Comparison of the roles of nucleotide synthesis, polymerization, and recombination in the origin of autocatalytic sets of RNAs

Ribozymes that act as polymerases and nucleotide synthases are known experimentally, even though no fully self-replicating system has yet been found. If the RNA World hypothesis is true, ribozymes must have arisen initially from within a random abiotic polymerization system. To investigate the origin of the RNA world, we studied a mathematical model of a chemical reaction system describing RNA polymerization. It is supposed that, in absence of ribozymes, polymerization occurs at a small spontaneous rate, and that in the presence of polymerase ribozymes, polymerization occurs at a faster rate that is proportional to the ribozyme concentration. Chains must be longer than a minimum threshold length in order to have the possibility of acting as ribozymes. The reaction system has two stable states that we term dead and living. The dead state is controlled by the small spontaneous rate and has negligible concentration of ribozymes. The living state has high concentration of ribozymes, and the reaction rates are determined by the ribozymes; thus, the system is autocatalytic. Concentration fluctuations in a finite volume can cause a transition to occur from the dead to the living state, that is, an origin of life occurs within this model. We also consider ribozymes that catalyze nucleotide synthesis. We show that living and dead states arise in the presence of synthase ribozymes in the same way as for polymerases. It has been proposed that recombination reactions are a way of generating long RNA chains in the early stages of life. We show that if the possibility of random reversible recombination reactions is added to our model, this does not lead to an increase in long polymer concentration. Thus, if recombination is fully reversible, there is no autocatalytic state controlled by recombination. Nevertheless, recombination can play an important role in ribozyme synthesis if there is an additional process that keeps the recombination reactions out of equilibrium. We modeled a case studied experimentally in which building block strands of moderate length associate due to RNA secondary structure formation. A recombination reaction then occurs between these strands to form a longer sequence that catalyzes its own formation via the recombination reaction. This system has an autocatalytic state, and it is possible for it to arise within our random polymerization system. If complexes formed by associations of shorter strands can act as catalysts without the requirement that the strands be covalently linked, this would alleviate the need for synthesis of very long strands; hence, it makes the emergence of an autocatalytic system from an abiotic random polymerization system much more likely.

Long-range tertiary interactions in single hammerhead ribozymes bias motional sampling toward catalytically active conformations

Enzymes generally are thought to derive their functional activity from conformational motions. The limited chemical variation in RNA suggests that such structural dynamics may play a particularly important role in RNA function. Minimal hammerhead ribozymes are known to cleave efficiently only in ∼ 10-fold higher than physiologic concentrations of Mg(2+) ions. Extended versions containing native loop-loop interactions, however, show greatly enhanced catalytic activity at physiologically relevant Mg(2+) concentrations, for reasons that are still ill-understood. Here, we use Mg(2+) titrations, activity assays, ensemble, and single molecule fluorescence resonance energy transfer (FRET) approaches, combined with molecular dynamics (MD) simulations, to ask what influence the spatially distant tertiary loop-loop interactions of an extended hammerhead ribozyme have on its structural dynamics. By comparing hammerhead variants with wild-type, partially disrupted, and fully disrupted loop-loop interaction sequences we find that the tertiary interactions lead to a dynamic motional sampling that increasingly populates catalytically active conformations. At the global level the wild-type tertiary interactions lead to more frequent, if transient, encounters of the loop-carrying stems, whereas at the local level they lead to an enrichment in favorable in-line attack angles at the cleavage site. These results invoke a linkage between RNA structural dynamics and function and suggest that loop-loop interactions in extended hammerhead ribozymes-and Mg(2+) ions that bind to minimal ribozymes-may generally allow more frequent access to a catalytically relevant conformation(s), rather than simply locking the ribozyme into a single active state.

Generation and development of RNA ligase ribozymes with modular architecture through "design and selection"

In vitro selection with long random RNA libraries has been used as a powerful method to generate novel functional RNAs, although it often requires laborious structural analysis of isolated RNA molecules. Rational RNA design is an attractive alternative to avoid this laborious step, but rational design of catalytic modules is still a challenging task. A hybrid strategy of in vitro selection and rational design has been proposed. With this strategy termed “design and selection,” new ribozymes can be generated through installation of catalytic modules onto RNA scaffolds with defined 3D structures. This approach, the concept of which was inspired by the modular architecture of naturally occurring ribozymes, allows prediction of the overall architectures of the resulting ribozymes, and the structural modularity of the resulting ribozymes allows modification of their structures and functions. In this review, we summarize the design, generation, properties, and engineering of four classes of ligase ribozyme generated by design and selection.

Inhibition of HIV-1 replication and dimerization interference by dual inhibitory RNAs

The 5'-untranslated region (5'UTR) of the HIV-1 RNA is an attractive target for engineered ribozymes due to its high sequence and structural conservation. This region encodes several conserved structural RNA domains essential in key processes of the viral replication and infection cycles. This paper reports the inhibitory effects of catalytic antisense RNAs composed of two inhibitory RNA domains: an engineered ribozyme targeting the 5' UTR and a decoy or antisense domain of the dimerization initiation site (DIS). These chimeric molecules are able to cleave the HIV-1 5'UTR efficiently and prevent viral genome dimerization in vitro. Furthermore, catalytic antisense RNAs inhibited viral production up to 90% measured as p24 antigen levels in ex vivo assays. The use of chimeric RNA molecules targeting different domains represents an attractive antiviral strategy to be explored for the prevention of side effects from current drugs and of the rapid emergence of escape variants of HIV-1.

