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A covalent crosslink converts the hammerhead ribozyme from a ribonuclease to an RNA ligase

Nature Structural Biology volume 8, pages 863–867 (2001)Cite this article

Abstract

The hammerhead ribozyme is a more efficient ribonuclease than an RNA ligase. Under typical reaction conditions, the rate of RNA chain cleavage is ∼100-fold faster than the rate of the reverse ligation reaction such that virtually all of the hammerhead is in its cleaved form at equilibrium. Here we show that the introduction of a crosslink away from the catalytic core of the hammerhead has little effect on the cleavage rate but dramatically increases the ligation rate, thereby making the hammerhead an efficient RNA ligase. This experiment emphasizes the role of molecular flexibility in defining the properties of a macromolecular catalyst and suggests why other small ribozymes are more efficient ligases than ribonucleases.

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Figure 1: An intermolecular ribozyme–substrate crosslink.
Figure 2: The rate of ligation is increased for the crosslinked hammerhead.
Figure 3: The intermolecular crosslink alters the cleavage-ligation equilibrium.

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Acknowledgements

Special thanks to S. Cohen for assistance with the thiol–disulfide interchange crosslinking and W. Pieken for supplying the 2′ amino phosphoramidites used in this study. This research was supported by a grant from the National Institutes of Health.

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  1. Tracy K. Stage-Zimmermann

    Present address: Variagenics, Inc., 60 Hampshire St., Cambridge, Massachusetts, 02139, USA

Authors and Affiliations

  1. Department of Chemistry and Biochemistry, University of Colorado, Boulder, 80309-0215, Colorado, USA

    Tracy K. Stage-Zimmermann & Olke C. Uhlenbeck

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  1. Tracy K. Stage-Zimmermann
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  2. Olke C. Uhlenbeck
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Correspondence to Olke C. Uhlenbeck.

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Stage-Zimmermann, T., Uhlenbeck, O. A covalent crosslink converts the hammerhead ribozyme from a ribonuclease to an RNA ligase. Nat Struct Mol Biol 8, 863–867 (2001). https://doi.org/10.1038/nsb1001-863

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