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PubMedDate not supplied

[Interaction of tripeptides containing arginine and tyrosine (or phenylalanine) residues with synthetic polynucleotides and DNA of various origins].

Model peptides--L-Arg-Gly-L-Arg, L-Arg-L-Tyr-L-Arg and L-Arg-L-Phe-L-Arg bind to different DNAs and synthetic polynucleotides and are found in the major groove of the double helix. Polynucleotide complexes containing L-Arg-Gly-L-Arg were studied in order to consider the influence of the arginine residues on the polynucleotide melting temperature. It was shown, that L-Arg-L-Tyr-L-Arg and L-Arg-L-Phe--L-Arg lowers the melting temperature in all polynucleotides studied. The dependence of the melting temperature of polynucleotide (DNA)--L-Arg-L-Tyr(L-Phe)-L-Arg complexes upon the polynucleotide GC-content has been detected. These effects reflect the intercalation of peptide tyrosyl (or phenylalanyl) residues into the double-stranded polynucleotide.

Arginine↗
PubMed1985

3'-Deoxy-3'-fluorothymidinetriphosphate: inhibitor and terminator of DNA synthesis catalysed by DNA polymerase beta, terminal deoxynucleotidyl transferase and DNA polymerase I.

3'-deoxy-3'-fluorothymidine-5'-triphosphate (dFTTP) was examined with respect to its capacity to inhibit and to terminate DNA-synthesis catalysed by DNA polymerases alpha and beta, terminal deoxynucleotidyl transferase (TdT) and E. coli DNA polymerase I (Klenow fragment). In analogy with 2', 3'-dideoxythymidine-5'-triphosphate (ddTTP) it was found that DNA polymerase beta was much more sensitive to dFTTP inhibition than DNA polymerase alpha. Moreover, the activity of TdT is strongly inhibited by both dFTTP and ddTTP, whereas the two compounds displayed a lower inhibitory potency on DNA polymerase I. Except for DNA polymerase alpha, the other investigated DNA polymerases are able to incorporate dFTTP into poly (dA).oligo (dT) and oligo (dG), respectively. The specific chain-terminating activity of dFTTP has proved for DNA sequencing to be at least equivalent to ddTTP.

Animals↗
PubMedDate not supplied

[Reaction of fluorescent labeled analogs of the antibiotic distamycin A with synthetic polydeoxyribonucleotides].

Interaction of DNA with the analogs of the antibiotic distamycin A having different numbers of pyrrolcarboxamide units and labeled with dansyl was studied. The intensity of fluorescence of these analogs increases markedly when they bind to DNA. It is shown that the introduction of dansyl into the analog molecules does not change their binding characteristics. The binding isotherms of the analogs to synthetic polydeoxyribonucleotides were obtained. Analysis of the experimental data leads to the following conclusions: 1. The free energy of binding of the analogs to poly(dA1 . poly(dT) depends linearly on the number of pyrrolcarboxamide units in the molecule of the analog whereas attachment of each pyrrolcarboxamide unit produces change of 2 kcal/mole in the free energy. 2. Attachment of a pyrrolcarboxamide unit to GC pair results in the free energy change of 0.95 kcal/mole. 3. Adenine and thymine are close but not equivalent by the energy of binding to the analogs of distamycin A. 4. The binding of analogs to poly(dA . poly(dT) is a cooperative process, presumably dependent on the conformational changes induced by the binding of analogs to DNA.

Chemical Phenomena↗
PubMedDate not supplied

[Structure of the B-form of DNA using the homopolymer poly(dA) . poly(dT) as an example. Refinement in accordance with x-ray and energy criteria].

The refinement of the B-form DNA structure was made using homopolymer poly(dA) (dT) as a model system. In the course of refinement 9 conformational and 22 independent experimental parameters (20 intensities of reflections and 2 helical parameters) were used. After the goal-function, including R-factor, helical and conformational parameters, was optimised, the structures with the values of potential energy and R-factor close correspondingly to the optimal values were selected. "The best" conformations obtained according to energy criteria have the value of an axial projection per one nucleotide pair of about 2,9 A that is equal to the corresponding value in the recently discovered relaxed form of DNA in solution. The most probable conformations according to combine energy and structural criteria have better value of the R-factor in comparison with those derived on the basis of X-ray only, although they are slightly less satisfactory according to the energy criteria. The conformation of DNA which have the values of an axial projection per one nucleotide pair--3,29 A; of the angle of rotation of neighboring nucleotide pair relative each other--36 degrees and of the angle of nucleotide pair with an axis of the helix -13,7 degrees seems to be the most accurate description of the doublehelical structure of poly(dA) . poly(dT). The atomic coordinates of the new model may be used in analysis of stereochemistry of the complexes of nucleic acids with polypeptide and proteins, that is in consideration of the problem of protein-nucleic acid recognition.

