In vitro polyoma DNA synthesis: inhibition by 1-beta-d-arabinofuranosyl CTP

Interaction of polymerases with 2'-deoxyuridine-5'-triphosphate spin-labeled at the 5-position

2'-Deoxyuridine-5'-triphosphate spin-labeled at the 5-position with N-[1-oxyl-2,2,6,6-tetramethyl-4-piperidinyl]-O- was found to be an inhibitor of some DNA and RNA polymerases including avian myeloblastosis virus reverse transcriptase. Furthermore, the spin-labeled nucleotide was found to be incorporated internally into polydeoxythymidylic acid via reverse transcriptase to an extent of 1.0 spin-labeled base per 10(3) bases. The incorporation, monitored by electron spin resonance, is analogous to some other nucleotide inhibitors of polymerases, and the results indicate that it may be feasible to obtain sequence specific, spin-labeled DNA, enzymatically.

Adenovirus DNA replication in vivo: properties of short DNA molecules extracted from infected cells

Adenovirus type 5 (Ad5) DNA replicating in intact HeLa cells was pulse-labeled with [3H]thymidine extracted by the procedure of Hirt and analyzed on neutral sucrose gradients. In addition to viral replicative forms (over 33 kb), slowly sedimenting species of DNA (0.05-3 kb) was observed. Hybridization analysis showed that this DNA contained about 30% Ad5 DNA sequences. Analysis of the sensitivity of this DNA to the 5' OH-specific spleen exonuclease after alkali or RNAase treatment revealed that about 80% of these molecules contained ribonucleotides. DNA in this fraction was labeled at the 5' end with 32P and hybridized together with control 3H-labeled Ad5 DNA to Hpa I restriction fragments immobilized on nitrocellulose paper. Many of these small molecules were located near the termini. Alkali treatment prior to hybridization decreased the 32P/3H ratio throughout the genome. This suggests that some of these Ad5 molecules possess ribonucleotides and therefore may be intermediates in discontinuous DNA replication. Longer molecules (over 0.5 kb) were found sedimenting with viral replicative forms and mature DNA. The Ad5 molecules in this fraction showed no evidence of alkali-labile termini.

Effect of ARA-C incorporation on deoxyribonucleic acid synthesis in cells

Recent work using isolated DNA polymerase-template complexes has shown that arabinofuranosyl derivatives con slow DNA synthesis by being incorporated into DNA. Our results suggest that these agents act by a similar mechanism in L1210 cells. The results demonstrate that inhibition of cellular DNA synthesis by cytosine arabinoside (ara-C) was significantly related to the extent of ara-C incorporation in DNA over a wide range of drug concentrations and times of exposure. Furthermore, treatment with increasing concentrations of ara-C resulted in a greater proportion of ara-C residues at the 3'-terminus of the elongating DNA chain. These observations suggest that ara-C incorporation results in poor primer termini for further chain elongation.

Effects of hydroxyurea on DNA synthesis in mouse L-cells

The effect of the anti-metabolite hydroxyurea on DNA synthesis in mouse L-cells has been examined. It was shown previously that when DNA synthesis was diminished to very low levels by treatment with the drug there was preferential incorporation of added [3H]dThd into low molecular weight fragments (Martin, R.F., Radford, I. And Pardee, M. (1977) Biochem. Biophys. Res. Commun. 74, 9-15). On the basis of several criteria it is concluded here that these fragments are a product of semi-conservative nuclear DNA replication. The preferential labelling of DNA fragments, but not their size, is shown to be dependent on the hydroxyurea concentration used. These DNA fragments are also shown, by comparison with normal DNA replication intermediates, to comprise a heterogeneous population of 'larger-than-normal' fragments. Different models to account for these findings are considered and it is concluded that the results are compatible with a loss of coordination of DNA synthesis following drug treatment.

Effect of arabinosyl cytosine on the level of DNA polymerase and thymidine kinase activity in PHA-stimulated human tonsillar lymphocytes

The effect of arabinosyl cytosine (ara-C) was studied on the uptake, phosphorylation and incorporation of 3H-thymidine in human tonsillar lymphocyte cultures is described along with its effect on the level of DNA polymerase and thymidine Kinase activities induced by phytohaemagglutinin (PHA). Freshly isolated tonsillar lymphocytes are stimulated cells with a remarkably high activity of DNA polymerase alpha and thymidine kinase. During in vitro culture, these stimulated cells are transformed to the resting state with low DNA polymerase and thymidine kinase activity. However, a new DNA synthesising cycle can be induced by PHA with maximum at 48 h. 10(-6) M ara-C inhibited the incorporation of 3H-thymidine by 90-95%. This inhibition may be reversed by rinsing the cells. The inhibition of the transport of 3H-thymidine seems to be only a consequence of the inhibitory effect of ara-C on the DNA polymerisation reaction, because at 10 degrees C, where DNA synthesis was arrested, ara-C does not influence the uptake and the phosphorylation of 3H-thymidine. Ara-C (10(-6) M) abolished also the PHA induced elevation of DNA polymerase alpha and thymidine kinase activities without influencing protein synthesis of the cell. This supports a coordinated regulation mechanism between DNA synthesis and the synthesis of enzymes involved in DNA replication.

