An abnormal profile of DNA replication intermediates in Bloom's syndrome

Bloom's syndrome (BS) cells display a characteristic genomic instability, notably an elevated frequency of sister-chromatid exchange. Replicating DNA in cultured BS cells was labeled with [3H]thymidine using several time schedules. Separation of DNA in agarose gels showed high molecular weight DNA and three classes of DNA replication intermediates: 20-kilobase DNA, 10-kilobase DNA, and Okazaki fragments. In contrast newly replicated DNA from normal cells showed no 20-kilobase DNA replication intermediates. Certain BS cells, exceptional in that their characteristic genomic instability has for unknown reasons been corrected, also differed from normal cells in having the 20-kilobase intermediate, but they differed from both normal cells and the other (the uncorrected) BS cells in lacking the 10-kilobase DNA replication intermediates.

Increased levels of 5-fluorouracil-induced DNA lesions in Bloom's syndrome

In Bloom's syndrome (BS) the regulation of uracil-DNA glycosylase, an enzyme involved in the repair of DNA containing 5-FU, is altered. 5-FU induces higher levels of DNA fragmentation in BS cells than in non-BS cells. The increase in DNA fragmentation is connected to the cytotoxic mechanism where 5-FU is incorporated into DNA. When 5-FU induces DNA fragmentation by a mechanism not involving the incorporation of drug into DNA, the levels of DNA fragmentation in BS and non-BS cells remain similar.

Bleomycin-induced DNA lesions are dependent on nucleosome repeat length

Treatment of cells or nuclei with bleomycin induces DNA lesions. We detect the presence of lesions as the release of fragments from bulk DNA when cells (or nuclei) are lysed in dilute alkali. To further characterize the lesions we have altered experimentally the average nucleosome repeat length and probed the lysate with nuclease S1 in order to remove single-stranded DNA. In salt-incubated nuclei with short average nucleosome repeat length (140-145 base pairs) (and also with long nucleosome-free stretches of DNA) one can induced fewer DNA lesions in the nucleosome-containing DNA as compared to nuclei with 190-195 base pairs average nucleosome repeat length. Hence the ability of bleomycin to induce DNA lesions is dependent on nucleosome repeat length.

Altered formation of DNA in human cells treated with inhibitors of DNA topoisomerase II (etoposide and teniposide)

We have investigated the importance of DNA topoisomerase II for the formation of mammalian DNA replication intermediates. Treatment with the DNA topoisomerase II inhibitor etoposide (teniposide) prevents the formation of large intermediates, such as 10-kilobase DNA, but allows the formation of small intermediates, i.e., Okazaki fragments. In untreated cells, there is a distinct stage in which the 10-kilobase DNA intermediates are joined before the appearance of mature chromatin. We find that pretreatment with etoposide (teniposide) prevents the appearance of this stage. When the protocol is reversed and the cells contain labeled 10-kilobase DNA before exposure to the drugs, one can detect the stage.

Appearance of a late stage during mammalian DNA replication when cells resume formation of 10 kb DNA replication intermediates

After the joining of human large DNA replication intermediates and before the appearance of mature chromatin DNA, there exists a distinct stage--'the post-elongation stage'. This stage reappears during recovery of DNA synthesis simultaneously with the reappearance of a large DNA replication intermediate, 10 kb DNA.

Altered formation of DNA replication intermediates in human 46 BR fibroblast cells hypersensitive to 3-aminobenzamide

The appearance of DNA replication intermediates was investigated in a human fibroblast strain (46 BR) which is hypersensitive to the lethal effects of 3-aminobenzamide. 3-Aminobenzamide is an inhibitor of poly(ADP-ribose) synthetase and modulates DNA ligase activity. We detected the same intermediates (10 kb DNA and Okazaki-fragments) as in normal fibroblasts, but kinetics and amounts of intermediates were altered, either as a result of, or in order to overcome the defect in the cells.

Reduced DNA damage induced in human melanoma cells by dacarbazine in the presence of deoxyribonucleosides

Decarbazine induces DNA lesions in replicating DNA. We show here that deoxyribonucleosides, with the exception of thymidine, in doses of 250 microM or higher, prevent dacarbazine-induced DNA lesions. The DNA lesions that appear in the presence of thymidine can be prevented by aphidicolin, an inhibitor of DNA synthesis. Cytotoxicity analyses confirm that the combination thymidine-dacarbazine prevents cell outgrowth only partially, while other deoxyribonucleosides completely abolish the dacarbazine effect.