DNA↗
PubMed1979

Thymidine photoproducts of non-cyclobutane type as a crucial event in the conformation of UV-irradiated DNA.

The UV-light induced conformational effects in deoxyoligonucleotides and polynucleotides have been analyzed by CD measurements and isolation of the photoproducts. The results demonstrate that the essential photoproduct formed on irradiation of thymidylyl-thymidine at 254 nm is of non-cyclobutane type and may be correlated to the primary photoproduct formed in DNAs at low doses Formation of thymine dimers of cyclobutane-type structure appears to be a secondary product generated by treatment with formic acid.

Chromatography, Paper↗
PubMedDate not supplied

[Effect of the protein product of phage f1, gene 5, on heat denaturation of synthetic polynucleotides].

The influence of phage f1 gene 5 protein on melting of the synthetic polynucleotides has been investigated, using UV-spectroscopy. In our experiments we have varied the proteins concentration. It has been shown, that the protein lowers the melting temperature of the studied polynucleotides (d/A--Tn dAndTn, rAndTn, rAn.r n, dAn.rn). The melting temperatures and the shapes of melting curves of various polynucleotides differ when the same protein concentrations are used. We have shown that the protein binds to the double-stranded polynucleotides, containing ribo-ribo-, deoxyribo-ribo-chains. The difference in melting temperatures and shapes of melting curves was explained using the data about the differences in the secondary structure of these polynucleotides. Only for d/A-Tn renaturation was observed after sample cooling. It may reflect the single-stranded hairpin structure of this polynucleotide.

Bacteriophages↗
PubMed1977

Characterization of a new reverse transcriptase of possibly cellular origin in the chicken system.

The properties of an RNA-dependent DNA polymerase, which occurs ubiquitously in the allantoic fluid of uninfected, leukosis-virus-free eggs, are described. It is shown that the enzyme can synthesize faithful transcripts from natural RNA (globin mRNA). With biochemical and immunological methods, the enzyme can be clearly distinguished from the reverse transcriptases of the known chicken RNA tumour viruses and therefore seems to be a member of a so far unknown class of chicken polymerases. Our data show that in the chicken system reverse transcriptase can occur without connection to the replication of RNA tumour viruses and without relationship to the induction of malignancy.

Animals↗
PubMed1977

On the fidelity of DNA replication. Effect of metal activators during synthesis with avian myeloblastosis virus DNA polymerase.

The effect of metal activators on the fidelity of DNA synthesis has been examined. Using the DNA polymerase from avian myeloblastosis virus, the accuracy of Co2+-, M2+-, and Ni2+-activated DNA synthesis was determined with different polynucleotide templates. With poly[d(A-T)] as the template, the error frequency for dCMP incorporation was 1:1400, 1:1100, and 1:600 for Mg2+, Co2+, and Mn2+, respectively, at maximally activating concentrations. The error frequency was invariant with respect to [Mg2+] but increased with greater than activating concentrations of Co2+ and Mn2+. This increase resulted from differential rates of complementary and noncomplementary nucleotide incorporation. The enhanced error frequency was nonspecific as it occurred with all polynucleotide templates and with all noncomplementary deoxy- and ribonucleotides which were tested. Nearest neighbor analyses of the reaction products indicated that the noncomplementary deoxynucleotides were incorporated as single base substitutions. The fidelity of Ni2+-activated DNA synthesis was invariant with respect to [Ni2+] and was similar to that obtained using Mg2+. During DNA synthesis with Mg2+, the addition of Co2+, Mn2+, or Ni2+ resulted in a decrease in the fidelity of DNA synthesis. The relationship between decreases in the fidelity of DNA synthesis and metal mutagenesis, or carcinogenesis, or both, is considered.

Avian Myeloblastosis Virus↗
PubMed1987

O-Alkyl deoxythymidines are recognized by DNA polymerase I as deoxythymidine or deoxycytidine.

