Intrinsic termination

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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 stop and release the newly made RNA.[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. C-G base pairs have significant base-stacking interactions (especially repeated G-C pairs) and can form three hydrogen bonds between each other, resulting in a stable RNA duplex.[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.[4]

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. PMC 327222Freely accessible. PMID 7012794. doi:10.1093/nar/9.3.563. 
  2. ^ Lewin, Benjamin (2007). Genes IX. Sudbury, MA: Jones and Bartlett Publishers. ISBN 0-7637-4063-2. 
  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. PMC 41053Freely accessible. PMID 7568019. doi:10.1073/pnas.92.19.8793. Retrieved 2010-09-20. 
  4. ^ Krebs, Jocelyn E.; Goldstein, Elliott S.; Kilpatrick, Stephen T. (2014). Lewin's Genes XI. (11th ed.). Burlington, Mass.: Jones & Bartlett Learning. p. 531-533. ISBN 978-1-4496-5985-1. 

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