[Substrate properties of dioxolane analogs of 3'-deoxythymidine-5'-triphosphate in DNA synthesis reactions, catalyzed by various DNA polymerases]. / Substratnye svoistva dioksolanovykh analogov 3'-dezoksitimidin-5'-trifosfata v reaktsiiakh sinteza DNK, kataliziruemykh razlichnymi DNK-polimerazami.

The substrate properties of 3'-deoxythymidine 5'-triphosphate analogs prepared on the basis of 2,4-disubstituted 1,3-dioxolanes were investigated in reactions of the DNA synthesis catalyzed by various DNA polymerases. The 4'-triphosphates of (+/-)-cis-4-hydroxymethyl-2-(1-thyminylmethyl)-1,3-dioxolane and the corresponding (+/-)-trans-isomer were shown to be terminating substrates of terminal deoxynucleotidyl transferase. 4'-Triphosphate of (+/-)-cis-4-hydroxymethyl-2-(1-thyminylmethyl)- 1,3-dioxolane terminates the DNA synthesis catalyzed by HIV reverse transcriptase, whereas 2'-triphosphate of (+/-)-cis-2-hydromethyl-4-(1-thyminylmethyl)-1,3-dioxolane is a terminator in the DNA synthesis catalyzed by HIV reverse transcriptase and the Klenow fragment of DNA polymerase I.

[2'-Deoxynucleoside-5'-triphosphate, modified via the carbohydrate and triphosphate residues, in the DNA synthesis reaction]. / 2'-Dezoksinukleozid-5'-trifosfaty, modifitsirovannye po uglevodnomu i trifosfatnomu ostatkam, v reaktsii sinteza DNK.

We have investigated the substrate properties of deoxyribonucleoside 5'-triphosphate analogues, modified in the carbohydrate and triphosphate moieties, in DNA synthesis catalyzed by different DNA polymerases and reverse transcriptases. It was shown that (3'-azido-2',3'-dideoxythymidine-5'-O-methylenephosphonate) diphosphate, (3'-azido-2',3'-dideoxythymidine 5'-phosphate) dibromomethylenediphosphonate, (3'-azido-2',3'-dideoxythymidine 5'-phosphate) phosphonoacetate terminate DNA synthesis catalyzed by reverse transcriptases. (2'-Deoxythymidine 5'-phosphate) phosphonoacetate displays substrate properties for DNA polymerase beta, different reverse transcriptases, terminal deoxynucleotidyl transferase, but not for DNA polymerase alpha, Klenow's fragment DNA polymerase I. The Km value for this substance in DNA synthesis reactions catalyzed by reverse transcriptases was two of orders magnitude higher than that for native 2'-deoxythymidine 5'-triphosphate.

[Reverse transcriptase of the human immunodeficiency virus: isolation and substrate specificity]. / Obratnaia transkriptaza virusa immunodefitsita cheloveka: vydelenie i substratnaia spetsifichenost'.

Human immunodeficiency virus (HIV-I) reverse transcriptase was expressed in E. coli and purified to homogeneity (E. coli strain RRI (pRC-RT, pRK 248cIts)). We have investigated the substrate properties toward to DNA synthesis, catalyzed by this enzyme, of some nucleoside-5'-triphosphate analogues, previously studied in the same reactions, catalyzed by AMV and M-MLV reverse transcriptases. We have investigated substrate properties of new analogues of 2',3'-dideoxy-2',3'-didehydro- and 2',3'-dideoxytubercidin-5'-triphosphates. We have compared the relative efficiency of incorporation of different analogues tested in the DNA chain. It has been shown that expressed and purified HIV reverse transcriptase had the same specificity to analogues of 2'-deoxyribonucleoside-5'-triphosphates as was described for reverse transcriptases and natural HIV reverse transcriptase as well. These properties allow to apply the expressed HIV reverse transcriptase in different model systems.

[Acyclic analogs of 2',3'-dideoxy-2',3'-didehydronucleoside-5'-triphosphates--terminators of DNA synthesis, catalyzed by a broad set of DNA polymerases]. / Atsiklicheskie analogi 2',3'-didezoksi-2',3'-didegidronukleozid-5'-trifosfatov--terminatory sinteza DNK, kataliziruemogo shirokim naborom DNK-polimeraz.

