The endonuclease activity of FENs was initially identified as acting on a DNA duplex which has a single-stranded 5' overhang on one of the strands (termed a "5' flap", hence the name flap endonuclease).
Initially, researchers found that FENs had an endonuclease activity targeting a specific type of DNA structure: a double-stranded DNA with a single 5' overhang on one strand, known as a "flap".