Hairpin ribozyme

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A kind of ribozyme resembling a hairpin, and was first detected as a self-cleaving satellite RNA in tobacco ringspot virus


Ribozymes are RNAs that are capable of becoming biological catalysts. They may be distinguished by their structure, such as their characteristic loops and helices. For instance, hammerhead ribozyme has a secondary structure resembling a hammerhead shark. Another ribozyme is the hairpin ribozyme. In the minimal functional structure of a hairpin ribozyme, there are two domains in which each contains two helices separated by a conserved internal loop.1 The first domain, domain A, contains the substrate and the primary substrate–recognition region. The second domain, domain B, is the larger region and contains the primary catalytic determinants. The two domains are joined via a phosphodiester linkage. When inactive, the domains stack on top of the other, consequently resembling a hairpin.2

The hairpin ribozyme can reversibly cleave RNA substrates and generate 2', 3'-cyclic phosphate and 5'-hydroxyl termini. It was first discovered in the negative strand of the tobacco ringspot virus satellite RNA. It differs from a hammerhead ribozyme in a way that its cleavage and litigation proceed through catalysis that does not require direct coordination of metal cations to phosphate or water oxygens.3

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1 Adamatzky, A., Costello, B., Bull, L., Stepney, S. & Teuscher, C. (2007). Unconventional computing 2007. England: Luniver Press. p.78.
2 Esteban, J. A., Walter, N. G., Kotzorek, G., Heckman, J. E., & Burke, J. M. (1998). "Structural basis for heterogeneous kinetics: Reengineering the hairpin ribozyme". Proceedings of the National Academy of Sciences of the United States of America 95 (11): 6091–6096.
3 Fedor, M. J. (2000). Structure and function of the hairpin ribozyme. Journal of Molecular Biology 297 (2): 269–291.