Extended Data Fig. 9: The proposed pathways of hairpin extension after the TTC -hairpin intermediate.

The choice between the alternative pathways of hybrid-shearing and hypertranscloation depends on terminator sequences²⁶. It is also possible that hairpin completion follows a third alternative pathway, ‘hairpin invasion’^12,25,28,36, in which the RNAP clamp opens to allow hairpin extension into the main cleft. Although clamp opening cannot be obligatory for RNA release³⁰, the RNAP clamp is in constant thermal motion^52,53, can open fully in some conditions^36,37,38,39, and thus in principle could open upon DNA rewinding and allow the hairpin stem to extend into the main cleft without steric hinderance. After hairpin extension aided by bubble collapse, RNA release leads to TTC release (see Fig. 4).