Implementing Fluorescence Enhancement, Quenching, and FRET for Investigating Flap Endonuclease 1 Enzymatic Reaction at the Single-Molecule Level

Mohamed A. Sobhy, Muhammad Tehseen, Masateru Takahashi, Amer Bralić, Alfredo De Biasio, Samir M. Hamdan

Research output: Contribution to journalArticlepeer-review

3 Scopus citations


Flap endonuclease 1 (FEN1) is an important component of the intricate molecular machinery for DNA replication and repair. FEN1 is a structure-specific 5′ nuclease that cleaves nascent single-stranded 5′ flaps during the maturation of Okazaki fragments. Here, we review our research primarily applying single-molecule fluorescence to resolve important mechanistic aspects of human FEN1 enzymatic reaction. The methodology presented in this review is aimed as a guide for tackling other biomolecular enzymatic reactions by fluorescence enhancement, quenching, and FRET and their combinations. Using these methods, we followed in real-time the structures of the substrate and product and 5’ flap cleavage during catalysis. We illustrate that FEN1 actively bends the substrate to verify its features and continues to mold it to induce a protein disorder-to-order transitioning that controls active site assembly. This mechanism suppresses off-target cleavage of non-cognate substrates and promotes their dissociation with an accuracy that was underestimated from bulk assays. We determined that product release in FEN1 after the 5′ flap release occurs in two steps; a brief binding to the bent nicked-product followed by longer binding to the unbent nicked-product before dissociation. Based on our cryo-electron microscopy structure of the human lagging strand replicase bound to FEN1, we propose how this two-step product release mechanism may regulate the final steps during the maturation of Okazaki fragments.
Original languageEnglish (US)
JournalComputational and Structural Biotechnology Journal
StatePublished - Jul 2021
Externally publishedYes

Bibliographical note

KAUST Repository Item: Exported on 2021-07-29
Acknowledgements: This research was supported by King Abdullah University of Science and Technology through the KAUST Competitive Research Grant URF/1/3764-01-01 to S.M.H.
This publication acknowledges KAUST support, but has no KAUST affiliated authors.

ASJC Scopus subject areas

  • Biophysics
  • Biotechnology
  • Genetics
  • Biochemistry
  • Structural Biology
  • Computer Science Applications


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