, their morphology becoming similar to that of the senescent ones. The process was reversible: after inhibitor removal, the cells, including the giant ones, entered mitoses. All these data suggest that reverse transcriptase inhibitors block telomerase function in mouse cells.

3T3 Cells↗

PubMed1996

Should the asymmetry of enzymatic active centers always correlate with the asymmetry of their substrates?

Analysis of the substrate specificity of DNA polymerases and in part some other enzymes of nucleic acid metabolism towards unnatural L-stereomeric nucleosides and nucleotides was made. As a result, the hypothesis is proposed that when the chiral part of the substrate molecule does not interact specifically with the enzyme, substitution of natural D enantiomers by L compounds is possible.

Binding Sites↗

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↗

PubMed1995

Purine arabinonucleoside 5'-triphosphates with substituents at 2' position as substrates for DNA polymerases.

Analogues of araNTPs carrying an azido or aminogroup instead of the 2' hydroxyl exhibited substrate properties towards several mammalian and viral DNA polymerases. At the same time, introduction of a bulky hydrophobic DNP group into the 2' position inactivated the compounds as substrates. HSV-1 and CMV DNA polymerases were an interesting exception: they effectively incorporated the modified nucleotide residues with DNP group into the 3'-termini of the DNA chain. This is a reliable distinction of these enzymes from cellular DNA polymerases.

Amines↗

PubMed1994

Selectivity of DNA polymerases toward alpha and beta nucleotide substrates of D and L series.

The substrate properties of four carbocyclic D and L nucleoside 5'-triphosphate analogs toward HIV and AMV reverse transcriptases and terminal deoxynucleotidyl transferase were evaluated. The compounds of the D-beta and L-beta series were found to be terminating substrates for these enzymes, while the derivatives of the D-alpha and L-alpha series were recognized only by terminal deoxynucleotidyl transferase, suggesting that for the template-independent enzyme the mutual orientation of the two fragments is of no significance. A hypothesis for binding of nucleotides to the DNA polymerase active center was proposed.

Adenosine Triphosphate↗

PubMed1994

Novel acyclic nucleotides and nucleoside 5'-triphosphates imitating 2',3'-dideoxy-2',3'-didehydronucleotides: synthesis and biological properties.

A series of pyrophosphoryl (Z)-(phosphonomethoxy)but-2-enyl derivatives of pyrimidines and purines 9a-d and the corresponding phosphonates 10a-d were synthesized. The prepared compounds contain the phosphonate group as an alpha-phosphate mimic as well as an acyclic residue emulating the sugar moiety in 2',3'-dideoxy-2',3'-didehydronucleoside 5'-triphosphates known as highly potent chain terminators of DNA polymerases. Phosphonates 10a-d were obtained by alternative alkylations of the nucleic bases followed by condensation with ethyl [[(p-tolylsulfonyl)oxy]methyl]phosphonate. Pyrophosphorylation of 10a-d afforded phosphonate diphosphates 9a-d. Their substrate properties were evaluated in cell-free systems containing various DNA polymerases including viral reverse transcriptases. Compounds 9a-d manifested good terminating substrate properties toward HIV-1 and AMV reverse transcriptases. They exhibited high selectivity and were not recognized by human DNA polymerases alpha and epsilon, DNA polymerase beta from rat liver, Escherichia coli DNA polymerase I, and HSV-1 and CMV DNA polymerases. Phosphonates 10b-d displayed no activity in HIV-1-infected MT-4 cells cultures; 10a was moderately effective (ED50 = 9 microM).

Animals↗