flap endonuclease

Flap endonucleases (FENs, also known as 5' durgs 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.{{cite journal |doi=10.1006/jtbi.1994.1202 |title=Computer Aided Identification of a Potential 5′-3′ Exonuclease Gene Encoded by Escherichia coli |year=1994 |last1=Sayers |first1=Jon R. |journal=Journal of Theoretical Biology |volume=170 |issue=4 |pages=415–21 |pmid=7996866}}{{cite journal |doi=10.1146/annurev.biochem.73.012803.092453 |title=FLAP ENDONUCLEASE 1: A Central Component of DNA Metabolism |year=2004 |last1=Liu |first1=Yuan |last2=Kao |first2=Hui-I |last3=Bambara |first3=Robert A. |journal=Annual Review of Biochemistry |volume=73 |pages=589–615 |pmid=15189154}}{{cite journal |doi=10.1016/S0968-0004(98)01259-6 |title=Structure-specific DNA cleavage by 5′ nucleases |year=1998 |last1=Ceska |first1=T |journal=Trends in Biochemical Sciences |volume=23 |issue=9 |pages=331–6 |pmid=9787638 |last2=Sayers |first2=JR}}

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{{cite journal |doi=10.1126/science.7683443|title=Structure-specific endonucleolytic cleavage of nucleic acids by eubacterial DNA polymerases|year=1993 |last1=Lyamichev |first1=Victor |last2=Brow |first2=Mary Ann D. |last3=Dahlberg |first3=James E. |journal=Science |volume=260 |issue=5109 |pages=778–783|pmid=7683443|bibcode=1993Sci...260..778L}} (termed a "5' flap", hence the name flap endonuclease{{cite journal |pmid=8131753 |year=1994 |last1=Harrington |first1=John J. |last2=Lieber |first2=Michael R. |title=The characterization of a mammalian DNA structure-specific endonuclease |volume=13 |issue=5 |pages=1235–46 |pmc=394933 |journal=The EMBO Journal |doi=10.1002/j.1460-2075.1994.tb06373.x}}). FENs catalyse hydrolytic cleavage of the phosphodiester bond at the junction of single- and double-stranded DNA.{{cite journal |doi=10.1074/jbc.274.30.21387 |title=A Comparison of Eubacterial and Archaeal Structure-specific 5′-Exonucleases|year=1999 |last1=Kaiser |first1=Michael W. |last2=Lyamicheva |first2=N. |last3=Ma|first3=W. |last4=Miller|first4=C. |last5=Neri|first5=B. |last6=Fors|first6=L. |last7=Lyamichev |first7=V. |journal=Journal of Biological Chemistry |volume=274|issue=30|pages=21387–21394|pmid=10409700|doi-access=free }} Some 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.{{cite journal |doi=10.1038/382090a0 |title=A helical arch allowing single-stranded DNA to thread through T5 5'-exonuclease |year=1996 |last1=Ceska |first1=T. A. |last2=Sayers |first2=J. R. |last3=Stier |first3=G. |last4=Suck |first4=D. |journal=Nature |volume=382 |issue=6586 |pages=90–3 |pmid=8657312|bibcode=1996Natur.382...90C |s2cid=11159640 }}

Flap endonucleases have been used in biotechnology, for example the Taqman PCR assay {{Cite web |url=http://www.med.unc.edu/anclinic/Tm.htm |title=Taqman Principles |access-date=2006-12-27 |archive-date=2006-12-09 |archive-url=https://web.archive.org/web/20061209021601/http://www.med.unc.edu/anclinic/Tm.htm |url-status=dead }}{{full citation needed|date=November 2012}} and the Invader Assay for mutation and single nucleotide polymorphism (SNP) detection.{{cite journal |doi=10.1038/7044|title=Polymorphism identification and quantitative detection of genomic DNA by invasive cleavage of oligonucleotide probes|year=1999 |last1=Lyamichev |first1=V. |last2=Mast |first2=A.L. |last3=Hall |first3=J.G. |last4=Prudent |first4=J.R. |last5=Kaiser |first5=M.W. |last6=Takova |first6=T. |last7=Kwiatkowski |first7=R. |last8=Sander |first8=T. |last9=deArruda |first9=M. |last10=Arco |first10=D. |last11=Neri |first11=B.P. |last12=Brow|first12=M.A. |journal=Nature Biotechnology |volume=17|issue=3|pages=292–296|pmid=10096299|s2cid=37888925}}{{cite journal |doi=10.1016/j.mrfmmm.2004.08.016 |title=The Invader® assay for SNP genotyping |year=2005 |last1=Olivier |first1=Michael |journal=Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis |volume=573 |pmid=15829241 |pages=103–10 |issue=1–2 |pmc=2771639}}