Hairpin Ribozyme

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==Kinetics==
==Kinetics==
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There are at least four steps in the reaction pathway of the hairpin ribozyme. They are: (1) substrate binding to ribozyme, (2) cleavage in the ribozyme-substrate complex, (3) release of 5' products, and (4) release of 3' products. The rates and equilibrium constants for individual steps have been studied. Substrate binding can reach a minimum of <math>6*10^6 M^-1 min^-1</math>
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There are at least four steps in the reaction pathway of the hairpin ribozyme. They are: (1) substrate binding to ribozyme, (2) cleavage in the ribozyme-substrate complex, (3) release of 5' products, and (4) release of 3' products. The rates and equilibrium constants of these individual steps have been studied. Substrate binding by the naturally occurring hairpin ribozyme can reach a minimum of 6x10^6 M^-1 min^-1 and modified versions can reach 5x10^8 M^-1 min^-1.
==References==
==References==
<references/>
<references/>

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Contents

Hairpin Ribozyme Overview

Crystal Structure of the Hairpin Ribozyme in the catalytically-active conformation (PDB entry 1m5k)

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Structure

In the transition state, the

The secondary structure of the hairpin ribozyme contains two independently folding domains, called A and B. In each domain there is an internal loop flanked by two helices(H1 and H2 in domain A and H3 and H4 in domain B). The RNA substrate is bound in domain A through Watson-Crick base pairs in H1 and H2. Once bound to domain A, the substrate is reversibly cleaved. Linkers of varying lengths were inserted between the 5' end of the substrate and the 3' end of the ribozyme in order to test what proximity is preferred by the two domains. The results of the test showed that the two domains prefer to be relatively close to one another and use H2 and H3 as a sort of hinge. In the naturally occurring hairpin ribozyme, this hinge is occupied by a four-way junction, which is believed to regulate inter-domain interactions by alternative stacking of helices.[2]

Kinetics

There are at least four steps in the reaction pathway of the hairpin ribozyme. They are: (1) substrate binding to ribozyme, (2) cleavage in the ribozyme-substrate complex, (3) release of 5' products, and (4) release of 3' products. The rates and equilibrium constants of these individual steps have been studied. Substrate binding by the naturally occurring hairpin ribozyme can reach a minimum of 6x10^6 M^-1 min^-1 and modified versions can reach 5x10^8 M^-1 min^-1.

References

  1. ↑ Fedor MJ. Structure and function of the hairpin ribozyme. J Mol Biol. 2000 Mar 24;297(2):269-91. PMID:10715200 doi:http://dx.doi.org/10.1006/jmbi.2000.3560
  2. ↑ Walter NG, Burke JM. The hairpin ribozyme: structure, assembly and catalysis. Curr Opin Chem Biol. 1998 Feb;2(1):24-30. PMID:9667918

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