Figure 5. Hypothetical model for formation of a ligatable nick by hairpin realignment accompanying LP-BER.

In the context of CAG repeats, the single-stranded BER intermediates with a 5′-sugar phosphate ( ) may undergo spontaneous DNA slippage resulting in formation of multi-nucleotide gaps and a CAG repeat-containing hairpin with 5′-sugar phosphate (i). Pol β performs multi-nucleotide gap-filling synthesis to produce a newly synthesized CAG repeat strand, eventually colliding with the 5′-base of the hairpin. Pol β pauses at the base of the hairpin and dissociates from this product (ii). The CAG repeat hairpin undergoes spontaneous DNA realignment. This leads to formation of intermediates with alternate conformations (iii) of an annealed 5′-region consisting of 3 nucleotides (one CAG repeat) and various lengths of 5′-repeat flap, consisting of 3 nt [(CAG)₁], 6 nt [(CAG)₂], 9 nt [(CAG)₃], etc. FEN1 loading and alternate cleavage (iv) then removes the 5′-CAG repeat-containing flaps, creating the ligatable nick for ligation, resulting in TNR expansion (v). During the spontaneous DNA realignment and formation of alternate conformations proposed, the hairpin migrates to the right, as illustrated by the arrow.