Full-length hammerhead ribozymes were subjected to in vitro selection to identify variants that are allosterically regulated by theophylline in the presence of a physiologically relevant concentration of Mg(2+). The hammerhead ribozyme–substrate complex is comprised of an intramolecular helix (helix II) and two intermolecular helices generated after the substrate interaction (helix I and III). 2003; Khvorova et al. Ribozymes with 9-mer HAL were relatively ineffective in transfected cells. Ribozyme parameters, namely hybridization arm length (HAL) and nonhybridizing extraneous sequences (NES), were found to have rate-determining properties. In cell-free reactions, ribozymes with 13-mer HAL were up to 10-fold more efficient than those with 9-mer HAL. Helen A. James, in Encyclopedia of Cancer (Second Edition), 2002 II.C.1 Hammerhead Ribozymes. Hammerhead ribozyme kinetics TRACY K. STAGE-ZIMMERMANN1 and OLKE C. UHLENBECK Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, USA Keywords: catalytic RNA; RNA conformations INTRODUCTION The hammerhead ribozyme is a small RNA motif that self cleaves at a specific phosphodiester bond to pro- However, the mechanistic source of the catalytic rate increase generated by twister was unknown. [12] as a template, the positions of the catalytic core whose 2'-OH groups were involved in tertiary interactions were replaced by 2'-C-methylnucleosides (U 4 , G 5 , U 7 , G 8 , and G 12 ). The hammerhead motif most commonly used is a 35-nt-long RNA molecule, but this varies depending on the length of the substrate binding arms . In 2003, two groups revealed that “full-length” hammerhead ribozymes derived from natural sequences, which included a previously neglected tertiary contact between helices I and II in a region with little sequence conservation, were up to 1000-fold more active than minimal hammerheads (De la Peña et al. activity, the hammerhead ribozyme requires the presence of sequences in stems I and II that interact to form tertiary contacts (De la Pena et al., 2003; Khvorova et al., 2003) (Figure 1b), making it clear that a crystal structure of the full-length hammerhead ribozyme in which these distal tertiary contacts were present might be of some interest. The hammerhead ribozyme was the first reported and the most extensively studied member of this family. The hammerhead ribozyme consists of a catalytic core flanked by two arms, the sequence of which can be modified to base pair with the substrate RNA on either side of the cleavage site. The hammerhead is a small self-cleaving RNA motif that is found embedded in the genomes of plant viroids and virus satellite RNAs, where it is used for genome cleavage and possibly ligation in a rolling circle replication pathway (1, 2).The hammerhead has also been found in the transcripts of certain satellite DNAs and in the 3′ untranslated regions of a few Arabodopsis mRNAs (), … Then, by using the X-ray structure of a hammerhead ribozyme ± inhibitor complex elucidated by Pley et al. 3E) that is similar to that of HD3, and also attains a maximum k obs (~0.2 min −1) that exceeds the speed limit projected for γ catalysis but falls within the range of rate constants that is projected for combined αγ catalysis. Hammerhead ribozymes are intrinsically cis-acting: that is, their natural activity is to cleave and hence to inactivate themselves. For example, the MR11 ribozyme exhibits a pH profile (Fig. The population of allosteric ribozymes resulting from 15 rounds of in vitro selection yi … 2003). Twister is a small self-cleaving ribozyme similar in size to the hammerhead ribozyme but uses an orthogonal fold for a similar catalytic rate constant. Small nucleolytic ribozymes are a family of naturally occurring RNA motifs that catalyse a self-transesterification reaction in a highly sequence-specific manner.