Substrate sequence effects on 'hammerhead' RNA catalytic efficiency

M. J. Fedor, O. C. Uhlenbeck*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

97 Scopus citations


The 'hammerhead' RNA self-cleaving domain can be assembled from two RNA molecules: a large (~34 nucleotide) ribozyme RNA containing most of the catalytically essential nucleotides and a small (~13 nucleotide) substrate RNA containing the cleavage site. Four such hammerheads that contained identical catalytic core sequences but differed in the base composition of the helices that are involved in substrate binding had been reported to vary in cleavage rates by more than 70-fold under similar reaction conditions. Steady-state kinetic analyses reveal that k(cat) values are nearly the same for these hammerheads but K(m) values vary nearly 60-fold. The substrates for reactions having high K(m) values form aggregates that are virtually nonreactive. These observations demonstrate that the secondary structure of substrate RNA can be a major determinant of hammerhead catalytic efficiency.

Original languageEnglish (US)
Pages (from-to)1668-1672
Number of pages5
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number5
StatePublished - 1990


  • RNA enzymes
  • RNA secondary structure
  • antisense RNA

ASJC Scopus subject areas

  • General


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