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Nucleic Acids Research, Vol 24, Issue 14 2685-2689, Copyright © 1996 by Oxford University Press

ARTICLES

The loop B domain is physically separable from the loop A domain in the hairpin ribozyme

C Shin, JN Choi, SI Song, JT Song, JH Ahn, JS Lee and YD Choi
Research Center for New BioMaterials in Agriculture, Seoul National University, Suwon, Korea.

In order to understand the catalysis mechanism of the hairpin ribozyme, mutant ribozymes were constructed. The distance between the loop A domain and the loop B domain was extended by inserting various lengths of nucleotide linkers at the hinge region in cis mutants, or the domains were separated physically in a trans mutant. All the mutant ribozymes, including the trans mutant, could cleave substrate RNA at the predicted site. A cis mutant with a single nucleotide insertion exhibited cleavage activity about twice as high as that of the wild- type (wt) ribozyme. The insertion of 2-5 nucleotides (nt) gradually reduced the activity to the level of the wt ribozyme. Insertion of a longer linker, up to 11 nt, resulted in the reduction of activity to one half of that of the wt ribozyme. The ribozyme with a single nucleotide insertion at the hinge region seems to form a more suitable conformation for catalysis by three-dimensional fold-back of the loop B to loop A containing the cleavage site. The trans mutant, in which the A and B domains were physically separated, maintained a significant level of activity, suggesting that both domains are necessary for catalysis, but separable. These results demonstrate that interaction between the A and B domains results in catalysis.
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C. Schmidt, R. Welz, and S. Muller
RNA double cleavage by a hairpin-derived twin ribozyme
Nucleic Acids Res., February 15, 2000; 28(4): 886 - 894.
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