Design and function of triplex hairpin ribozymes

Triplex ribozymes allow for the individual activity of multiple trans-acting ribozymes producing higher target cleavage relative to tandem-expressed RZs. A triplex expression system based on a single hairpin ribozyme for the multiple expression (multiplex) vectors can be engineered to target RNAs with single or multiple antisense-accessible sites. System construction relies on triplex expression modules consisting of hairpin ribozyme cassettes flanked by ribozymes lacking catalytic domains. Multiplex vectors can be generated with single or multiple specificity by tandem cloning of triplex expression modules. Triplex ribozymes are initially tested in vitro using cis- and trans-cleavage assays against radioactive-labeled targets. In addition, triplex ribozymes are tested for cis and trans cleavage in vivo by transfection in cultured cells followed by ribonuclease protection assays (RPAs) and RT-PCR. The use of triplex configurations with multiplex ribozymes will provide the basis for the development of future RZ-based therapies and technologies.

Cleavage of the Ewing tumour-specific EWSR1-FLI1 mRNA by hammerhead ribozymes

BACKGROUND

Ewing family tumours (EFT) are the second most common bone tumours in children and adolescents. In the majority of EFT, EWSR1-FLI1 (Ewing sarcoma breakpoint region 1-Friend leukaemia virus integration 1) fusion proteins can be detected and EWSR1-FLI1 substantially contributes to the malignant phenotype of EFT. Therefore, inactivation of EWSR1-FLI1 is an interesting strategy for EFT therapy.

MATERIALS AND METHODS

A ribozyme with specificity for EWSR1-FLI1 was developed and the activity in vitro was investigated. Synthetic RNAs corresponding to EWSR1-FLI1 were used as substrates. In addition, the total RNA from EFT cells was used as substrate and the rapid amplification of cDNA ends method for the detection of the cleavage products was used.

RESULTS

The ribozyme cleaved the synthetic RNA in a sequence specific manner with high efficiency in vitro. Furthermore, the expected cleavage products were detected after digestion of the total cellular RNA with this ribozyme. A point mutation in the catalytic centre of the ribozyme abolished enzymatic activity.

CONCLUSION

The RNA corresponding to EWSR1-FLI1 is accessible for ribozyme mediated inactivation and ribozymes are able to cleave EWSR1-FLI1 specific RNA in the presence of a high background of normal cellular RNAs.

In vitro selection of glmS ribozymes

Riboswitches modulate gene expression in eubacteria and eukaryotes in response to changing concentrations of small molecule metabolites. In most examples studied to date, riboswitches achieve both metabolite sensing and gene control functions without the obligate involvement of protein factors. These findings validate the hypothesis that RNA molecules could be engineered to function as designer gene control elements that sense and respond to different ligands. We believe that reverse engineering natural riboswitches could provide an intellectual foundation for those who wish to build synthetic riboswitches. Also, natural riboswitches might serve as starting points for efforts to change ligand specificity or gene control function through mutation and selection in vitro. In this chapter, we describe how in vitro selection can be used to create variant glmS ribozymes. Additionally, we discuss how these techniques can be extended to other riboswitch classes.

Preparations of hammerhead ribozymes for investigations of their cleavable sequences

Recently, in hammerhead ribozymes, newly identified loop-loop interaction was found to be important for their activation. Therefore, we chemically synthesized a hammerhead ribozyme with this extra loop sequences and its mutant ribozymes, as well as their substrate RNA strands in order to clarify their cleavable sequences. After purification with an anion exchange column chromatography, we were able to obtain 44mer and 20mer RNA.

RNA and RNP as new molecular parts in synthetic biology

Synthetic biology has a promising outlook in biotechnology and for understanding the self-organizing principle of biological molecules in life. However, synthetic biologists have been looking for new molecular "parts" that function as modular units required in designing and constructing new "devices" and "systems" for regulating cell function because the number of such parts is strictly limited at present. In this review, we focus on RNA/ribonucleoprotein (RNP) architectures that hold promise as new "parts" for synthetic biology. They are constructed with molecular design and an experimental evolution technique. So far, designed self-folding RNAs, RNA (RNP) enzymes, and nanoscale RNA architectures have been successfully constructed by utilizing Watson-Crick base-pairs together with specific RNA-RNA or RNA-protein binding motifs of known defined 3D structures. Riboregulators for regulating targeted gene expression have also been designed and produced in vitro as well as in vivo. Lately, RNA and ribonucleoprotein complexes have been strongly attracting the attention of molecular biologists because a variety of noncoding RNAs discovered in nature perform spatiotemporal gene expressions. Thus we hope that newly accumulating knowledge on naturally occurring RNAs and RNP complexes will provide a variety of new parts, devices and systems for synthetic biology.

A posteriori design of crystal contacts to improve the X-ray diffraction properties of a small RNA enzyme

The hairpin ribozyme is a small catalytic RNA comprising two helix-loop-helix domains linked by a four-way helical junction (4WJ). In its most basic form, each domain can be formed independently and reconstituted without a 4WJ to yield an active enzyme. The production of such minimal junctionless hairpin ribozymes is achievable by chemical synthesis, which has allowed structures to be determined for numerous nucleotide variants. However, abasic and other destabilizing core modifications hinder crystallization. This investigation describes the use of a dangling 5'-U to form an intermolecular U.U mismatch, as well as the use of synthetic linkers to tether the loop A and B domains, including (i) a three-carbon propyl linker (C3L) and (ii) a nine-atom triethylene glycol linker (S9L). Both linker constructs demonstrated similar enzymatic activity, but S9L constructs yielded crystals that diffracted to 2.65 A resolution or better. In contrast, C3L variants diffracted to 3.35 A and exhibited a 15 A expansion of the c axis. Crystal packing of the C3L construct showed a paucity of 6(1) contacts, which comprise numerous backbone to 2'-OH hydrogen bonds in junctionless and S9L complexes. Significantly, the crystal packing in minimal structures mimics stabilizing features observed in the 4WJ hairpin ribozyme structure. The results demonstrate how knowledge-based design can be used to improve diffraction and overcome otherwise destabilizing defects.

