The 'two-state' mechanism and insight into target recognition. (A) Confirmation of the 'two-state' model for guide anchoring. The figure displays the binary complex  and early (12 mer ternary) and late (19 mer ternary) propagation complexes , illustrating release of the 3' end of the guide (red) from PAZ (green) upon formation of a sufficient number of guide - target base pairs (12-14). Dotted lines indicate connectivity where atoms are invisible in the structures (due to disorder). (B) Exposure of the seed nucleotides in the binary complex. The figure displays the binary complex  with the seed nucleotides (red) in a cavity in the narrowed nucleic acid binding channel in TtAgo. The backbone in a quasi-helical conformation is bedded against the MID and PIWI domains (pale green) whilst the base edges face outwards. (C) Regions of seed and 3' supplementary base pairing in the 19 mer ternary complex. The figure highlights base pairing in the 19 mer ternary complex  mediated by positions 2-8 of the guide (the seed, in red, with corresponding target nucleotides in blue) and positions 13-16 of the guide (positions of 3' supplementary pairing , with guide in pink and target in pale blue).
Parker Silence 2010 1:3 doi:10.1186/1758-907X-1-3