O-4'-nor-2', 3'-dideoxy-2', 3'-didehydronucleoside 5'-triphosphates are shown to be effective termination substrates of DNA biosynthesis catalyzed by human placental DNA polymerases alpha and epsilon, rat liver DNA polymerase beta, reverse transcriptases of human immunodeficiency virus and avian myeloblastosis virus, and calf thymus terminal deoxynucleotidyl transferase. These compounds do not interact only with the Escherichia coli DNA polymerase I (Klenow fragment). The probable reasons of interaction of acyclo-d4NTP with the DNA synthesizing complexes are discussed.

[Fluorescent analogs of nucleoside-5'-phosphates for the study of nucleic acids by nonradioactive methods]. / Fluorestsentnye analogi nukleozid-5'-trifosfatov dlia izucheniia nukleinovykh kislot neradioaktivnymi metodami.

The synthesis of 2'-deoxyuridine 5'-triphosphate analogues with fluorescent residues of fluorescein and rhodamine nature at C5 of the uracil base was performed. Reverse transcriptase of avian myeloblastosis virus, DNA polymerase beta of rat liver, terminal deoxynucleotidyl transferase of calf thymus and E. coli DNA polymerase I, Klenow fragment, were shown to be capable to incorporate a nucleotide residue with fluorescent label into 3'-terminus of oligonucleotide. These fluorescent labeled oligonucleotides were used as primers for synthesis of (-)-chain of M13mp10 phage. Fluorescently labeling template-primer complexes were used for DNA sequencing.

[Conformation limited nucleoside-5'-phosphates as termination substrates for DNA-polymerases]. / Konformatsionno ogranichennye nukleozid-5'-trifosfaty kak terminatornye substraty DNK-polimeraz.

We have investigated the ability of some nucleoside 5'-triphosphate analogues to terminate the DNA synthesis catalyzed by calf thymus DNA polymerase alpha and terminal deoxynucleotidyl transferase, rat liver DNA polymerase beta, E. coli DNA polymerase I (Klenow's fragment) and AMV reverse transcriptase. It has been shown that lyxoanhydronucleoside 5'-triphosphates terminate DNA synthesis catalyzed by reverse transcriptase and terminal deoxynucleotydil transferase. 2',3'-O-Isopropylidenecytidine 5'-triphosphate inhibits the DNA synthesis catalyzed by reverse transcriptase and DNA polymerase beta and its moiety was incorporated in the place of dTMP residue. Riboanhydroadenosine 5'-triphosphate reveals the properties of an effective termination substrate for all the DNA polymerases studied. This is the first attempt to investigate nucleotide analogues with the restricted conformation of the carbohydrate moiety as termination substrates for several prokaryotic and eukaryotic DNA polymerases.

[Analogs of pyrophosphate in a pyrophosphorolysis reaction catalyzed by DNA polymerases]. / Analogi pirofosfata v reaktsii pirofosforoliza, kataliziruemoi DNK-polimerazami.

The reaction of pyrophosphorolysis catalyzed by Escherichia coli DNA polymerase I Klenov fragment, calf thymus DNA polymerase alpha, rat liver DNA polymerase beta and AMV reverse transcriptase was studied. Some pyrophosphate (PPi) analogs were taken as low molecular weight substrates. It was shown that only imidodiphosphonic acid acted as the PPi substrate analog for the reactions catalyzed by DNA polymerases I and alpha, both imidodiphosphonic acid and methylenediphosphonic acid were active in the case of DNA polymerase beta and reverse transcriptase. Other analogs tested were neither nucleotide residue acceptors, nor inhibitors of the pyrophosphorolysis reaction with PPi. The abilities of some PPi analogs to inhibit the DNA elongation catalyzed by reverse transcriptase were investigated. The principles of specificity of low molecular substrates recognition by DNA polymerases and some problems concerning the mechanisms of DNA synthesis inhibition by PPi analogues are discussed.

[DNA polymerase I, Klenow fragment of Escherichia coli: hydrolysis and pyrophosphorolysis of DNA containing phosphothioate groups]. / DNK-polimeraza I Escherichia coli, fragment Klenova: gidroliz i pirofosforoliz DNK, soderzhashchei fosfotioatnye gruppy.

