Flap endonuclease

Flap endonucleases (FENs, also known as 5' nucleases in older references) are a class of nucleolytic enzymes that act as both 5'-3' exonucleases and structure specific endonucleases on specialised DNA structures that occur during the biological processes of DNA replication, DNA repair and DNA recombination. Flap endonucleases have been identified in eukaryotes, prokaryotes, archaea and some viruses. Organisms can have more than one FEN homologue, this redundancy may give an indication of the importance of these enzymes. In prokaryotes, the FEN enzyme is found as an N-terminal domain of DNA polymerase I, but some prokaryotes appear to encode a second homologue. [ Sayers JR (1994) J Theor Biol, 170(4):415. PMID 7996866 ]

The endonuclease activity of FENs was initially identifed 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) [ Harrington JJ and Lieber MR (1994) EMBO J., 13, 1235-1246. PMID 8131753 ] . FENs catalyse hydrolytic cleavage of the phosphodiester bond at the junction of single and double stranded DNA. FENs can also act as 5'-3' exonucleases on the 5' terminus of the flap strand and on 'nicked' DNA substrates.

Protein structure models based on X-ray crystallography data suggest that FENs have a flexible arch created by two α-helices through which the single 5' strand of the 5' flap structure can thread [ Ceska TA "et al.," (1996) Nature, 382, 90-93. PMID 8657312 ] .

Flap endonucleases have been used in biotechnology, for example the Taqman PCR assay [ [http://www.med.unc.edu/anclinic/Tm.htm Taqman Principles ] ] and the Invader single nucleotide polymorphism (SNP) assay [ Olivier M (2005) Mutat. Res. 573, 103-110. PMID 15829241] .

For a more detailed reviews of FENs see [ Liu Y "et al"., (2004) Annu. Rev. Biochem., 73, 589-615. PMID 15189154 ] [ Ceska TA and Sayers JR, (1998) Trends Biochem. Sci., 23, 331-336. PMID 9787638]

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* Endonucleases