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. Author manuscript; available in PMC: 2013 Apr 1.

Published in final edited form as: Trends Biochem Sci. 2012 Jan 27;37(4):162–172. doi: 10.1016/j.tibs.2011.12.002

FEN1 modulates trinucleotide repeat stability in different ways during DNA replication and long-patch BER. During DNA replication (a), pol δ/ε strand-displacement DNA synthesis creates a repeat containing 5′-flap that subsequently folds back into a hairpin. The repeat-containing hairpin competes with upstream repeats to anneal to the template strand resulting in a dynamic equilibration between the repeat-containing hairpin configuration and a double-flap configuration with a long 3′-flap and a short 5′-flap. FEN1 subsequently captures the 5′-short flap, loads from the 5′-end of the flap and tracks down through the flap along with DNA branch migration until FEN1 captures an intermediate with a 1 nt-3′-flap. FEN1 then cleaves the repeat-containing 5′-flap or hairpin, and expansion does not occur. However, during BER of a base lesion such as 8-oxoG (b), single-strand DNA breaks in the context of trinucleotide repeats (induced by base removal and APE1 5′-incision of the AP site) often results in DNA slippage. This is especially the case when the 5′-sugar phosphate group ( ) cannot be removed by pol β’s dRP lyase. Strand slippage results in formation of intermediates with multi-nucleotide gaps and repeat-containing hairpins. Pol β conducts gap-filling synthesis to fill the gaps, but terminates synthesis at the base of the hairpin. Formation of a stable hairpin structure inhibits conventional FEN1 cleavage activity for removing the entire length of the hairpin. Instead, FEN1 “alternate cleavage” of a short flap generated at the 5′-end of the hairpin by DNA realignment is allowed, resulting in removal of the flap with the 5′-end dRP group, a ligatable nick, ligation and repeat expansion.

Inline graphic — FEN1 modulates trinucleotide repeat stability in different ways during DNA replication and long-patch BER. During DNA replication (a), pol δ/ε strand-displacement DNA synthesis creates a repeat containing 5′-flap that subsequently folds back into a hairpin. The repeat-containing hairpin competes with upstream repeats to anneal to the template strand resulting in a dynamic equilibration between the repeat-containing hairpin configuration and a double-flap configuration with a long 3′-flap and a short 5′-flap. FEN1 subsequently captures the 5′-short flap, loads from the 5′-end of the flap and tracks down through the flap along with DNA branch migration until FEN1 captures an intermediate with a 1 nt-3′-flap. FEN1 then cleaves the repeat-containing 5′-flap or hairpin, and expansion does not occur. However, during BER of a base lesion such as 8-oxoG (b), single-strand DNA breaks in the context of trinucleotide repeats (induced by base removal and APE1 5′-incision of the AP site) often results in DNA slippage. This is especially the case when the 5′-sugar phosphate group ( ) cannot be removed by pol β’s dRP lyase. Strand slippage results in formation of intermediates with multi-nucleotide gaps and repeat-containing hairpins. Pol β conducts gap-filling synthesis to fill the gaps, but terminates synthesis at the base of the hairpin. Formation of a stable hairpin structure inhibits conventional FEN1 cleavage activity for removing the entire length of the hairpin. Instead, FEN1 “alternate cleavage” of a short flap generated at the 5′-end of the hairpin by DNA realignment is allowed, resulting in removal of the flap with the 5′-end dRP group, a ligatable nick, ligation and repeat expansion.