Reaction of DNA synthesis catalyzed by DNA polymerase I KF in the presence of 2'-deoxynucleoside 5'-alpha-thiotriphosphates (dNTP alpha S) was investigated. DNA with thiophosphate groups (DNA[P=S]) obtained by such a way was studied in reactions of hydrolysis and pyrophosphorolysis catalyzed by DNA polymerase I KF. It is shown that the rate of DNA elongation is decreased both on the step of incorporation of dNMP alpha S residues and on the step of incorporation of the next dNMP residue. The rate of pyrophosphorolysis of 3'-terminal dNMP alpha S was demonstrated to be one order of magnitude less in comparison with the corresponding reaction with the natural dNMP residue. Contrary, the rate of 3'----5'-exonuclease hydrolysis of both DNA[P=S] and DNA of the same structure revealed no distinguishable differences.

[Analogs of deoxyribonucleoside-5'-triphosphates modified in the base and sugar moieties: substrate properties in DNA biosynthesis in cell-free systems]. / Analogi dezoksiribonukleozid-5'-trifosfatov, modifitsirovannye po osnovaniiu i sakharnomu ostatku: substratnye svoistva pri biosinteze DNK v beskletochnykh sistemakh.

Incorporation of 2'-deoxyribonucleotide 5'-triphosphate derivatives, chemically modified both in the base and at 3'-position, into DNA by four different DNA polymerases was investigated. It is shown that 3'-azido- and 3'-amino-2',3'-dideoxy-(E)-5-(2-bromovinyl)-uridine 5'-triphosphates effectively terminate DNA synthesis catalyzed by E. coli DNA polymerase I, rat liver DNA polymerase beta, and AMV reverse transcriptase. Calf thymus DNA polymerase alpha incorporates only the 3'-amino derivative. DNA polymerases I and beta catalyse DNA synthesis in the presence of beta-D-(2'-deoxyribofuranosyl)-1-benzimidazol 5'-triphosphate, inserting the corresponding monophosphate in place of -dGTP, whereas 3'-substituted analogues of this compound were inactive in the reactions.

[Pyrophosphate analogs in the pyrophosphorolysis reaction catalyzed by Escherichia coli RNA polymerase]. / Analogi pirofosfata v reaktsii pirofosforoliza, kataliziruemoi RNK-polimerazoi Escherichia coli.

Processive pyrophosphorolysis of RNA from ternary RNA polymerase-nascent RNA-delta D111 T7 DNA complex has been followed in the absence of nucleoside triphosphates. Series of inorganic pyrophosphate analogs were investigated for their ability to sustain the reaction and to compete with inorganic pyrophosphate for the reaction. Methylenediphosphonic, imidodiphosphonic, phosphonacetic acids, inorganic triphosphate, methylenediphosphonic and phosphate were found to be capable of substituting the inorganic pyrophosphate in RNA degradation reaction with tantamount efficiency. They give rise to nucleoside monophosphates for phosphonoacetic acid, nucleoside triphosphates for inorganic pyrophosphate and inorganic triphosphate, nucleoside triphosphates analogs for methylenediphosphonic, imidodiphosphonic acids and methylenediphosphonic acid phosphate as the low molecular weight product of the reaction. The problem of specific interaction of RNA polymerase with nucleoside triphosphates and inorganic pyrophosphate is discussed in the terms of structural requirements for the compounds to be a potent substrate for RNA polymerase.

[Reaction of pyrophosphorolysis catalyzed by Escherichia coli RNA polymerase]. / Reaktsiia pirofosforoliza, kataliziruemaia RNK-polimerazoi Escherichia coli.

E. coli RNA polymerase is shown to be capable of catalyzing consecutive DNA-dependent pyrophosphorolysis of RNA in the presence of inorganic pyrophosphate and Mg2+. Active ternary complex of the enzyme with DNA and nascent RNA is needed for the reaction, the mixure of all the components can not carry out pyrophosphorolysis. The reaction was realized in the absence of added nucleoside triphosphates. Nucleoside triphosphates are low molecular mass products of the reaction. The rate of pyrophosphorolysis of the RNA synthesised for the AI promoter of the DNA of wild type T7 phage and delta D III T7 mutant phage was followed as a function of primary structure of the DNA, temperature, ionic strength and inorganic pyrophosphate concentration. The relative rate pyrophosphorolysis for particular nucleotides in different regions of the RNA can differ by several orders of magnitude depending on the primary structure of the RNA that undergoes pyrophosphorolysis. Ternary complex containing partially pyrophosphorilised RNA is active on the RNA synthesis when pyrophosphate is removed and nucleoside triphosphates are added to the reaction mixture. RNA as short as 70-8 nucleotides long can be produced at the conditions used. It seems that efficient dissociation in this region of RNA limits the pyrophosphorolysis to proceed up to the 5' end of RNA. Ternary complex of RNA polymerase with nascent RNA and DNA is shown to undergo site specific dissociation. The specificity of the dissociation is shown to be a function of the primary structure of RNA and the direction of the reaction. Dissociation occurs at different places along RNA sequence when the RNA is synthesised and when it is pyrophosphorilised.