Design and switch of catalytic activity with the DNAzyme-RNAzyme combination

Design and switch of catalytic activity in enzymology remains a subject of intense investigation. Here, we employ a DNAzyme-RNAzyme combination strategy for construction of a 10-23 deoxyribozyme-hammerhead ribozyme combination that targets different sites of the beta-lactamase mRNA. The 10-23 deoxyribozyme-hammerhead ribozyme combination gene was cloned into phagemid vector pBlue-scriptIIKS (+). In vitro the single-strand recombinant phagemid vector containing the combination sequence exhibited 10-23 deoxyribozyme activity, and the linear transcript displayed hammerhead ribozyme activity. In bacteria, the 10-23 deoxyribozyme-hammerhead ribozyme combination inhibited the beta-lactamase expression and repressed the growth of drug-resistant bacteria. Thus, we created a DNAzyme-RNAzyme combination strategy that provides a useful approach to design and switch of catalytic activities for nucleic acid enzymes.

Aptazyme-based riboswitches as label-free and detector-free sensors for cofactors

We constructed a label-free and detector-free aptazyme-based riboswitch sensor for detecting the cofactor of the aptazyme. This riboswitch, which usually suppresses the gene expression with its anti-RBS sequence bound to the RBS of its own mRNA (OFF), activates the translation only when a cofactor is added to release the anti-RBS sequence from itself as a result of cofactor-induced self-cleavage by the aptazyme (ON). The rationally optimized one with beta-galactosidase as a reporter gene enabled us to detect the cofactor of the aptazyme visibly with high ON/OFF efficiency.

Design of Hammerhead Ribozymes that Cleave Murine Sry mRNA In Vitro and In Vivo

As the first step in investigating the possiblity of applying ribozyme technology to artificial control of the sex ratios at birth in farm animals, where the demand for females exceeds that for males, we designed a hammerhead ribozyme (HHRz) and 2 tRNA(val)-hammerhead ribozyme complexes (tRNARz3 and tRNARz4), and examined their effects upon murine Sry mRNA in vitro and in cells. We demonstrated that HHRz and tRNARz3 could effectively cleave the target Sry mRNA in vitro. For the purpose of experiments in vivo, HHRz was cloned into the highly efficient pUC-CAGGS mammalian expression vector (pCAG/HHRz), and the tRNA ribozyme complexes were cloned into the pol III promoter-driven pPUR-KE vector (pPUR/tRNARz3 and pPUR/tRNARz4); the ribozyme vectors were co-transfected with the target vector (pCAG/Sry). A suppressive action (up to approx. 60%) was confirmed for pCAG/HHRz and pPUR/tRNARz3 upon the transiently expressed exogenously introduced Sry in M15 cultured cells.

Synthetic hammerhead ribozymes as therapeutic tools to control disease genes

Ribozymes are RNA molecules that have the ability to catalyse the cleavage and formation of covalent bonds in RNA strands at specific sites. The "hammerhead" motif, approximately 30-nucleotide long, is the smallest endonucleolytic cis-acting ribozyme structure found in natural circular RNAs of some plant viroids. Hammerhead ribozymes became appealing when it was shown that it is possible to produce trans-acting ribozymes directed against RNA sequences of interest. Since then, gene-tailored ribozymes have been designed, produced and given to cells to knock down the expression of specific genes. At present, this technology has advanced so much that many hammerhead ribozymes are being used in clinical trials. With this work we would provide some guidelines to design efficient trans-acting hammerhead ribozymes as well as review the recent results obtained with them as gene therapy tools.

Stereoselective synthesis using immobilized Diels-Alderase ribozymes

Development of artificial ribozymes by in vitro selection has so far, mostly been addressed from the viewpoint of fundamental research. However, such ribozymes also have high potential as selective catalysts in practical syntheses. Immobilization of an active and selective ribozyme is an important step towards this end. A 49-nucleotide RNA molecule that was previously found to stereoselectively catalyze Diels-Alder reactions between various anthracene dienes and maleimide dienophiles was quantitatively immobilized on an agarose matrix by periodate oxidation of the 3'-terminal ribose and coupling to a hydrazide moiety. Typical loadings were 45 pmol microL(-1) gel. The specific activity was comparable to that of soluble ribozyme, and high enantioselectivities were obtained in catalyzed cycloadditions. The catalytic matrix was found to be stable and could be regenerated about 40 times with only minimal reduction of catalytic activity. Like the soluble ribozyme, the immobilized catalyst stereoselectively converts various diene and dienophile substrates. By using either natural D-RNA or enantiomeric L-RNA, both product enantiomers were made synthetically accessible with similar selectivities.

A peptidyl transferase ribozyme capable of combinatorial peptide synthesis

The formation of peptide bonds is a key step in both the chemical and biological synthesis of peptides. The ribozyme can use a wide range of amino acids as its substrate for the dipeptide synthesis. A library containing 29 peptides whose synthesis was catalyzed by this unique ribozyme was analyzed by mass spectrometry. These results implicate that ribozyme may have potential application in the peptide synthesis.

Properties of antigenomic hepatitis delta virus ribozyme that consists of three RNA oligomer strands

A three-strand ribozyme, a derivative of antigenomic hepatitis delta virus (HDV) ribozyme, which consists of subfragments of 16 (L), 17 (S), and 33 nucleotides (B), has been constructed. The ternary B-L-S complex formed by the subfragments in stoichiometric ratio was able to catalyze a self-cleavage reaction. Kinetics of this reaction exhibited biphasic behavior and the same parameters as in the case of natural cis-ribozyme. Study of kinetics of reaction initiated by adding various reaction components and the study of binary complex formation between subfragments B and L, B and S, and also ternary B-L-S complex formation revealed that: 1) in the presence of Mg2+, B and S form a stoichiometric complex, L and S do not form complex at all, while B and L form 2 types of complexes, probably B-L and 2B-L; and addition of S subfragment prevented the formation of the latter complex; 2) the reaction initiated by S subfragment proceeds much slower than that initiated by other components pointing to the possibility that in the absence of S L may form a nonproductive complex with B, which is slowly displaced by S followed by productive ternary complex formation. Dissociation constants for binary B-L, B-S and ternary B-L-S complexes have been estimated.

