Transcription Termination: Intrinsic Hairpin vs Rho Factor

RNA polymerase transcribes a modeled 120-nucleotide DNA template in real time while you choose how the process ends. In intrinsic (Rho-independent) mode, reaching the terminator folds the nascent RNA into a hairpin that pauses the enzyme, and a tunable stability value decides whether the weak downstream RNA-DNA hybrid actually breaks or reads through. In Rho-dependent mode, a Rho ATPase loads onto the growing transcript at its rut site and chases the polymerase down the RNA at its own translocation speed, catching it only if it closes the gap before the template runs out. Live readouts track transcript length, the polymerase's state, and either the hairpin's stability or the shrinking Rho-to-RNAP gap.