TheAtaxia telangiectasia-mutated (ATM) and the ATM-Rad3-related (ATR) kinases are master regulators of the DNA damage-signaling pathways that respond to a wide variety of DNA damage. In this chapter, we describe an in vitro biochemical assay to study the activation of ATM and ATR by double-stranded DNA breaks (DSBs) (Shiotani and Zou, 2009,Mol Cell33, 547–58). In this assay, DNA fragments with different structural features are used to activate ATM and ATR in human cell extracts, and the activation of ATM and ATR is monitored by the phosphorylation of specific ATM and ATR substrates. Importantly, in this assay both ATM and ATR are activated in a DNA structure-regulated manner, providing a useful tool to characterize the DNA structural determinants for their activation. The four primary steps of this assay are as follows: (1) preparation of nuclear extracts from cultured human cells; (2) generation of various DNA fragments using DNA oligonucleotides or plasmids; (3) incubation of DNA fragments in extracts; (4) analysis of the phosphorylation of specific ATM or ATR substrates.
