When a hairpin loop forms in the nascent mRNA: The hairpin will destabilize the interaction and possibly lead to transcriptional termination.
Transcription in prokaryotes like E. coli is terminated either by a rho-dependent process or a rho-independent process. Intrinsic termination is controlled by the specific sequences of RNA .
When the termination process starts, the transcribed mRNA forms a stable secondary structural hairpin loop, also known as a stem-loop. Several uracil nucleotides follow this RNA hairpin. The uracil and adenine connections are exceedingly weak. NusA, a protein attached to RNA polymerase, attaches to the stem-loop structure so firmly that it momentarily stalls the polymerase.
The polymerase is pausing at the same time that the poly-uracil sequence is being transcribed. The RNA-DNA duplex can unwind and separate from the RNA polymerase because the weak adenine-uracil interactions reduce the energy of destabilization for the RNA-DNA duplex. Overall, transcription is terminated by the modified RNA structure.
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