TRANSCRIPTION STOP SIGNALS
RNA polymerase continues transcribing DNA until it reaches a termination signal. In bacteria, the Rho-independent terminator is a region of DNA with two inverted repeats separated by about six bases, followed by a stretch of A’s. As RNA polymerase makes these sequences, the two inverted repeats form a hairpin structure. The secondary structure causes RNA polymerase to pause. As the stretch of A’s is transcribed into U’s, the DNA/RNA hybrid molecule becomes unstable (A/U base pairs only have two hydrogen bonds). RNA polymerase “stutters” and then falls off the template strand of DNA in the middle of the A’s.
Bacteria also have Rho-dependent terminators that have two inverted repeats but lack the string of A’s. Rho (r) protein is a special helicase that unwinds DNA/RNA hybrid double helices. Rho binds upstream of the termination site in a region containing many cytosines but very few guanines. After RNA polymerase passes the Rho binding site, Rho attaches to the RNA and moves along the RNA transcript until it catches RNA polymerase at the hairpin structure. Rho then unwinds the DNA/RNA helix and separates the two strands. The RNA is then released.
Transcription terminates either in a Rho-independent manner or in a Rho-dependent manner.