Human cells remove bulky adducts from DNA by excising single-stranded fragments 27-29 nucleotides in length by an enzyme system consisting of at least 14 polypeptides. All of the previous work on characterizing the excision reaction was conducted with plasmids 3 or 8 kilobases in length. To determine if the size and tertiary structure of DNA play a role in the excision reaction and to find out if large DNA fragments are necessary to contact all of the subunits of the excinuclease, we performed experiments with circular DNA and with linear DNA fragments of various sizes. We found that the human excinuclease is capable of removing DNA adducts from linear and covalently closed circular DNAs with about the same efficiency. Furthermore, we found that the excinuclease can remove a thymine dimer or a psoralen-thymine monoadduct from linear fragments provided that the distance between the lesion and the 5'-terminus of the damaged strand is > or = 60 nucleotides and the distance between the lesion and the 3'-terminus is > or = 44 nucleotides. Thus, the minimum size substrate for human excinuclease is approximately 100 base pairs in length.