Probing the hammerhead ribozyme structure with ribonucleases

RNAdigest: a web-based tool for the analysis and prediction of structure-specific RNAse digestion results

Despite recent developments in analyzing RNA secondary structures, relatively few RNA structures have been determined. To date, many investigators have relied on the traditional method of using structure-specific RNAse enzymes to probe RNA secondary structures. However, if these data were combined with novel computational approaches, investigators would have an informative and valuable tool for RNA structural analysis. To this end, we created the web server “RNAdigest.” RNAdigest uses mfold RNA structural models in order to predict the results of RNAse digestion experiments. Furthermore, RNAdigest also utilizes both RNA sequence and the experimental digestion patterns to formulate the constraints for predicting secondary structures of the RNA. Thus, RNAdigest allows for the structural interpretation of RNAse digestion experiments. Overall, RNAdigest simplifies RNAse digestion result analyses while allowing for the identification of unique fragments. These unique fragments can then be used for testing predicted mfold structures and for designing structural-specific DNA/RNA probes.

Length variation of helix III in a hammerhead ribozyme and its influence on cleavage activity

The previously described HIV-1 directed hammerhead ribozyme 2as-Rz12 can form with its target RNA 2s helices I and III of 128 and 278 base pairs (bp). A series of derivatives was made in which helix III was truncated to 8, 5, 4, 3, and 2 nucleotides (nt). These asymmetric hammerhead ribozymes were tested for in vitro cleavage and for inhibition of HIV-1 replication in human cells. Truncation of helix III to 8 bp did not affect the in vitro cleavage potential of the parental catalytic antisense RNA 2as-Rz12. Further truncation of helix III led to decreased cleavage rates, with no measurable cleavage activity for the 2 bp construct. All catalytically active constructs showed complex cleavage kinetics. Three kinetic subpopulations of ribozyme-substrate complexes could be discriminated that were cleaved with fast or slow rates or not at all. Gel purification of preformed ribozyme-substrate complexes led to a significant increase in cleavage rates. However, the complex cleavage pattern remained. In mammalian cells, the helix III-truncated constructs showed the same but no increased inhibitory effect of the comparable antisense RNA on HIV-1 replication.

In vitro selection of a purine nucleotide-specific hammerheadlike ribozyme

The in vitro selection for an intramolecular AUG-cleaving hammerhead-like ribozyme is described. One of the ribozymes selected was found to cleave after this triplet, both intramolecularly and intermolecularly, with rates comparable to the rate of the native GUC-cleaving hammerhead ribozyme. Although the selection was designed for cleavage 3' of the AUG triplet, the ribozyme also cleaves 3' of the AUA triplet. AUU and AUC triplets are, however, not cleaved, and thus the selected ribozyme is purine-specific for the third position in the triplet. In addition, cleavage 3' of the AAG triplet has been observed, thus the central U is not essential. Nuclease digestion indicates that the selected ribozyme has a secondary structure similar to that of the native hammerhead ribozyme, although with an altered core and stem-loop II sequence. All nucleotides in the core, except one, are essential for activity. The nucleotides in loop II are sensitive to changes and cannot, as in the hammerhead ribozyme, be replaced by other sequences or a nonnucleotide linker. Thus there are differences between these two ribozymes even though they have similar two-dimensional structures. The new ribozyme enlarges the application of hammerhead ribozymes for the inhibition of gene expression by extending the range of cleavable triplets.

Hammerhead ribozyme structure probed by cell extracts

To examine hammerhead ribozyme structure and vulnerability to cellular nucleases, ribozymes were incubated with soluble extracts from Escherichia coli, and cleavage sites were identified by primer extension analysis. Mapping of endonuclease-sensitive sites revealed that the most sensitive were in the 3'-substrate-binding region of the ribozyme. The catalytic domain was much less susceptible, although some cleavage preference was seen at two positions known to be twisted out of parallel stacking in a ribozyme-substrate analogue complex. Changes in substrate-binding domain nucleotide sequence had no effect on cleavage patterns of catalytic domains. Hammerhead ribozymes, in solution and free from substrate, appear to have structurally independent, asymmetrically arranged domains.

RNA cleavage by small catalytic RNAs

Recent studies of the hammerhead ribozyme have provided an insight into its three-dimensional structure. In addition, studies using chemical probes, functional-group modification and mutational analysis, in combination with computer modelling, have led to proposals for the structure of both the hairpin and hepatitis delta virus ribozymes. Such structural elucidations will aid understanding of the mechanism of ribozyme catalysis. The discovery that certain RNA-binding proteins can increase the catalytic efficiency of ribozymes in encouraging for their use in the inhibition of gene expression in vivo.

Ionic interactions and the global conformations of the hammerhead ribozyme

Here we investigate the global conformation of the hammerhead ribozyme. Electrophoretic studies demonstrate that the structure is folded in response to the concentration and type of ions present. Folding based on colinear alignment of arms II and III is suggested, with a variable angle subtended by the remaining helix I. In the probable active conformation, a small angle is subtended between helices I and II. Using uranyl photocleavage, an ion binding site has been detected in the long single-stranded region. The folded conformation could generate a preactivation of the scissile bond to permit in-line attack of the 2'-hydroxyl group, with a bound metal ion playing an integral role in the chemistry.

Global conformation of a self-cleaving hammerhead RNA

Phylogenetic and biochemical studies of RNA have provided a wealth of information regarding secondary structure; however, knowledge of tertiary structure has been more difficult to obtain. In the current work, electrophoretic and hydrodynamic measurements have yielded the global conformations of a self-cleaving "hammerhead" RNA, both prior to and following self-cleavage. The pre- and post-cleavage structures appear to have nearly identical conformations in which the three helices assume a roughly coplanar arrangement with well-defined interhelix angles. Following self-cleavage, one of the three helix stems (stem I) undergoes a slight (< 10 degrees) realignment, although the relative positions of the other two stems remain unchanged. Extension of stem III from (nominally) three base pairs to nine base pairs, known to dramatically enhance the rate of self-cleavage, results in a substantial (approximately 70 degrees) realignment of stems I and II. The current study represents an approach for studying other nonhelical elements in RNA.

A three-dimensional model for the hammerhead ribozyme based on fluorescence measurements

For the understanding of the catalytic function of the RNA hammerhead ribozyme, a three-dimensional model is essential but neither a crystal nor a solution structure has been available. Fluorescence resonance energy transfer (FRET) was used to study the structure of the ribozyme in solution in order to establish the relative spatial orientation of the three constituent Watson-Crick base-paired helical segments. Synthetic constructs were labeled with the fluorescence donor (5-carboxyfluorescein) and acceptor (5-carboxytetramethylrhodamine) located at the ends of the strands constituting the ribozyme molecule. The acceptor helix in helix pairs I and III and in II and III was varied in length from 5 to 11 and 5 to 9 base pairs, respectively, and the FRET efficiencies were determined and correlated with a reference set of labeled RNA duplexes. The FRET efficiencies were predicted on the basis of vector algebra analysis, as a function of the relative helical orientations in the ribozyme constructs, and compared with experimental values. The data were consistent with a Y-shaped arrangement of the ribozyme with helices I and II in close proximity and helix III pointing away. These orientational constraints were used for molecular modeling of a three-dimensional structure of the complete ribozyme.