Substrate sequence effects on "hammerhead" RNA catalytic efficiency.

• DOI: 10.1073/pnas.87.5.1668
• Publication Date: 2006-05-31T11:35:50Z
• Authors: M J Fedor; O C Uhlenbeck
• Keywords: Hammerhead ribozyme; Hairpin ribozyme; Cleavage (geology); Ligase ribozyme; VS ribozyme; Enzyme Kinetics

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