The synthesis and properties of oligoribonucleotide-spermine conjugates

Polyamines stabilise nucleic acids against chemical and enzymatic degradation, facilitate the formation of secondary and tertiary structures and enhance cellular uptake. Therefore methods for the syntheses of polyamine-nucleic acid conjugates are of interest. A route for the syntheses of RNA-spermine conjugates has been developed. The polyamine was introduced to the C-5 position of uridine via an ethyl tether and the molecule elaborated into a synthon suitable for oligoribonucleotide assembly. The resultant oligomers were components of the hairpin ribozyme. Characterisation of the spermine-conjugated catalytic RNA revealed that attachment of the polyamine was well tolerated in three of four positions, namely U41, U37 and U34, suggesting that conjugation to C-5 brings about minimal structural perturbation.

Synthesis of ribozyme against vascular endothelial growth factor165 and its biological activity in vitro

AIM: To investigate the designation, synthesis and biological activity of against vascular endothelial growth factor₁₆₅ (VEGF₁₆₅) ribozyme.

METHODS: The ribozyme against VEGF₁₆₅ was designed with computer. The transcriptional vector was constructed which included the anti-VEGF₁₆₅ ribozyme and 5’, 3’ self-splicing ribozymes. The hammerhead ribozyme and substrate VEGF₁₆₅ mRNA were synthesized through transcription in vitro. The cleavage activity of the ribozyme on target RNA was observed in a cell-free system.

RESULTS: The anti-VEGF₁₆₅ ribozyme was released properly from the transcription of pGEMRz212 cleaved by 5’ and 3’ self-splicing ribozymes which retained its catalytic activity, and the cleavage efficiency of ribozyme reached 90.7%.

CONCLUSION: The anti-VEGF₁₆₅ ribozyme designed with computer can cleave VEGF₁₆₅ mRNA effectively.

Enhancing the second step of the trans excision-splicing reaction of a group I ribozyme by exploiting P9.0 and P10 for intermolecular recognition

We previously reported that a group I intron-derived ribozyme can catalyze the excision of targeted sequences from within RNAs in vitro and that dissociation of the bridge-3' exon intermediate between the two reaction steps is a significant contributing factor to low product yields. We now analyze the effects of increasing the length, and thus the strength, of helices P9.0 and P10, which occur between the ribozyme and the bridge-3' exon region of the substrate, on this trans excision-splicing reaction. Using substrates where lengthy targeted regions are excised, these modifications can significantly increase product yields, specifically by enhancing the second reaction step. A threshold for product formation is obtained, however, at around five base pairs for P10 and eight base pairs for P9.0. Nevertheless, elongating P9.0 appears to be the more effective strategy, as both substrate binding and the rate of the second reaction step increase. In addition, P10 is required when P9.0 is not elongated. Also, a strong P9.0 helix cannot replace a weaker P10 helix, indicating that P9.0 and P10 play somewhat distinct roles in the reaction. We also show that second-step inhibition stems from the formation of an extended P1 helix (P1ex), consisting of as little as a single Watson-Crick base pair, as well as the mere presence of substrate nucleosides immediately downstream from P10. Both of these inhibitory components can be overcome by utilizing P9.0 and P10 elongated ribozymes. This work sets forth an initial framework for rationally designing more effective trans excision-splicing ribozymes.

Helicase-Attached Novel Hybrid Ribozymes

Ribozymes have potential as therapeutic agents and in functional studies of genes of interest. The activities of ribozymes in vivo depend on the accessibility of ribozymes to a cleavage site in the target RNA. At present, the selection of a target site for ribozymes is often based on a computer-aided structural analysis of the target RNA or trial-and-error experiments in which vast numbers of ribozymes are tested systematically. To overcome this problem, we have engineered intracellularly produced ribozymes with unwinding activity in vivo. We found that attachment to ribozymes (hybrid ribozymes) of an RNA motif with the ability to interact with intracellular RNA helicases, which create hybrid ribozymes, enhances ribozyme activity significantly in vivo. Thus, hybrid ribozymes can catalyze cleavage at the specified target site within an RNA in vivo almost independently of the secondary or tertiary structure of the target RNA around the cleavage site.

Peripheral regions of natural hammerhead ribozymes greatly increase their self-cleavage activity

Natural hammerhead ribozymes are mostly found in some viroid and viroid-like RNAs and catalyze their cis cleavage during replication. Hammerheads have been manipulated to act in trans and assumed to have a similar catalytic behavior in this artificial context. However, we show here that two natural cis-acting hammerheads self-cleave much faster than trans-acting derivatives and other reported artificial hammerheads. Moreover, modifications of the peripheral loops 1 and 2 of one of these natural hammerheads induced a >100-fold reduction of the self-cleavage constant, whereas engineering a trans-acting artificial hammerhead into a cis derivative by introducing a loop 1 had no effect. These data show that regions external to the central conserved core of natural hammerheads play a role in catalysis, and suggest the existence of tertiary interactions between these peripheral regions. The interactions, determined by the sequence and size of loops 1 and 2 and most likely of helices I and II, must result from natural selection and should be studied in order to better understand the hammerhead requirements in vivo.

In vitro selection of ribozymes dependent on peptides for activity

A peptide-dependent ribozyme ligase (aptazyme ligase) has been selected from a random sequence population based on the small L1 ligase. The aptazyme ligase is activated > 18,000-fold by its cognate peptide effector, the HIV-1 Rev arginine-rich motif (ARM), and specifically recognizes the Rev ARM relative to other peptides containing arginine-rich motifs. Moreover, the aptazyme ligase can preferentially recognize the Rev ARM in the context of the full-length HIV-1 Rev protein. The only cross-reactivity exhibited by the aptazyme is toward the Tat ARM. Reselection of peptide- and protein-dependent aptazymes from a partially randomized population yielded aptazymes that could readily discriminate against the Tat ARM. These results have important implications for the development of aptazymes that can be used in arrays for the detection and quantitation of multiple cellular proteins (proteome arrays).