Studies on the mechanism of action of cytosine arabinoside

We have demonstrated that Ara-C incorporates in leukemic cell DNA and that the extent of this incorporation correlates significantly with loss of clonogenic survival. This relationship between formation of (Ara-C)DNA and cytotoxicity is also obtained in the presence of modulating agents such as thymidine. Further, the (Ara-C)DNA is structurally abnormal and undergoes strand scission upon exposure to alkali. We have also demonstrated that the incorporated Ara-C residue serves as a poor primer terminus for further chain elongation and thereby results in inhibition of DNA synthesis. These findings provide new insights into the mechanism of action of the most effective agent in the treatment of acute myelogenous leukemia. These findings have also been extended to demonstrate that Ara-C results in the induction of leukemic cell differentiation as well as lethal cellular events.

Transcription of tRNA genes in vivo: single-stranded compared to double-stranded templates

The expression of cloned tRNA genes has been studied by injecting single-stranded and double-stranded DNA templates into Xenopus oocyte nuclei. In both forms the genes are faithfully transcribed after injection. Some single-stranded DNA is converted into double-stranded DNA in the oocyte nucleus. This conversion is necessary for the expression of the injected tRNA gene: no tRNA transcription is observed when DNA synthesis is inhibited. We conclude that single-stranded DNA does not serve as a template for faithful transcription of this gene in injected oocytes.

Effect of 2',3'-dideoxythymidine-5'-triphosphate on HeLa cell in vitro DNA synthesis: evidence that DNA polymerase alpha is the only polymerase required for cellular DNA replication

We have studied the effects of the nucleotide analogue, 2',3'-dideoxythymidine-5'-triphosphate (ddTTP) on replicative DNA synthesis in HeLa cell lysates. As previously demonstrated (1), such lysates carry out extensive DNA synthesis in vitro, at rates and in a fashion similar to in vivo DNA replication. We report here that all aspects of DNA synthesis in such lysates (total dNTP incorporation, elongation of continuous nascent strands, and the initiation, elongation, and joining of Okazaki pieces) are only slightly inhibited by concentrations of ddTTP as high as 100-500 micrometer when the dTTP concentration is maintained at 10 micrometer. This finding is consistent with the report by Edenberg, Anderson, and DePamphilis (2) that all aspects of replicative in vitro simian virus 40 DNA synthesis are also resistant to ddTTP. We also find, in agreement with Edenberg, Anderson, and DePamphilis (2), that DNA synthesis catalyzed by DNA polymerases beta or gamma is easily inhibited by ddTTP, while synthesis catalyzed by DNA polymerase alpha is very resistant. These observations suggest that DNA polymerase alpha may be the only DNA polymerase required for all aspects of cellular DNA synthesis.

DNA sequencing with chain-terminating inhibitors

A new method for determining nucleotide sequences in DNA is described. It is similar to the "plus and minus" method [Sanger, F. & Coulson, A. R. (1975) J. Mol. Biol. 94, 441-448] but makes use of the 2',3'-dideoxy and arabinonucleoside analogues of the normal deoxynucleoside triphosphates, which act as specific chain-terminating inhibitors of DNA polymerase. The technique has been applied to the DNA of bacteriophage varphiX174 and is more rapid and more accurate than either the plus or the minus method.

In vitro polyoma DNA synthesis: self-annealing properties of short DNA chains

Short DNA chains, isolated from in vitro pulse-labeled replicating polyoma DNA, exhibit some degree of self-complementarity (28% resistance to S1 nuclease after self-annealing to plateau levels). This level of self-annealing is not increased if short DNA chains present as free single-stranded DNA after extraction are included in the hybridization, excluding a selective loss of chains from one side of the growing fork and supporting a semi-discontinuous mode of chain growth. This mode also applies to restricted synthesis conditions under which a relative excess of short chains is made, since no increase in the self-annealing of such short chains is observed. The self-annealing that can be measured is higher for the faster sedimenting portion (46%) of the short DNA chains than for the slower sedimenting portion (18.5%), indicating that it is most likely due to contaminating continuously growing strands from the other side of the fork. High self-annealing values (up to 60%) are obtained if virus stocks generating defective DNA are used for infection. Restriction endonuclease (Hpall) characterization of such DNA shows evidence for the presence of multiple origins of replication. One of several possible mechanisms is discussed by which replicating defective DNA can generate self-complementary short chains despite a semi-discontinuous mode of replication.