The O2- and O4-methyldeoxythymidine triphosphates (O-alkyl dTTP) can be used to substitute for dTTP in Escherichia coli DNA polymerase I (Pol I)-catalysed synthesis of poly[deoxyadenosine-deoxythymidine] (dA-dT). When incorporated into the polynucleotide, no detectable perturbation of structure occurred with even 20% O-methyldeoxythymidine in place of dT. However, on replication of such polymers with Pol I, significant amounts of deoxyguanosine triphosphate (dGTP) were incorporated, as well as high levels of deoxyadenosine triphosphate (dATP), indicating tautomer-like behaviour. Higher homologues, such as O4-ethyl (e4) dTTP or O4-isopropyl (ip4) dTTP, could also replace dTTP, but with lower efficiency. Nevertheless, their presence, like O4-methyl (m4) dT substitutions, caused transitions as well as inhibiting enzyme digestion with a variety of 3' nucleases, particularly to the 3'----5' exonuclease activity (proofreading) of polymerases. Further proof of mutagenicity comes from site-directed experiments placing m4dT or e4dT in place of dT at position 587 in am3 of phi X174, in which all revertants sequenced had A----G transitions. This implies that, since m4dT and e4dT are poorly repaired in eukaryotes, it is likely that they will remain in the DNA and lead to effects on enzyme activity, as well as mutations which contribute to the carcinogenicity of N-nitroso compounds.

Alkylation↗
PubMed1987

Catalytic activities of synthetic octadeoxyribonucleotides as coenzymes of poly(ADP-ribose) polymerase and the identification of a new enzyme inhibitory site.

The catalytic activity of highly purified poly(ADP-ribose) polymerase was determined at constant NAD+ concentration and varying concentrations of sDNA or synthetic octadeoxyribonucleotides of differing composition. The coenzymic activities of deoxyribonucleotides were compared in two ways: graphic presentation of the activation of poly(ADP-ribose) polymerase in the presence of a large concentration range of deoxyribonucleotides and by calculating kD values for the deoxyribonucleotides. As determined by method i, auto-mono-ADP-ribosylation of the enzyme protein at 25 nM NAD+ was maximally activated at 1:1 octamer/enzyme molar ratios by the octadeoxyribonucleotide derived from the regulatory region of SV40 DNA (duplex C). At a 0.4:1 sDNA/enzyme ratio, sDNA was the most active coenzyme for mono-ADP-ribosylation. At 200 microM NAD+, resulting in polymer synthesis and with histones as secondary polymer acceptors, duplex C was the most active coenzyme, and the octamer containing the steroid hormone receptor binding consensus sequence of DNA was a close second, whereas sDNA exhibited an anomalous biphasic kinetics. sDNA was effective on mono-ADP-ribosylation at a concentration 150-200 -times lower than on polymer formation. When comparison of deoxyribonucleotides was based on method ii (kD values), by far the most efficiently binding coenzyme for both mono and polymer synthesis was sDNA, followed by duplex C, with (dA-dT)8 exhibiting the weakest binding. The synthetic molecule 6-amino-1,2-benzopyrone (6-aminocoumarin) competitively inhibited the coenzymic function of synthetic octadeoxyribonucleotides at constant concentration of NAD+, identifying a new inhibitory site of poly(ADP-ribose) polymerase.

ADP Ribose Transferases↗
PubMed1990

Molecular recognition in the minor groove of the DNA helix. Studies on the synthesis of oligonucleotides and polynucleotides containing 3-deaza-2'-deoxyadenosine. Interaction of the oligonucleotides with the restriction endonuclease EcoRV.

An improved procedure for the preparation of 3-deaza-2'-deoxyadenosine (d3CA) is described which is suitable for the synthesis of gram quantities of this analogue. Using phosphoramidite chemistry d3CA has been incorporated into the Eco RV restiction endonuclease recognition sequence (underlined) present in the self-complementary dodecamer d(GACGATATCGTC). The modified oligonucleotides have been thoroughly characterised by nucleoside composition analysis, circular dichroism and thermal melting studies. Studies with Eco RV show that incorporation of d3CA into either the central or outer dA-dT base-pair results in a substantial reduction in the rate of cleavage. The two-step conversion of d3CA to 3-deaza-2'-deoxyadenosine-5'-O-triphosphate (d3CATP) via the 5'-O-tosylate is also described. d3CATP is not a substrate in the poly[d(AT)].poly[d(AT)] primed polymerisation for either E. coli DNA polymerase I or Micrococcus luteus DNA polymerase. In a more detailed kinetic analysis d3CATP was shown to be a competitive inhibitor of E. coli DNA polymerase I with respect to dATP.

Adenosine Triphosphate↗