FEN-catalysed reactions

The main activity of the FENs is of course their flap endonuclease activity. In its simplest form FENs can cleave 5' flap or "pseudo Y" structures one nucleotide into the double-stranded region immediately downstream of a single-stranded 5' arm.

They can also carry out exonucleolyticactivity on free 5' ends of single-stranded or double-stranded DNA. Single strands of DNA are represented as black lines for simplicity, parallel lines indicate double-helical DNA.

The length of the 5' arm can be anything from one or a few nucleotides to several hundred. The exonucleotytic products are usually short, 1 to 3 nucleotides in length but there does seem to be some dependence upon the sequence of the single-stranded DNA. For example, oligo G tracts resist cleavage (probably due to quadruplex formation Sayers & Eckstein, JBC).

Some FENs can cleave single-stranded closed-circular DNA such as the Taq Polymerase-associated FEN and bacteriophage T5 FEN (also known as T5 D15 5'-3' exonuclease see Sayers & Eckstein). They have also been reported to have "gap specific endonuclease" activity or GEN.

The term gap endonuclease (GEN) was coined by Shen and coworkers in 2005 when they observed such an activity in human FEN but such and activity was observed for T5FEN much earlier (Sayers & Eckstein 1991).

DNA is represented here as a black line for simplicity, parallel lines represent double-helical DNA.