Engineered catalytic RNA and DNA : new biochemical tools for drug discovery and design

Since the fundamental discovery that RNA catalyzes critical biological reactions, the conceptual and practical utility of nucleic acid catalysts as molecular therapeutic and diagnostic agents continually develops. RNA and DNA catalysts are particularly attractive tools for drug discovery and design due to their relative ease of synthesis and tractable rational design features. Such catalysts can intervene in cellular or viral gene expression by effectively destroying virtually any target RNA, repairing messenger RNAs derived from mutant genes, or directly disrupting target genes. Consequently, catalytic nucleic acids are apt tools for dissecting gene function and for effecting gene pharmacogenomic strategies. It is in this capacity that RNA and DNA catalysts have been most widely utilized to affect gene expression of medically relevant targets associated with various disease states, where a number of such catalysts are presently being evaluated in clinical trials. Additionally, biotechnological prospects for catalytic nucleic acids are seemingly unlimited. Controllable nucleic acid catalysts, termed allosteric ribozymes or deoxyribozymes, form the basis of effector or ligand-dependent molecular switches and sensors. Allosteric nucleic acid catalysts promise to be useful tools for detecting and scrutinizing the function of specified components of the metabolome, proteome, transcriptome, and genome. The remarkable versatility of nucleic acid catalysis is thus the fountainhead for wide-ranging applications of ribozymes and deoxyribozymes in biomedical and biotechnological research.

Ribozyme-mediated selective induction of new gene activity in hepatitis C virus internal ribosome entry site-expressing cells by targeted trans-splicing

Although hepatitis C virus (HCV) causes worldwide health problems, efficient and specific therapy is not available so far. In this study, we describe a new genetic approach to the specific HCV therapy that is based upon trans-splicing ribozymes that can selectively replace HCV transcripts with a new RNA that exerts anti-HCV activity. We have developed a group I intron-based ribozyme targeting the internal ribosome entry site (IRES) of HCV with high fidelity and specificity. The ribozyme was designed to trans-splice its 3' tagging sequence comprising a new coding RNA, such as firefly luciferase transcript, that is linked to the 3' part of the HCV 5' UTR encompassing the downstream sequence of the targeted residue in the IRES. This ribozyme was then demonstrated to induce HCV IRES-dependent translation of the firefly luciferase gene selectively in HCV IRES-expressing cells with trans-splicing reaction. Moreover, a specific ribozyme with the coding sequence of the diphtheria toxin A chain in place of the firefly luciferase selectively triggered expression of the cytotoxin in cells expressing HCV IRES and specifically activated apoptosis of the cells. These results suggest that the trans-splicing ribozyme could be a potent anti-HCV agent to deliver therapeutic new gene activities specifically and selectively in HCV-infected cells.

Hammerhead ribozyme-mediated cleavage of the fusion transcript NPM-ALK associated with anaplastic large-cell lymphoma

OBJECTIVE

Approximately 60% of all anaplastic large-cell lymphomas (ALCL) contain a specific t(2;5)(p23;q35) chromosomal translocation leading to overexpression of NPM-ALK. As the chimeric tyrosine kinase is involved in tumorigenesis and pathogenesis of ALCL, we were interested to inhibit NPM-ALK expression using an exogenous and an endogenous ribozyme approach.

METHODS

We designed five anti-ALK hammerhead ribozymes that were targeted to cleave the ALK proportion of NPM-ALK. The ribozyme with the highest cleavage activity was used as a modified RNA/DNA chimera (RZ1*) for transient transfection and as a self-splicing ribozyme vector (pRZ1) for endogenous expression. Ribozyme performance was tested in 293 cells (cotransfected with NPM-ALK) and in the ALCL cell line Karpas 299 by transient and stable transfection and Western blotting. The half-life time of NPM-ALK was determined by pulse-chase experiments.

RESULTS

In vitro cleavage assays demonstrated different catalytic efficiencies depending on the targeted site of the substrate. Constant transfection of Karpas 299 cells with RZ1* for 96 hours did not lead to a significant reduction of NPM-ALK protein, presumably due to the long half-life of NPM-ALK (48 hours). In contrast, NPM-ALK protein expression was almost completely suppressed in transiently transfected 293 cells. Stable transfection of Karpas 299 cells with pRZ1 also resulted in significant reduction of NPM-ALK expression.

CONCLUSION

These results suggest that ribozymes targeted against NPM-ALK are able to inhibit expression of this oncogenic kinase efficiently and will be a useful tool to analyze its role in the pathophysiology of ALCL.

Factors that contribute to efficient catalytic activity of a small Ca2+-dependent deoxyribozyme in relation to its RNA cleavage function

Recently, we found a small Ca(2+)-dependent deoxyribozyme (unmodified), d(GCCTGGCAG(1)G(2)C(3)T(4)A(5)C(6)A(7)A(8)C(9)G(10)A(11)GTCCCT), with cleavage activity for its RNA substrate, r(AGGGACA downward arrow UGCCAGGC) ( downward arrow denotes the RNA cleavage site), in the presence of Ca(2+) and developed a functional SPR sensor chip with this deoxyribozyme [Okumoto, Y., Ohmichi, T., and Sugimoto, N. (2002) Biochemistry 41, 2769-2773]. In the study presented here, to clarify the factors contributing to the efficient catalytic activity of the unmodified deoxyribozyme, RNA cleavage reactions were carried out using 24 mutant deoxyribozymes containing one unnatural DNA nucleotide, such as dI (2'-deoxyinosine), 7-deaza-dG, 2-aminopurine, 7-deaza-dA, 2-amino-dA, dm(5)C (5-methyl-2'-deoxycytosine), or d(P)C (5-propynyl-2'-deoxycytosine). The K(m) values (Michaelis constants) with the mutants that lacked N7 and O6 of G(1) and O6 of G(2) were 4.5 and 6.6 times that of the unmodified one, respectively. The k(cat) value (cleavage rate constant) with the mutants that lacked O6 of G(10) was 0.025 times that of the unmodified one. The results of UV melting curves, SPR kinetics, and CD spectra supported the quantitative idea that the catalytic activity of the unmodified form was achieved using Ca(2+). On the basis of these results, a preliminary model for two G(1) x A(8) and G(2) x A(7) mismatched base pairs such as G(anti) x A(anti) formed in the catalytic loop is proposed. The factor of 10 increase in the k(cat)/K(m) value of the mutant deoxyribozyme, which has C(9) substituted with d(P)C, suggests that the base stacking interaction between the substituted propynyl group in dC and the nearest-neighbor base grew stronger. Thus, substituting d(P)C for dC in the catalytic loop would be one of the best ways to increase the catalytic activity of the deoxyribozyme.