[Modification of Escherichia coli RNA polymerase by diethylpyrocarbonate. II. Binding and unwinding of double-stranded DNA]. / Mosidikatsiia RNK-polimerazy Escherchia coli dietilpirokarbonatom. II. sviazyvanie i destabilizatsiia dvoinoi spirali DNK.

E. coli DNA dependent RNA polymerase was modified by diethylpyrocarbonate. Binding to a double-stranded DNA and unwinding of the DNA at the enzyme binding site by the modified enzyme were examined. It was found that RNA polymerase reversibly lost the ability to unwind DNA helix as well as the RNA synthetic activity when 9 to 11 histidyl residues of the enzyme were modified. In addition ot modification of the most reactive sulfhydryl or amino groups of the enzyme accompanying histidyl residues modification results in irreversible decrease of the salt concentration which is necessary to remove the enzyme from DNA cellulose column. Further modification of the less reactive sulfhydryl or amino groups leads to irreversible loss of the DNA binding ability and to the enzyme structure alteration.

[Modification of the RNA-polymerase of Escherichia coli by diethylpyrocarbonate]. / Modifikatsiia RNK-polimerazy Escherichia coli diétilpirokarbonatom.

E. coli DNA dependent RNA polymerase was modified by diethylpyrocarbonate. Optical and kinetic properties of the reaction were studied. More than 90% of RNA polymerase activity is inhibited by introduction of 9--11 ethoxyformyl groups per enzyme molecule without loss of its ability to bind DNA template. Furthermore the modified enzyme is able to form tight complexes with DNA and to compete with native enzyme for the formation of rifampicin-resistant complex. The ratio of the complex formation constants for the native and modified enzyme was determined to be equal to 10. The enzyme modified to such extent loses the activity in DNA dependent RNA as well as pppApU synthesis. Vmax value rather than Km value for both ATP and UTP decreases following the modification reaction. Incubation of the enzyme modified to the 10% of residual activity with 0.2 M hydroxylamine for 2 hours results in restoration of RNA polymerase activity. Most but not all of the modified histidyl residues restore their native structure. Two of 13 histidyl residues were modified irreversibly due to Bamberger's cleavage reaction, but these two residues were found to be unessential for RNA polymerase activity. Reaction with higher concentration of the diethylpyrocarbonate induces modification of more than 15--20 histidyl residues and leads to irreversible inactivation of the enzyme. Nevertheless the modification of the additional histidyl redidues was reversible as well as the modification of the first 11 residues. RNA polymerase modified to such extent loses the ability to bind DNA. Preformation of the initiated ternary complex of RNA polymerase with template and product fails to protect the enzyme from reversible inactivation at a low reagent concentration, but markedly decreases the rate of the irreversible and unspecific modification of sulfhydryl or amino groups of the enzyme. Reaction with the ternary complex results in reversible inactivation of the enzyme with respect to elongation of RNA chains as well as the pyrophosphate exchange reaction. The complex itself was, however, completely stable under the reaction conditions and the enzyme subunit structure was also conserved after the reaction. Evidently, the mild modification of the histidyl residues with diethylpyrocarbonate selectively inhibits RNA chain elongation.

[Addition of the fluorescent label to the 3'-OH end of DNA and the 3'-OH end of nascent RNA]. / Vvedenie fluorestsentnoi metki na 3'OH-konets DNK i 3'-OH-konets rastushchei tsepi RNK.

3'(2')-O-acyl derivatives of the uridine triphosphate were synthesized. Acyl residues contained fluorescent dye; fluoresceine or rodamine C. Optical properties and stability of UTP analogues were studied. Their ability to serve as the substrates for calf thymus terminal deoxyribonucleotidyl transferase and E. coli RNA polymerase was also examined. It was shown that both enzymes were able to use tested analogues as substrates. Incorporation of the analogues into nascent RNA and DNA chains inhibited the synthetic reaction because of primer inactivation. The rate of the incorporation of the analogues showed an exponential time dependence