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Intrinsic termination

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Title: Intrinsic termination  
Author: World Heritage Encyclopedia
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Subject: WebGeSTer, Attenuator (genetics), Neisseria sigma-E sRNA, Abortive initiation, Bacteria
Collection: Gene Expression, Molecular Biology
Publisher: World Heritage Encyclopedia

Intrinsic termination

A predicted conserved secondary structure and sequence conservation annotation for 90 bacterial Rho-independent termination elements.

Intrinsic termination (also called Rho-independent termination) is a mechanism in prokaryotes that causes RNA transcription to be stopped.[1] In this mechanism, the mRNA contains a sequence that can base pair with itself to form a stem-loop structure 7-20 base pairs in length that is also rich in cytosine-guanine base pairs. These bases form three hydrogen bonds between each other and are therefore particularly strong.[2] Following the stem-loop structure is a chain of uracil residues. The bonds between uracil and adenine are very weak. A protein bound to RNA polymerase (nusA) binds to the stem-loop structure tightly enough to cause the polymerase to temporarily stall.[3] This pausing of the polymerase coincides with transcription of the poly-uracil sequence. 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.[2]

Stem-loop structures that are not followed by a poly-Uracil sequence cause the RNA polymerase to pause, but it will typically continue transcription after a brief time because the duplex is too stable to unwind far enough to cause termination.

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


  1. ^ Farnham, PJ; Platt, T (1981-02-11). "Rho-independent termination: dyad symmetry in DNA causes RNA polymerase to pause during transcription in vitro.". Nucleic Acids Research 9 (3): 563–77.  
  2. ^ a b Lewin, Benjamin (2007). Genes IX. Sudbury, MA: Jones and Bartlett Publishers.  
  3. ^ Wilson KS, von Hippel PH (September 1995). "Transcription termination at intrinsic terminators: the role of the RNA hairpin". Proc. Natl. Acad. Sci. U.S.A. 92 (19): 8793–7.  

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