Molecular recognition by the Candida albicans group I intron: tertiary interactions with an imino G.A pair facilitate binding of the 5' exon and lower the KM for guanosine

A G.A pair at position -5 in the P1 helix of the Candida albicans ribozyme contributes to tertiary binding of the 5' exon substrate [Disney, M. D., Haidaris, C. G., and Turner, D. H. (2001) Biochemistry 40, 6507-6519]. Here, the G in the G.A pair is replaced with inosine (I) in both semisynthetic ribozymes and oligonucleotide mimics of the internal guide sequence. Comparisons of oligonucleotide binding affinity for these and other sequences indicate that the G.A pair is in an imino conformation where the exocyclic amine of G contributes approximately 1.4 kcal/mol to tertiary interactions that help dock the ribozyme's P1 helix. Furthermore, replacement of the G.A pair with a G-C pair produces less favorable interactions with the 2'-hydroxyl group at the -3 position and a less favorable K(M) for pG in a ribozyme-catalyzed transesterification reaction. These results are also consistent with the G.A pair promoting docking of the P1 helix into the catalytic core. Evidently, tertiary interactions with the exocyclic amino group of a G in a single G.A pair can increase the equilibrium constant for tertiary folding of RNA by roughly 10-fold at 37 degrees C. Results with a G.U or G.G pair replacing the G.A pair at the -5 position suggest similar tertiary interactions with these pairs.

Ribozyme-mediated suppression of G protein gamma subunits

Efforts to determine the sequence of the human genome have resulted in sequence information on thousand of genes. Now, the challenge is to determine the functions of this myriad of genes, including those encoding the G protein subunit families. In this chapter, we describe the successful use of ribozymes to inactivate mRNAs expressed from the G protein gamma subunit genes. Ribozymes are unique in that they can inactivate specific gene expression, and thereby can be used to help identify the function of a protein or the role of a gene in a functional cascade. Compared to other means of identifying the role of a gene (i.e., transgenic or knockout animals), ribozymes are specific and relatively easy to use. Moreover, ribozymes are able to discriminate closely related, or even mutated, sequences within gene families. Thus, in addition to elucidating functions, ribozymes have the potential to be used in treating genetic disorders associated with mutations of G protein subunits.

Synthetic hammerhead ribozymes as tools in gene expression

The assessment of genetic controls for sequential developmental processes such as tooth formation and biomineralization is often difficult in transgenic "knockout" models, where phenotypes reflect only the permanent eradication of a gene, and reveal little about the dynamic range of expression for the gene(s) involved. One promising strategy to overcome this problem is through the use of ribozymes, a class of metalloenzymes made entirely of ribonucleic acid (RNA), that are capable of cleaving other RNA molecules in a catalytic fashion. Their activity can be targeted against specific mRNAs by selection of unique sequences flanking a conserved catalytic motif. In synthetic ribozymes, specificity, stability, and cell permeability can be dramatically improved by the incorporation of chemically modified ribonucleotides. This review focuses on the design and application of hammerhead ribozymes, the best-known and most widely used class of RNA-based enzymes. So far, except for a few conserved structures at the catalytic core, no one particular model or superior ribozyme design has been identified. It may well be that each cell, tissue, and organism has different requirements for the uptake, activity, and stability of hammerhead ribozymes. However, designed ribozymes can be highly effective agents for timed and localized elimination of gene products. As the 3D structures of active hammerhead molecules are revealed, more effective ribozymes will be developed. Today, developments in ribozyme-mediated sequence-specific blocking of gene expression hold great promise for active RNA enzymes as tools in biomolecular research and for eliminating unwanted gene expression in human diseases.

A circular RNA-DNA enzyme obtained by in vitro selection

A circular RNA-DNA enzyme with higher activity to target RNA cleavage and higher stability than that of the hammerhead ribozyme in the presence of RNase A was obtained by in vitro selection. The molecule is composed of a catalytic domain of 22-mer ribonucleotides derived from the hammerhead ribozyme and a fragment of 55-mer deoxyribonucleotides. The DNA fragment contains two substrate-binding domains (9-mer and 6-mer, respectively) and a "regulation domain" (assistant 40-mer DNA with 20-mer random deoxyribonucleotides sequence), which probably play the role in the regulation of flexibility and rigidity of the circular RNA-DNA enzyme. The above results suggest that the circular RNA-DNA enzyme will have a great prospect in gene-targeting therapies.

Imino proton NMR analysis of HDV ribozymes: nested double pseudoknot structure and Mg2+ ion-binding site close to the catalytic core in solution

Minimized trans-acting HDV ribozyme systems consisting of three (Rz-3) and two (Rz-2) RNA strands were prepared and their folding conformations were analyzed by NMR spectroscopy. The guanosine residues in one of the enzyme components of Rz-3 were labeled with 13C and 15N. Imino proton signals were assigned by analysis of NOESY and HSQC spectra. The results are consistent with the nested double pseudoknot model, which contains novel base pairs (P1.1), as observed in the crystal structure of a genomic HDV ribozyme. The NOE connectivities suggest an additional G:G pair at the bottom of P1.1 and at the top of P4. The effects of temperature and Mg2+ ions on base pairs for Rz-3 were examined. The temperature variation experiment on Rz-3 showed that P3 is the most stable and that P1.1 is as stable as P1 and P2. The imino proton signals of the G:U pair at the bottom of P1 and the top of P1.1, which are close to the cleavage site, showed the largest changes upon Mg2+ titration of Rz-3. The results suggest that the catalytic Mg2+ ion binds to the pocket formed by P1 and L3.

