Kinase experiment:

For DNA topoisomerase IIα assays, the 161-bp fragment from pBluescript SK(-) phagemid DNA or single stranded oligonucleotides are 5'-end labeled with [32P]ATP and T4 polynucleotide kinase. Labeling mixtures are subsequently centrifuged through Mini Quick Spin DNA columns (for pSK fragments) or Oligo columns (for oligonucleotides) to remove the unincorporated label. Annealing to the complementary strand of the oligonucleotides is done by heating the reaction mixture to 95℃ and overnight cooling to room temperature in 10 mM Tris-HCl (pH 7.8), 100 mM NaCl, and 1 mM EDTA. DNA substrates (10 pmol/reaction) are incubated with 500 ng of top2a or top2h in the presence or absence of Dp44mT for the indicated times at 25℃ in 10 μL of reaction buffer. Reactions are stopped by adding SDS (final concentration 0.5%). Samples are separated on 16% (for pSK DNA) or 20% (for the oligonucleotides) denaturing polyacrylamide gels (7 M urea). Imaging and quantitation are done using a PhosphorImager[1].

Cell experiment:

Cell proliferation is measured using a sulforhodamine B dye–based assay. MDA-MB-231(breast cancer) and MCF-12A (healthy mammary epithelial) cells are incubated with increasing concentrations of Dp44mT (0.01, 0.1, 1, 10, 100 μM). Results are expressed relative to control[1].

Dp44mT is an iron chelator that selectively inhibit topoisomerase IIα, with an GI50 value of ~100 nmol/L in the human breast cancer cell line MDA-MB-231 [1].

Topoisomerases play important roles in chromosome segregation, DNA synthesis, and transcription. Topoisomerase I and topoisomerase II are two major types of topoisomerases in eukaryotes. Human cells contain two isozymes of topoisomerase II, named topo IIa and topo IIβ [2].

In control experiments, the Nalm-6 leukemic top2α+/- cells expressed ~57% as much levels of top2α enzyme as the wild type cells. Treated with Dp44mT at 100 nmol/L, compared with the top2α+/+ cells, top2α+/- cells showed partial resistance to the cytotoxic effects of the drug.After the exposure to Dp44mT at 100 nmol/L, the top2α+/+ cells showed 31.7%, while the top2α+/- cells only showed 9.4% sub-G1 containing cells. In HeLa cells, transient siRNA-mediated knockdown of top2α resulted in a reduction of ~78% in the protein level for top2α. In top2α siRNA cells, a partial resistance to Dp44mT (0.1 and 0.3 μmol/L) was found at 72 hours, compared with the control siRNA-treated cells [1].

In vivo, 6 and 24 hours after the treatment with 0.1 and 1 μmol/L of Dp44mT, the treatment resulted in the covalent complex formation between DNA and top2α. No complex formation was found after the treatment when probed for top1 or top2β. Caspase inhibitor pretreatment did not rescue the formation of top2α complex, so the formed top2α-DNA complexes were not the secondary effect of apoptosis [1].

References:
[1].  Rao VA, Klein SR, Agama KK, et al. The iron chelator Dp44mT causes DNA damage and selective inhibition of topoisomerase IIα in breast cancer cells. Cancer research, 2009, 69(3): 948-957.
[2].  Tan KB, Dorman TE, Falls KM, et al. Topoisomerase IIα and topoisomerase IIβ genes: characterization and mapping to human chromosomes 17 and 3, respectively. Cancer Research, 1992, 52(1): 231-234.