In 1990, two secretive British record producers remixed "Tom's Diner" without Suzanne Vega's permission, grafting her vocals onto an infectious dance beat from Soul II Soul, and turning her simple ad-libbed outro - "Doo doo doo doo, doo da-doo doo" - into the song's driving hook. They took the name "DNA", later calling themselves The DNA Disciples to distinguish themselves from no wave band DNA, and released their work on a limited basis for distribution to clubs as "Oh Suzanne", by "DNA featuring Suzanne Vega". Vega's record company of the time, A&M, decided to buy the single and release it themselves rather than taking DNA to court for copyright infringement after consultation with Vega, who liked the interpretation, and DNA, who conducted the whole deal through intermediaries in order to hide their true identities. The remix became a much larger hit than Vega had with the song originally, and spawned a number of rap, dance, and rock remixes and remakes from artists such as Peter Behrens and "Bingo Hand Job", a whimsical one-time collaboration between Billy Bragg and R.E.M. It was also sampled in songs by Public Enemy and Lil Kim, among other rap acts.

In 1991, Vega, noting the huge number of remakes of the song, released Tom's Album, a compilation of different versions of the song, spanning a variety of musical genres, including a parody that worked in references to I Dream Of Jeannie, called "Jeannie's Diner." The album also featured another DNA remix of one of her songs, "Rusted Pipe."