Then, by using the X-ray structure of a hammerhead ribozyme ± inhibitor complex elucidated by Pley et al. In cell-free reactions, ribozymes with 13-mer HAL were up to 10-fold more efficient than those with 9-mer HAL. Small nucleolytic ribozymes are a family of naturally occurring RNA motifs that catalyse a self-transesterification reaction in a highly sequence-specific manner. However, the mechanistic source of the catalytic rate increase generated by twister was unknown. 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. 2003). 2003; Khvorova et al. 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. Ribozyme parameters, namely hybridization arm length (HAL) and nonhybridizing extraneous sequences (NES), were found to have rate-determining properties. Hammerhead ribozymes are intrinsically cis-acting: that is, their natural activity is to cleave and hence to inactivate themselves. 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. 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 (), … 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- 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+). Helen A. James, in Encyclopedia of Cancer (Second Edition), 2002 II.C.1 Hammerhead Ribozymes. 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 population of allosteric ribozymes resulting from 15 rounds of in vitro selection yi … 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. 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 . 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). [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 ribozyme was the first reported and the most extensively studied member of this family. Ribozymes with 9-mer HAL were relatively ineffective in transfected cells. For example, the MR11 ribozyme exhibits a pH profile (Fig.
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