5-Fluoropyrimidine-induced DNA damage in human colon adenocarcinoma and its augmentation by the nucleoside transport inhibitor dipyridamole

5-Fluorouracil and 5-fluorodeoxyuridine induce DNA lesions via two different mechanisms, one involving and the other not involving the incorporation of drug into DNA. The DNA lesions are detected by lysing cells in dilute alkali and then separating the DNA in agarose gel electrophoresis. We examine here the effect of dipyridamole, a nucleoside transport inhibitor, on the DNA lesions. We find that dipyridamole augments the levels of DNA fragmentation when the lesions are induced by the mechanism not involving the incorporation of drug. In parallel cytotoxicity is increased.

Altered formation of DNA replication intermediates in cells growing in different culture conditions

In human melanoma cells one can detect two discrete DNA replication intermediates, 10-kb DNA intermediates and Okakzaki fragments. Both intermediates are seen when cells are rapidly growing in medium supplemented with fetal calf serum. When the medium is supplemented with newborn calf serum, one can detect Okakzaki fragments but not 10-kb DNA intermediates. In contrast we do not detect changes in the replicon sizes in the two media.

Step-wise progression of mammalian 10-kb DNA replication intermediates to mature chromatin

In mammalian DNA synthesis the primary replication intermediates are joined to larger intermediates. After the joining process is complete one can detect a distinct stage called the post-elongation stage. Furthermore a 10-kb DNA1 population is detected before the post-elongation stage whereas a 10-kb DNA2 population is part of this stage DNA. When cells are treated with 3-aminobenzamide, an inhibitor of poly(ADP-ribose) synthetase, an altered post-elongation-stage DNA was detected, which does not contain 10-kb fragments. The step(s) affected by 3-aminobenzamide prevents the appearance of 10-kb DNA in the post-elongation stage. The drug effect is reversible with the appearance of 10-kb DNA in the post-elongation stage when the cells are washed free of drug. Hence there is a step-wise progression from 10-kb DNA, via the post-elongation stage, to mature chromatin.

Cytotoxicity, calmodulin and DNA lesions in cells treated with streptozotocin

Streptozotocin is a nitrosourea-derivative containing a methyl group instead of a haloethyl group. Treatment of human adenocarcinoma cells with streptozotocin induces DNA lesions. The presence of the lesions is visualized during cell lysis in dilute alkali as changes in fragmentation of prelabelled DNA. The increase in DNA fragmentation is paralleled by increased cytotoxicity. Furthermore prolonged duration of treatment reduces the level of DNA fragmentation. The repair of the DNA lesions is prevented by treating the cells with W-7, an inhibitor of calmodulin.

Increased levels of DNA lesions induced by leucovorin-5-fluoropyrimidine in human colon adenocarcinoma

Leucovorin augments the growth inhibitory effect of 5-fluoropyrimidines on neoplastic cells. The effect is paralleled by much higher levels of DNA fragmentation than in cells treated with 5-fluoropyrimidines alone at the same concentration. The lesions are induced by a mechanism independent of incorporation of the drug into DNA, in all probability due to reduced repair of DNA lesions induced independently of the drug treatment. Thymidine added after the treatment with fluoropyrimidines partly rescues the cells and reduces the level of DNA fragmentation.

Progressive formation of DNA lesions during treatment with anti-metabolites without incorporation of the drugs into DNA

Anti-metabolites, such as methotrexate, 5-fluoropyrimidines or hydroxyurea, induce progressive formation of DNA lesions. 5-Fluoropyrimidines induce DNA lesions either by incorporation of the drug into DNA or by a mechanism not involving incorporation. The second mechanism, not involving incorporation, is also seen with methotrexate and hydroxyurea. The three anti-metabolites have in common their ability to reduce intracellular levels of nucleotides, resulting in reduced efficiency of repair of DNA lesions. The lesions probably appear spontaneously, independently of the drug treatment.

Increased growth inhibition and DNA lesions in human colon adenocarcinoma cells treated with methotrexate or 5-fluorodeoxyuridine followed by calmodulin inhibitors

The antineoplastic agents methotrexate and 5-fluorodeoxyuridine induce DNA lesions, although the drugs are not incorporated into DNA. The lesions arise as a result of reduced repair of damage occurring in DNA independently of the treatment with antineoplastic agents. When cells containing DNA lesions are treated with calmodulin inhibitors (W-7, phenothiazine, promethazine), the amount of lesions is increased, in all probability due to reduced DNA repair. This is paralleled by increased growth inhibition. Hence by inhibiting calmodulin, one can modulate the levels of DNA lesions and change the growth-inhibitory effect induced by methotrexate or 5-fluorodeoxyuridine. This strongly supports the importance of this type of DNA lesion in the toxic effects induced by the drugs.