Selection, design, and characterization of a new potentially therapeutic ribozyme

An in vitro selection was designed to identify RNA-cleaving ribozymes predisposed for function as a drug. The selection scheme required the catalyst to be trans-acting with phosphodiesterase activity targeting a fragment of the Kras mRNA under simulated physiological conditions. To increase stabilization against nucleases and to offer the potential for improved functionality, modified sequence space was sampled by transcribing with the following NTPs: 2'-F-ATP, 2'-F-UTP, or 2'-F-5-[(N-imidazole-4-acetyl) propylamine]-UTP, 2'-NH2-CTP, and GTP. Active motifs were identified and assessed for their modified NMP and divalent metal dependence. The minimization of the ribozyme's size and the ability to substitute 2'-OMe for 2'-F and 2'-NH2 moieties yielded the motif from these selections most suited for both nuclease stability and therapeutic development. This motif requires only two 2'-NH2-Cs and functions as a 36-mer. Its substrate sequence requirements were determined to be 5'-Y-G-H-3'. Its half-life in human serum is >100 h. In physiologically relevant magnesium concentrations [approximately 1 mM] its kcat = 0.07 min(-1), Km = 70 nM. This report presents a novel nuclease stable ribozyme, designated Zinzyme, possessing optimal activity in simulated physiological conditions and ready for testing in a therapeutic setting.

In vitro selection of nonnatural ribozyme-catalyzing porphyrin metalation

A new macromolecular catalyst, which is composed of nonnatural ribonucleotide, was synthesized by the in vitro selection (SELEX) method. A pool of RNAs consisting of random sequences was obtained by transcription from a pool of synthetic random-sequence DNAs in the presence of 2'-aminocytidine triphosphate (2'-amino-CTP) instead of CTP. The pool was incubated with N-methylmesoporphyrin-immobilized gel; bound nonnatural RNAs were then collected and amplified by reverse-transcription following the polymerase chain reaction. The amplified DNAs were again transcribed in the presence of 2'-amino-CTP and applied to the gel. This selection process was repeated 10 times. The selected RNAs were cloned and sequenced. The RNAs not only bound to the ligand, N-methylmesoporphyrin but also catalyzed the metalation reaction of porphyrin.

Enhanced antiviral effect in cell culture of type 1 interferon and ribozymes targeting HCV RNA

We have recently shown that the replication of an HCV-poliovirus (PV) chimera that is dependent upon the hepatitis C virus (HCV) 5' untranslated region (UTR) can be inhibited by treatment with ribozymes targeting HCV RNA. To determine the antiviral effects of anti-HCV ribozyme treatment in combination with type 1 interferon (IFN), we analysed the replication of this HCV-PV chimera in HeLa cells treated with anti-HCV ribozyme and/or IFN-alpha2a, IFN-alpha2b, or consensus IFN. The anti-HCV ribozyme, or any of the IFNs alone have significant inhibitory effects on HCV-PV replication compared to control treatment (> or = 85%, P < 0.01). The maximal inhibition due to IFN treatment (94%, P < 0.01) was achieved with > or = 50 U/ml for either IFN-alpha2a or IFN-alpha2b compared to control treatment. A similar level of inhibition in viral replication could be achieved with a 5-fold lower dose of IFN if ribozyme targeting the HCV 5' UTR was given in combination. For consensus IFN, the dose could be reduced by > 12.5-fold if ribozyme targeting the HCV 5' UTR was given in combination. Conversely, the dose of ribozyme could be reduced 3-fold if given in combination with any of the IFN preparations. Moreover, treatment with low doses (1-25 U/mL) of IFN-alpha2a, IFN-alpha2b, or consensus IFN in combination with anti-HCV ribozyme resulted in > 98% inhibition of HCV-PV replication compared to control treatment (P < 0.01). These results demonstrate that IFN and ribozyme each have a beneficial antiviral effect that is augmented when given in combination.

Hammerhead ribozyme targeting human platelet-derived growth factor A-chain mRNA inhibited the proliferation of human vascular smooth muscle cells

Platelet-derived growth factor (PDGF) A-chain contributes to the pathogenesis of cardiovascular proliferative diseases, such as hypertensive vascular disease, atherosclerosis, and re-stenosis of an artery after angioplasty. To develop a ribozyme against human PDGF A-chain mRNA as a gene therapy for human arterial proliferative diseases, we designed and synthesized a 38-base hammerhead ribozyme to cleave human PDGF A-chain mRNA at the GUC sequence at nucleotide 591. In the presence of MgCl(2), synthetic hammerhead ribozyme to human PDGF A-chain mRNA cleaved the synthetic target RNA to two RNA fragments at a predicted size. Doses of 0.01-1.0 microM hammerhead ribozyme to human PDGF A-chain mRNA significantly inhibited angiotensin II (Ang II) and transforming growth factor (TGF)-beta(1)-induced DNA synthesis in vascular smooth muscle cells (VSMC) from human in a dose-dependent manner. One micromolor of hammerhead ribozyme to human PDGF A-chain mRNA significantly inhibited Ang II-induced PDGF A-chain mRNA and PDGF-AA protein expressions in VSMC from humans. These results indicate that the designed hammerhead ribozyme to human PDGF A-chain mRNA effectively inhibited growth of human VSMC by cleaving the PDGF A-chain mRNA and inhibiting the PDGF-AA protein expression in human VSMC. This suggests that the designed hammerhead ribozyme to PDGF A-chain mRNA is a feasible gene therapy for treating arterial proliferative diseases.

