Our recent work has focused on the roles of the FANCJ helicase in the DNA damage response. Mutations in the BRCA1-associated helicase BACH1 have been associated with early-onset breast cancer and cellular data suggest a role of the helicase in double strand break repair and checkpoint control. Recently, BACH1 (FANCJ) has been genetically linked to the chromosomal instability disorder Fanconi anemia (FA). To understand the molecular functions and biological substrates that FANCJ helicase acts upon, we have systematically evaluated the ability of purified recombinant FANCJ to unwind a panel of related DNA substrates with distinct tail variations including single-stranded versus double-stranded character, tail length, or backbone continuity. In addition, we have assessed the ability of BACH1 to catalytically unwind DNA structures proposed to be key intermediates of cellular DNA metabolism. The results from these unwinding studies provide a platform to investigate the molecular interactions of the FANCJ helicase with its protein partners in double strand break repair by homologous recombination. In terms of protein interactions, we have identified and characterized two novel FANCJ partners, the mismatch repair protein complex MutL alpha and the single-stranded DNA binding protein RPA. FANCJ interactions with these DNA repair factors play important roles in the DNA damage response. Our current efforts are directed toward understanding the roles of FANCJ in the classic FA pathway of cross-link repair as well as stabilization and progression of the replication fork.