Extensive regions of single-stranded DNA in aphidicolin-treated melanoma cells

We have looked for the presence of single-stranded DNA in human melanoma cells. Single-stranded DNA was observed by lysis of cells in dilute alkali (to partly denature the DNA) followed by CsCl gradient centrifugations. In normally growing cells we did not observe single-stranded DNA whereas large amounts were present in cells treated with aphidicolin (an inhibitor of DNA polymerase alpha). The single-stranded DNA is much larger (greater than 20 kb) than Okazaki fragments. When the cells were washed free of aphidicolin, the single-stranded DNA was converted to high molecular weight DNA. Furthermore, when DNA synthesis is recovering after drug treatment, the single-stranded DNA disappears. The single-stranded DNA represents a transient step during the maturation of newly synthesized DNA.

Treatment with dilute alkali-nuclease S1 permits the analysis of DNA damage: cells treated with platinum analogues

We describe here an approach to characterize various lesions induced in DNA by drug treatments, using three parameters: (a) release of single-stranded DNA fragments by cell lysis in dilute alkali, which result from enzymatic strand scission during DNA repair or chemical alterations of DNA; (b) the presence of high molecular weight DNA in cells after lysis in dilute alkali followed by nuclease S1 treatment which, due to drug-induced DNA cross-links and its level is a measure of the amount of DNA-containing cross-links; and (c) the appearance of small double-stranded DNA fragments, when the cell lysis is followed by digestion with nuclease S1 to remove single-stranded DNA. This DNA shows the same characteristics as DNA of untreated cells, but it may contain monoadducts. By following the flow of label through the three parameters, one can characterize both the lesions induced in DNA and how the lesions are repaired. We report here results of three platinum analogues: cis-Pt(II), trans-Pt(II), and cis-FLAP(II). A large proportion of DNA in treated cells appears as fragments (parameter c). The cis- compounds and trans- compounds differ with regard to appearance of high molecular weight DNA (parameter b) and the initial release of fragments (parameter a).

Conversion of post-elongation stage DNA to mature DNA occurs even if movement of the replication fork has stopped

During DNA synthesis there is a distinct stage immediately after the joining of large DNA replication intermediates (post-elongation stage). The conversion of this DNA to mature DNA was analysed in cells treated with aphidicolin to stop the movement of the replication fork. In such cells mature DNA is formed. In contrast, UV-A, which induces a wide spectrum of DNA lesions, inhibits the conversion to mature DNA. The data indicate that the maturation of the post-elongation stage can be uncoupled from the movement of the replication fork.

W-7, a calmodulin inhibitor, potentiates dacarbazine cytotoxicity in human neoplastic cells

Dacarbazine induces damage in replicative DNA, with a maximum level at 24 hr after treatment. Repair of these lesions does not occur when cells are post-treated with the calmodulin inhibitor W-7. In parallel cell cytotoxicity increases. The augmentation effect of W-7 is prevented by simultaneous incubation of cells with high levels of calmodulin and does not occur in cells pre-treated with aphidicolin (to stop DNA synthesis). Furthermore, W-5, an analogue of W-7 with a less inhibitory effect on calmodulin, does not interfere with DNA repair. The results show that calmodulin and/or calmodulin-regulated proteins are involved in the repair process of dacarbazine-induced DNA lesions.

5,6-Dichloro-1-beta-O-ribofuranosylbenzimidazole induces DNA damage by interfering with DNA topoisomerase II

We have examined DNA in cells treated with 5,6-dichloro-1-beta-O-ribofuranosylbenzimidazole (DRB), an adenosine analogue. The results show that DRB induces an partial fragmentation of DNA when the cells are lysed in dilute alkali. Fragmentation of DNA does not occur in control cells, nor in cells pretreated with novobiocin or VP-16/VM-26. The data show that DRB interferes with DNA topoisomerase II. In agreement with this interpretation, crude nuclear extracts of DRB-treated cells result in reduced in vitro KC1/SDS precipitation of covalent protein-DNA complexes. Formation of covalent complexes is typical of topoisomerase-DNA interaction.

