RNA polymerase (RNAP) elongates RNA 5'→3' by reading the DNA template inside a ~9 bp transient RNA-DNA hybrid ("transcription bubble"). Termination releases the finished transcript and the enzyme — two mechanisms do it very differently:
Intrinsic (Rho-independent):
GC-rich inverted repeat → RNA folds into a hairpin
right behind RNAP, followed by a weak rU·dA run.
Hairpin invades the hybrid → RNAP pauses once → the
weak rU·dA tract lets the hybrid fray → release, or
the pause resolves the other way and RNAP reads
straight through to the end of the template.
Rho-dependent:
Rho (hexameric ATPase) loads onto a C-rich, unstructured
"rut" site on the nascent RNA, then translocates 5'→3'
along the RNA using ATP hydrolysis. If it catches a
paused RNAP before the transcript ends, it unwinds the
hybrid and pulls the RNA free.
- Elongation rate — how fast RNAP adds nucleotides (nt/s); a rough proxy for how much time Rho has to catch up.
- Hairpin stability (ΔG) — higher values mean a more stable hairpin: longer RNAP pause at the terminator and a higher chance the weak hybrid actually breaks instead of reading through.
- Rho translocation rate — how fast the Rho ring runs along the RNA once it loads at the rut site (~nt 25); if it never reaches RNAP before the template ends, transcription reads through.
- A shallow natural pause site around nt 70 is included in Rho mode — real Rho-dependent terminators lean on RNAP pausing to give the trailing ATPase a chance to close the gap.
- Drag the canvas to pan along the template and scroll/pinch to zoom in on the terminator region; "Fit view" resets to the full 120 nt window.
Fixed here vs. the 3D version: the original engine re-armed the hairpin pause on every animation frame once RNAP passed the terminator (the pause condition just checked "position ≥ terminator", which stays true forever), so a low-stability run kept re-rolling the coin until it always terminated eventually — stability had no real effect on the terminate/read-through split. This build resolves the terminator exactly once per pass (a terminatorResolved latch), which was verified numerically: across 200 seeded runs per stability value, the unpatched logic terminated 100% of the time even at stability 0, while the patched logic gives ~12% termination at stability 0 and ~88% at stability 90 — matching the stated probability model.
Real-world relevance: intrinsic terminators dominate in bacteria and need no accessory factor; Rho-dependent termination also silences pervasive antisense/upstream transcription and couples termination to translation via the ribosome's own speed.