Human AIF-M2 is an unusual flavoprotein oxidoreductase that binds DNA, nicotinamide coenzyme, and the modified flavin 6-hydroxy-FAD. Using multiple solution methods to investigate the redox chemistry and binding interactions of AIF-M2, we demonstrate that binding of DNA and coenzyme to AIF-M2 is mutually exclusive. We also show that DNA binding does not perturb the redox chemistry of AIF-M2, but it has significant effects on the reduction kinetics of the 6-hydroxy-FAD cofactor by NAD(P)H. Based on quantitative analysis of ligand binding and redox chemistry, we propose a model for the function of AIF-M2. In this model, DNA binding suppresses the redox activity of AIF-M2 by preventing the binding of the reducing coenzyme NAD(P)H. This DNA-mediated suppression of AIF-M2 activity is expected to lower cellular levels of superoxide and peroxide, thereby lessening survival signaling by Ras, NF-B, or AP-1, as suggested from knock-out studies of the related AIF in human colon cancer cell lines. We show marked differences between AIF-M2 and AIF. DNA and coenzyme binding activity is retained in the C-terminal deletion mutant AIF-M2-(⌬319 -613), whereas DNA binds to the C-terminal D3 domain of AIF. Our work provides the first analysis of AIF-M2 ligand interactions and redox chemistry and identifies an important mechanistic connection between coenzyme and DNA binding, redox activity, and the apoptotic function of AIF-M2. Through its DNA binding activity, we suggest that AIF-M2 lessens survival cell signaling in the presence of foreign (e.g. bacterial and (retro)viral) cytosolic DNA, thus contributing to the onset of apoptosis.Apoptosis (programmed cell death), a cellular process in higher organisms by which cells die (1, 2), can be induced by toxic insult (e.g. chemical damage) or physical disruption of cells. It is critical in the development of multicellular organisms, including the development of the embryo and vital organs, and in cellular homeostasis (3). Up to 70 billion human adult cells undergo apoptosis each day (4). Lesions in the apoptotic process or its regulation result in developmental defects, immortalized cells, and cancers (3). The mitochondrion is a key apoptosis regulator, and pro-apoptotic and cell damage-controlled pathways feed back to the mitochondrion and induce permeabilization of mitochondrial membranes (5). In part, this is under the control of the Bcl-2 protein family, which contains members with either pro-(e.g. Bax) or anti-apoptotic (e.g. Bcl-2) functions (6). Cytotoxic molecules in the mitochondrial intermembrane space are released on membrane permeabilization and act as cell death effectors, some depending on activation by caspase proteases (7). Release of cytochrome c triggers activation of the initiator caspase-9. Downstream activation of other caspases leads to proteolytic cleavage of key target molecules (e.g. laminins) leading to cell morphology changes such as plasma membrane perturbations, condensation and fragmentation of nuclear chromatin, and compaction of cytoplasmic organelles and...