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.^[1][2][3]

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^[4] (termed a "5' flap", hence the name flap endonuclease^[5]). FENs catalyse hydrolytic cleavage of the phosphodiester bond at the junction of single- and double-stranded DNA.^[6] 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.^[7]

Flap endonucleases have been used in biotechnology, for example the Taqman PCR assay ^[8] and the Invader Assay for mutation and single nucleotide polymorphism (SNP) detection.^[9][10]

See also

• Endonucleases

References

1. Sayers, Jon R. (1994). "Computer Aided Identification of a Potential 5′-3′ Exonuclease Gene Encoded by Escherichia coli". Journal of Theoretical Biology. 170 (4): 415–21. doi:10.1006/jtbi.1994.1202. PMID 7996866.
2. Liu, Yuan; Kao, Hui-I; Bambara, Robert A. (2004). "FLAP ENDONUCLEASE 1: A Central Component of DNA Metabolism". Annual Review of Biochemistry. 73: 589–615. doi:10.1146/annurev.biochem.73.012803.092453. PMID 15189154.
3. Ceska, T; Sayers, JR (1998). "Structure-specific DNA cleavage by 5′ nucleases". Trends in Biochemical Sciences. 23 (9): 331–6. doi:10.1016/S0968-0004(98)01259-6. PMID 9787638.
4. Lyamichev, Victor; Brow, Mary Ann D.; Dahlberg, James E. (1993). "Structure-specific endonucleolytic cleavage of nucleic acids by eubacterial DNA polymerases". Science. 260 (5109): 778–783. Bibcode:1993Sci...260..778L. doi:10.1126/science.7683443. PMID 7683443.
5. Harrington, John J.; Lieber, Michael R. (1994). "The characterization of a mammalian DNA structure-specific endonuclease". The EMBO Journal. 13 (5): 1235–46. doi:10.1002/j.1460-2075.1994.tb06373.x. PMC 394933. PMID 8131753.
6. Kaiser, Michael W.; Lyamicheva, N.; Ma, W.; Miller, C.; Neri, B.; Fors, L.; Lyamichev, V. (1999). "A Comparison of Eubacterial and Archaeal Structure-specific 5′-Exonucleases". Journal of Biological Chemistry. 274 (30): 21387–21394. doi:10.1074/jbc.274.30.21387. PMID 10409700.
7. Ceska, T. A.; Sayers, J. R.; Stier, G.; Suck, D. (1996). "A helical arch allowing single-stranded DNA to thread through T5 5'-exonuclease". Nature. 382 (6586): 90–3. Bibcode:1996Natur.382...90C. doi:10.1038/382090a0. PMID 8657312. S2CID 11159640.
8. http://www.med.unc.edu/anclinic/Tm.htm^{[full citation needed]}
9. Lyamichev, V.; Mast, A.L.; Hall, J.G.; Prudent, J.R.; Kaiser, M.W.; Takova, T.; Kwiatkowski, R.; Sander, T.; deArruda, M.; Arco, D.; Neri, B.P.; Brow, M.A. (1999). "Polymorphism identification and quantitative detection of genomic DNA by invasive cleavage of oligonucleotide probes". Nature Biotechnology. 17 (3): 292–296. doi:10.1038/7044. PMID 10096299. S2CID 37888925.
10. Olivier, Michael (2005). "The Invader® assay for SNP genotyping". Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis. 573 (1–2): 103–10. doi:10.1016/j.mrfmmm.2004.08.016. PMC 2771639. PMID 15829241.

External links

External link Flap endonucleases, 5'-3' exonucleases & 5' nucleases