A Hammerhead Ribozyme
David Marcey & Cora Crenwelge
2003

I. Introduction
II. Structure
III. References


I. Introduction

Hammerhead ribozymes are small, catalytic RNAs that undergo self-cleavage of their own backbone to produce two RNA products. All hammerhead ribozymes contain three base-paired stems and a highly conserved core of residues required for cleavage. The cleavage reaction proceeds by an attack of a 2' hydroxyl oxygen of a catalytic site cytosine on the phosphorus atom attached to the 3' carbon of the same residue, breaking the sugar phosphate backbone and producing a 2', 3' cyclic phosphate. As for protein ribonucleases, a metal ion bound in the active site (Mg++) stabilizes the ionized form of the 2' hydroxyl oxygen, promoting the catalytic attack.

The wishbone-shaped structure at left is is a hammerhead ribozyme in which a portion of the RNA has been substituted with a stretch of DNA that acts as an inhibitor of catalysis, due to the absence of 2' hydroxyl groups in DNA. The structure was the first described for a hammerhead ribozyme.

return to beginning of exhibit


II. Structure

Stem I is formed by base pairing of complementary nucleotides through Watson-Crick hydrogen bonding. The 5' phosphate and 3' oxygen atoms mark the beginning and end of the ribozyme and are juxtaposed at the top of Stem I.

Stem II lies opposite Stem I in the other branch of the "wishbone." It also is formed by standard Watson-Crick base pairing and is capped by a four base loop at the top of the branch.

Stem III is formed by Watson-Crick base pairing and forms the base of the "wishbone." In a standard ribozyme, formed by a continuous RNA molecule instead of an RNA-DNA, two-chain hybrid, the nucleotides at the base of Stem III would be connected by a short loop.

The base sequences of the three stems can vary, depending on the hammerhead ribozyme under consideration. The only sequence restriction is that Watson-Crick base complementarity is maintained so that stem hydrogen bonding can form. The central core sequence, however, is highly conserved between ribozymes. The core contains two domains.

Domain 1 of the core comprises a CUGA sequence, the uridine turn, that follows Stem I.

Domain 2 is formed by non-Watson Crick base pairing, and connects Stem II and Stem III.

C17 is the conserved residue at which strand cleavage takes place (see Introduction).


reset molecule


return to beginning of exhibit


III. References

Pley, H. W., Flaherty, K. M., McKay, D. B.: Three-dimensional structure of a hammerhead ribozyme. Nature 372: 68-74 (1994).

return to beginning of exhibit