Inhibition of poly(ADP-ribose) synthetase potentiates cell dacarbazine cytotoxicity

Dacarbazine induces DNA lesions in cells synthesizing new DNA. When poly(ADP-ribosylation) is inhibited with 3-aminobenzamide, repair of the dacarbazine-induced DNA lesions is reduced. This is parallelled by increased cytotoxicity. Cells pre-treated with aphidicolin (to stop DNA synthesis) are resistant to dacarbazine.

DNA lesions in human neoplastic cells and cytotoxicity of 5-fluoropyrimidines

We have examined the induction of alkali-labile regions in DNA of human neoplastic cells treated with 5-fluorouracil and 5-fluorodeoxyuridine. 5-Fluorouracil induces DNA lesions by two mechanisms: incorporation of drug into DNA and a second mechanism not involving the incorporation. The second mechanism is seen in cells treated with aphidicolin, a specific inhibitor of DNA polymerase alpha, to stop the movement of the DNA replication forks. 5-Fluorodeoxyuridine is not incorporated into DNA of these cells; only the second mechanism of induction of alkali-labile DNA is detected. The second mechanism is in all probability due to inefficient DNA repair of normally occurring defects in purine and pyrimidine residues. Furthermore there is a correlation between increasing levels of alkali-labile regions in the DNA and cytotoxicity of the drugs. This may be one explanation for the cytocidal effects of 5-fluoropyrimidines.

Leucovorine prevents methotrexate from inducing DNA lesions

Methotrexate induces DNA strand fragmentation. We show here that the induction of DNA lesions can be overcome by treatment with leucovorine, a folic acid analogue.

Ca2+ and calmodulin are involved in the processes conferring stability to DNA in proliferating neoplastic cells

We have examined, in proliferating neoplastic cells, the effect on DNA of EGTA (a chelator of Ca2+) and W7 (an inhibitor of calmodulin). The treatment results in release of single-stranded DNA fragments (2-10 kb) from pre-labelled HMW DNA. When DNA from synchronized neoplastic cells in S phase is examined, almost all pre-labelled DNA appears as short fragments. However, fragmentation does not occur in growth-arrested cells or in normal cells. Furthermore, fragmentation can be prevented by incubating cells in excessive amounts of Ca2+. Hence Ca2+ and the Ca2+-binding protein calmodulin are involved in the processes conferring stability to DNA in proliferating neoplastic cells.

There exists a distinct stage during mammalian DNA synthesis immediately after joining of replication intermediates

We describe an approach, using alkaline cell lysis and digestion with nuclease S1, which permits to distinguish between newly ligated DNA and the DNA of mature chromatin. When cells with steady-state labelled DNA (mature DNA) are analyzed, the results show labelled "nucleosomal-sized" DNA. However, when DNA of cells pulse-labelled with thymidine for 45 seconds is examined one can detect only large DNA. The newly ligated DNA is not reduced to "nucleosomal-sized" DNA by nuclease S1. When the large DNA is denatured in formamide one can detect 10 kb DNA fragments. Furthermore in pulse-chase experiments there appear, after formamide-treatment, increasing amounts of "nucleosomal-sized" DNA with a parallel decrease in the amount of 10 kb DNA fragments. Hence the newly ligated, large, DNA differs from mature DNA and represents a distinct stage during DNA replication.

The increased cytotoxicity in colon adenocarcinoma of methotrexate-5-fluorouracil is not associated with increased induction of lesions in DNA by 5-fluorouracil

Sequential methotrexate-5-fluorouracil (Mtx-5-Fu) reduces proliferation of human colon adenocarcinoma cells. The DNA of treated cells was examined by cell lysis in dilute alkali in order to detect if there is any release of single-stranded DNA fragments, which occurs in cells treated with 5-Fu. The results showed that in spite of increased cytotoxicity of Mtx-5-Fu there is reduced release of DNA fragments. The findings are paralleled by a reduced incorporation of 5-Fu into DNA. Hypoxanthine reduces the growth inhibitory effect of Mtx-5-Fu. In treated cells grown in the presence of hypoxanthine, alkaline lysis causes release of DNA fragments from bulk DNA, in contrast to cells grown without hypoxanthine. Hence, the increased cytotoxicity of Mtx-5-Fu in human colon adenocarcinoma is not associated with enhanced lesions in DNA by 5-Fu.