Application of computational technologies to ribozyme biotechnology products

A structural analysis of in vitro catalytic activities of hammerhead ribozymes

BACKGROUND

Ribozymes are small catalytic RNAs that possess the dual functions of sequence-specific RNA recognition and site-specific cleavage. Trans-cleaving ribozymes can inhibit translation of genes at the messenger RNA (mRNA) level in both eukaryotic and prokaryotic systems and are thus useful tools for studies of gene function. However, identification of target sites for efficient cleavage poses a challenge. Here, we have considered a number of structural and thermodynamic parameters that can affect the efficiency of target cleavage, in an attempt to identify rules for the selection of functional ribozymes.

RESULTS

We employed the Sfold program for RNA secondary structure prediction, to account for the likely population of target structures that co-exist in dynamic equilibrium for a specific mRNA molecule. We designed and prepared 15 hammerhead ribozymes to target GUC cleavage sites in the mRNA of the breast cancer resistance protein (BCRP). These ribozymes were tested, and their catalytic activities were measured in vitro. We found that target disruption energy owing to the alteration of the local target structure necessary for ribozyme binding, and the total energy change of the ribozyme-target hybridization, are two significant parameters for prediction of ribozyme activity. Importantly, target disruption energy is the major contributor to the predictability of ribozyme activity by the total energy change. Furthermore, for a target-site specific ribozyme, incorrect folding of the catalytic core, or interactions involving the two binding arms and the end sequences of the catalytic core, can have detrimental effects on ribozyme activity.

CONCLUSION

The findings from this study suggest rules for structure-based rational design of trans-cleaving hammerhead ribozymes in gene knockdown studies. Tools implementing these rules are available from the Sribo module and the Srna module of the Sfold program available through Web server at http://sfold.wadsworth.org.

Boltzmann ensemble features of RNA secondary structures: a comparative analysis of biological RNA sequences and random shuffles

Ensemble-based approaches to RNA secondary structure prediction have become increasingly appreciated in recent years. Here, we utilize sampling and clustering of the Boltzmann ensemble of RNA secondary structures to investigate whether biological sequences exhibit ensemble features that are distinct from their random shuffles. Representative messenger RNAs (mRNAs), structural RNAs, and precursor microRNAs (miRNAs) are analyzed for nine ensemble features. These include structure clustering features, the energy gap between the minimum free energy (MFE) and the ensemble, the numbers of high-frequency base pairs in the ensemble and in clusters, the average base-pair distance between the MFE structure and the ensemble, and between-cluster and within-cluster sums of squares. For each of the features, we observe a lack of significant distinction between mRNAs and their random shuffles. For five features, significant differences are found between structural RNAs and random counterparts. For seven features including the five for structural RNAs, much greater differences are observed between precursor miRNAs and random shuffles. These findings reveal differences in the Boltzmann structure ensemble among different types of functional RNAs. In addition, for two ensemble features, we observe distinctive, non-overlapping distributions for precursor miRNAs and random shuffles. A distributional separation can be particularly useful for the prediction of miRNA genes.

Effect of target secondary structure on RNAi efficiency

RNA interference (RNAi) mediated by small interfering RNAs (siRNAs) or short hairpin RNAs (shRNAs) has become a powerful tool for gene knockdown studies. However, the levels of knockdown vary greatly. Here, we examine the effect of target disruption energy, a novel measure of target accessibility, along with other parameters that may affect RNAi efficiency. Based on target secondary structures predicted by the Sfold program, the target disruption energy represents the free energy cost for local alteration of the target structure to allow target binding by the siRNA guide strand. In analyses of 100 siRNAs and 101 shRNAs targeted to 103 endogenous human genes, we find that the disruption energy is an important determinant of RNAi activity and the asymmetry of siRNA duplex asymmetry is important for facilitating the assembly of the RNA-induced silencing complex (RISC). We estimate that target accessibility and duplex asymmetry can improve the target knockdown level significantly by nearly 40% and 26%, respectively. In the RNAi pathway, RISC assembly precedes target binding by the siRNA guide strand. Thus, our findings suggest that duplex asymmetry has significant upstream effect on RISC assembly and target accessibility has strong downstream effect on target recognition. The results of the analyses suggest criteria for improving the design of siRNAs and shRNAs.

