Potency and property of DNA conformational damage determine ATM activation: two new DNA topological probes.

We have shown previously the intercalation geometry of a series of acenaphtho [1,2-b] pyrrole derivatives with DNA double helix in vitro. In this report we chose a couple of intercalating analogues and a Chinese traditional medicine Tanshinone IIA as probes to investigate the response of DNA damage sensor ataxia-telangiectasia mutated (ATM) protein toward the DNA topological change in vivo. The two analogues (1)a (3-(4-Methyl-piperazin)-8-oxo-8H-acenaphtho [1,2-b]pyrrole -9-carbonitrile) and (3)a (3-(3-Dimethylamino-propylamino)-8-oxo-8H-acenaphtho[1,2-b]pyrrole-9- carbonitrile) could unwind double helix to different extents, whereas Tanshinone IIA could wind the double helix. Using a combination of circular dichroism (CD) studies and immunoflurescence assays, we found for the first time that the ATM protein kinase can respond to the unwinding chromatin conformational damage caused by (1)a and (3)a, while it could not be activated by the winding effects caused by Tanshinone IIA. Moreover, the amount of ATM protein phosphorylation is consistent with the degree of unwinding conformational damage. The average number of ATM foci in an MCF-7 cell is 32 +/- 1.5 at 6 microM (1)a, which is significantly higher than the 8 microM (3)a exposure (15 +/- 0.5, p < 0.5). A new couple of DNA topological probes, (1)a and (3)a have been found for the future semi-quantitative investigation of factors involved in the DNA damage pathway. Copyright (c) 2008 John Wiley & Sons, Ltd.