Page 22 - ebook

[A. Biochemistry/Molecular Biology] A-11

The mechanism of gap creation by a multifunctional nuclease

during base excision repair

Jungmin Yoo¹, Gwangrog Lee¹*

¹School of Life Sciences, GIST, Gwangju 61005, Korea

During base excision repair, a transient single-stranded DNA (ssDNA) gap is produced at the apurinic/apyrimidinic
(AP) site. Exonuclease III, capable of performing both AP endonuclease and exonuclease activity, are responsible for

gap creation in bacteria. We used single-molecule fluorescence resonance energy transfer to examine the mecha-
nism of gap creation. We found an AP site anchor-based mechanism by which the intrinsically distributive enzyme

binds strongly to the AP site and becomes a processive enzyme, rapidly creating a gap and an associated transient
ssDNA loop. The gap size is determined by the rigidity of the ssDNA loop and the duplex stability of the DNA and

is limited to a few nucleotides to maintain genomic stability. When the 3′ end is released from the AP endonuclease,
polymerase I quickly initiates DNA synthesis and fills the gap. Our work provides previously unidentified insights

into how a signal of DNA damage changes the enzymatic functions.