Clustering of RNA secondary structures with application to messenger RNAs

There is growing evidence of translational gene regulation at the mRNA level, and of the important roles of RNA secondary structure in these regulatory processes. Because mRNAs likely exist in a population of structures, the popular free energy minimization approach may not be well suited to prediction of mRNA structures in studies of post-transcriptional regulation. Here, we describe an alternative procedure for the characterization of mRNA structures, in which structures sampled from the Boltzmann-weighted ensemble of RNA secondary structures are clustered. Based on a random sample of full-length human mRNAs, we find that the minimum free energy (MFE) structure often poorly represents the Boltzmann ensemble, that the ensemble often contains multiple structural clusters, and that the centroids of a small number of structural clusters more effectively characterize the ensemble. We show that cluster-level characteristics and statistics are statistically reproducible. In a comparison between mRNAs and structural RNAs, similarity is observed for the number of clusters and the energy gap between the MFE structure and the sampled ensemble. However, for structural RNAs, there are more high-frequency base-pairs in both the Boltzmann ensemble and the clusters, and the clusters are more compact. The clustering features have been incorporated into the Sfold software package for nucleic acid folding and design.

Modeling hybridization kinetics

Formation of complementary base pairs between nucleic acids over a short region (<or=15 nucleotides) is described by a kinetic model in which the intermediate state is assumed to be locally single stranded. The model enables calculation of a rate factor that is proportional to the rate constant for hybridization under steady-state reaction conditions. Rate factors calculated for various sites in acetylcholinesterase mRNA correlated with sites found previously to be experimentally accessible for hybridization to antisense oligonucleotides. Hybridization rate of longer antisense oligodeoxynucleotides was modeled by calculation of a maximal rate factor for all possible 15-nucleotide segments of a given antisense molecule. Maximal rate factor calculated for a set of antisense oligonucleotides correlated (r=0.95) with initial rate of hybridization reported previously. Two other models proposed for identifying accessible sites for hybridization were less predictive than the rate factor calculation.

Designing ribozymes for the inhibition of gene expression

Ribozymes are being increasingly used for the sequence-specific inhibition of gene expression by the cleavage of mRNAs encoding proteins of interest. However, particular attention must be paid to the following points: the identification of regions on the mRNA accessible to the ribozyme; the delivery of ribozymes to cells by either exogenous or endogenous delivery; colocalization of the ribozyme with the target RNA in the cell; and differentiation between closely related sequences. This field is advancing rapidly, and results obtained with transgenic animals demonstrate the power of this strategy for the inhibition of gene expression.

The structure, function and application of the hammerhead ribozyme

The hammerhead ribozyme is one of the smallest ribozymes known and catalyses the site-specific hydrolysis of a phosphodiester bond. This small ribozyme is of interest for two reasons. It offers a convenient system to study the structure/function relationship of a nucleotide sequence, and is a potential vehicle for the inhibition of gene expression. The first part of the review summarizes the sequence requirements of the hammerhead, its three-dimensional structure and the proposed mechanism, in addition to ribozyme specificity and turnover. The second part of the review focuses on the in vivo application of the ribozyme. The processes involved in designing ribozymes for efficient cleavage in vivo are described, together with possible delivery strategies.

Optimizing the cell efficacy of synthetic ribozymes. Site selection and chemical modifications of ribozymes targeting the proto-oncogene c-myb

Expression of the proto-oncogene c-myb is necessary for proliferation of vascular smooth muscle cells. We have developed synthetic hammerhead ribozymes that recognize and cleave c-myb RNA, thereby inhibiting cell proliferation. Herein, we describe a method for the selection of hammerhead ribozyme cleavage sites and optimization of chemical modifications that maximize cell efficacy. In vitro assays were used to determine the relative accessibility of the ribozyme target sites for binding and cleavage. Several ribozymes thus identified showed efficacy in inhibiting smooth muscle cell proliferation relative to catalytically inactive controls. A combination of modifications including several phosphorothioate linkages at the 5'-end of the ribozyme and an extensively modified catalytic core resulted in substantially increased cell efficacy. A variety of different 2'-modifications at positions U4 and U7 that confer nuclease resistance gave comparable levels of cell efficacy. The lengths of the ribozyme binding arms were varied; optimal cell efficacy was observed with relatively short sequences (13-15 total nucleotides). These synthetic ribozymes have potential as therapeutics for hyperproliferative disorders such as restenosis and cancer. The chemical motifs that give optimal ribozyme activity in smooth muscle cell assays may be applicable to other cell types and other molecular targets.

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.