Intrinsic termination

Intrinsic, or rho-independent termination, is a process to signal the end of transcription and release the newly constructed RNA molecule.

When the termination process begins, the transcribed mRNA forms a stable secondary structure hairpin loop, also known as a stem-loop.

The weak adenine-uracil bonds lower the energy of destabilization for the RNA-DNA duplex, allowing it to unwind and dissociate from the RNA polymerase.

Rho-independent transcription termination is a frequent mechanism underlying the activity of cis-acting RNA regulatory elements, such as riboswitches.

The purpose function of intrinsic termination is to signal for the dissociation of the ternary elongation complex (TEC), ending the transcript.

Intrinsic termination thus regulates the level of transcription as well, determining how many Polymerase can transcribe a gene over a given period of time, and can help prevent interactions with neighboring chromosomes.

This is accomplished through interactions with single stranded RNA that corresponds to the upstream area of the loop, resulting in disruption of the termination process.

Furthermore, there is some implication that the nut site may also contribute to regulation, as it is involved in recruitment of some critical components in the formation of the hairpin.

G-C base pairs have significant base-stacking interactions, and can form three hydrogen bonds with each other, which makes them very thermodynamically favorable.

[citation needed] Generally, the absence of the uracil-rich sequence following the stem-loop will result in a delay or pause in transcription, but termination will not cease completely.

In absence of U-tract, hair pin formation does not result in efficient termination, indicating its importance in this process.

[7] The elongation destabilization process occurs in four steps[7] In terms of inhibitors of intrinsic termination, much is still unknown.

[10] Archaeal RNA polymerase is responsive to intrinsic signals both in vivo and in vitro such as the poly-U-rich regions.

In RNAP III, some poly(dT) sites are indeed occasionally read-through: some genes have multiple such regions, allowing transcripts of different lengths to be produced.