By using a band mobility shift assay, deoxyinosine 3-endonuclease, an Escherichia coli enzyme which recognizes deoxyinosine, AP site, urea residue, and base mismatches in DNA, was shown to bind tightly to deoxyinosine-containing oligonucleotide duplexes. Two distinct protein-DNA complexes were observed, the faster migrating complex (complex I, K d ؍ 4 ؋ 10 ؊9 M) contained one molecule of deoxyinosine 3-endonuclease, while the slower migrating complex (complex II, K d ؍ 4 ؋ 10 ؊7 M) contained two molecules of the protein bound to every molecule of duplex DNA. The endonucleolytic activity of deoxyinosine 3-endonuclease paralleled the formation of the complex I. Interestingly, deoxyinosine 3-endonuclease exhibited similar affinities for both the substrate and the nicked duplex product and thus remained bound to the DNA after the cleavage reaction. The formation of a stable complex required the presence of a duplex structure 5 to the deoxyinosine residue. DNase I footprinting revealed that deoxyinosine 3-endonuclease protected 4 -5 nucleotides 5 to the deoxyinosine, and when complex II was formed, at least 13 nucleotides 3 to deoxyinosine were protected. Based on these results, a model is proposed for the interaction of deoxyinosine 3-endonuclease with DNA containing deoxyinosine.Deoxyinosine in DNA can arise from deamination of deoxyadenosine, which can be spontaneous or promoted by exposure of DNA to ionizing radiation, UV light, or nitrous acid (1-3). Deoxyinosine in DNA is premutagenic and can lead to A/T to C/G transition mutations (4). Deoxyinosine in DNA was thought to be removed by hypoxanthine DNA glycosylase, which has been partially purified from Escherichia coli as well as other eukaryotic sources (5-8). However, it was reported recently (9) that a well characterized repair enzyme, 3-methyladenine DNA glycosylase II, encoded by alkA gene in E. coli possesses hypoxanthine DNA glycosylase activity and releases hypoxanthine from deoxyinosine-containing DNA, suggesting that both 3-methyladenine DNA glycosylase and hypoxanthine DNA glycosylase activities reside in the same protein. It has also been shown that 3-methyladenine DNA glycosylase from human (ANPG protein), rat (APDG protein), and yeast (MAG protein) are able to excise hypoxanthine from DNA (9).Recently, we identified and purified a novel deoxyinosine specific endonuclease from E. coli, deoxyinosine 3Ј-endonuclease (10). The enzyme hydrolyzes the second phosphodiester bond 3Ј to the deoxyinosine residue. In addition to deoxyinosine, deoxyinosine 3Ј-endonuclease also recognizes AP site, urea residue, and base mismatches in DNA and exhibits strand-specific cleavage of base mismatches in DNA (11). In contrast to hypoxanthine DNA glycosylase, deoxyinosine 3Ј-endonuclease does not remove deoxyinosine or other lesions from the DNA (10). Therefore, it is likely that other proteins are required to complete the repair process initiated by deoxyinosine 3Ј-endonuclease.The initial binding of a protein to DNA is critical for multiprotein interaction with DN...