SiDNA and Other Tools for the Indirect Induction of DNA Damage Responses

Abstract

Cells respond to DNA damage by activating an intricate signaling network leading to DNA repair, cell cycle arrest or apoptosis. In recent years, progress has been made in the discovery and characterization of a number of DNA repair pathways, and it has become apparent that the inhibition of specific components of these pathways could offer new targets for combating the resistance of tumors to chemotherapy or radiotherapy. A thorough understanding of the various DNA repair pathways and their regulation is therefore essential. The DNA damage response (DDR) is of great importance in determining cell fate decisions. It includes many signal amplification steps and several steps that are partly redundant due to the ability of different kinases to phosphorylate the same target. Furthermore, the timing and origin of the damage play an important role in determining the DNA repair pathway activated. All this makes it difficult to study the role of one particular protein in DNA damage signaling. In addition, the available tools for activating DNA repair pathways are mostly agents that systematically produce more than one type of DNA damage. Even if the damage caused is initially of one predominant type (as for topoisomerase inhibitors, alkylators or the I-SceI endonuclease system), the damage may rapidly be transformed by normal cellular processes, such as DNA replication, or specific nuclease activities. Studies of the DDR become evenmore complicated if the agent used to create DNA lesions also damages other cellular components, as is the case for ionizing radiation (IR), alkylators and hydrogen peroxide. Furthermore, the damage is transient, as DNA damage signaling is rapid and lesions are quickly repaired. The signal induced by the damage therefore disappears rapidly, soon after the induction of damage. In some cells, the DNA may not be successfully repaired, leading to apoptosis or senescence. These aspects make it difficult to study the signaling network induced by a given type of damage. In this chapter, we will provide an overview of the response of the cell to DNA damage and possible ways of inducing a DDR in cells without actually damaging chromatin. We will focus on stabilized short interfering DNAmolecules (siDNA), which mimic different types of damage and induce a pure damage-specific response. SiDNA and Other Tools for the Indirect Induction of DNA Damage Responses