The specific hydrolysis of HIV-1 TAR RNA element with the anti-TAR hammerhead ribozyme: structural and functional implications

The main transcriptional regulator of the human immunodeficiency virus is the Tat protein, which recognises and binds to a fragment RNA at the 5' end of viral mRNA, named transactivation response element (TAR) RNA. Extensive mutagenesis studies have shown that a region of TAR RNA important for Tat binding involves a set of nucleotides surrounding a characteristic UCU nucleotide bulge. The specific Tat-TAR complex formation enhances the rate of transcription elongation but inhibition of that interaction prevents the human immunodeficiency virus type 1 (HIV-1) replication. If so, a possibility of virus inactivation would be a site specific degradation of the TAR RNA element. To break down and inactivate TAR RNA, we designated the anti-hammerhead (HH) ribozyme to cleave nucleosides within the bulge. We showed for the first time the new type of the AUC hammerhead ribozyme, which hydrolyses specifically the TAR RNA element at C8 nucleotide in the bulge (C24 in the standard TAR RNA numbering). The cleavage reaction has broad magnesium requirements. Mn and particularly Ca are less efficient. Argininamide interferes with the cleavage of TAR RNA induced by the ribozyme. These results have two implications; (i) structural, where the HIV-1 TAR RNA element in solution occurs in equilibrium of only two forms, one of which, a double stranded RNA, meets structural requirements for ribozyme pairing and cleavage, and (ii) functional, the HH ribozyme can be explored for an inactivation of HIV-1 through the TAR RNA element deintegration.

Identifying ribozyme-accessible sites using NUH triplet-targeting gapmers

Accurately identifying accessible sites in RNA is a critical prerequisite for optimising the cleavage efficiency of hammerhead ribozymes and other small nucleozymes. Here we describe a simple RNase H-based procedure to rapidly identify hammerhead ribozyme-accessible sites in gene length RNAS: Twelve semi-randomised RNA-DNA-RNA chimeric oligonucleotide probes, known as 'gapmers', were used to direct RNase H cleavage of transcripts with the specificity expected for hammerhead ribozymes, i.e. after NUH sites (where H is A, C or U). Cleavage sites were identified simply by the mobility of RNase H cleavage products relative to RNA markers in denaturing polyacrylamide gels. Sites were identified in transcripts encoding human interleukin-2 and platelet-derived growth factor. Thirteen minimised hammerhead ribozymes, miniribozymes (Mrz), were synthesised and in vitro cleavage efficiency (37 degrees C, pH 7.6 and 1 mM MgCl2) at each site was analysed. Of the 13 Mrz, five were highly effective, demonstrating good initial rate constants and extents of cleavage. The speed and accuracy of this method commends its use in screening for hammerhead-accessible sites.

Selection and characterization of a high-activity ribozyme directed against the antineoplastic drug resistance-associated ABC transporter BCRP/MXR/ABCG2

Breast cancer resistance protein (BCRP) is a recently identified new member of the superfamily of ATP-binding cassette transporters. BCRP is a "half transporter" that may homo- or heterodimerize to form an active transport complex. A considerable overexpression of BCRP was reported from various atypical multidrug-resistant tumor cell lines, in particular from those which were established by treatment with mitoxantrone. Thus, BCRP represents a very interesting candidate molecule for reversal of a drug-resistant phenotype. Six hammerhead ribozymes directed against the BCRP-encoding mRNA were designed and tested for their ability to cleave their target molecule. The anti-BCRP ribozymes were in vitro synthesized using bacteriophage T7 RNA polymerase and oligonucleotide primers whereby one primer contains a T7 RNA polymerase promoter sequence. BCRP-encoding substrate RNA molecules were created by a reverse transcription polymerase chain reaction using total RNA prepared from the atypical multidrug-resistant gastric carcinoma cell line EPG85-257RNOV exhibiting a high BCRP mRNA expression level. One anti-BCRP ribozyme was found to show a very high endoribonucleolytic cleavage activity at physiologic pH and temperature. This ribozyme was characterized in a cell-free system with regard to its specific kinetic parameters using large target molecules.

Kinetic characterization of ribozymes directed against the cisplatin resistance-associated ABC transporter cMOAT/MRP2/ABCC2

The enhanced expression of the human ABC transporter, cMOAT (MRP2/ABCC2), is associated with resistance of tumor cells against platinum-containing compounds, such as cisplatin. Therefore, cMOAT represents an interesting candidate factor for modulation of antineoplastic drug resistance. Two different hammerhead ribozymes, which exhibit high catalytic cleavage activities towards specific RNA sequences encoding cMOAT, were designed. Cleavage sites of these ribozymes are the GUC sites in codons 704 and 708 of the open reading frame in the cMOAT-specific mRNA molecule. Hammerhead ribozymes were in vitro synthesized using bacteriophage T7 RNA polymerase and oligonucleotide primers whereby one primer contains a T7 RNA polymerase promoter sequence. cMOAT-encoding substrate RNA molecules were created by a reverse transcription polymerase chain reaction using RNA prepared from the cisplatin-resistant human ovarian carcinoma cell line A2780RCIS overexpressing the cMOAT-encoding transcript. In a cell-free system, both anti-cMOAT ribozymes cleaved their substrate in a highly efficient manner at a physiologic pH and temperature. The cleavage reaction was dependent on time and ribozyme:substrate ratio for determining specific kinetic parameters.

HIV-1 LTR as a target for synthetic ribozyme-mediated inhibition of gene expression: site selection and inhibition in cell culture

A library of three synthetic ribozymes with randomized arms, targeting NUX, GUX and NXG triplets, respectively, were used to identify ribozyme-accessible sites on the HIV-1 LTR transcript comprising positions -533 to 386. Three cleavable sites were identified at positions 109, 115 and 161. Ribozymes were designed against these sites, either unmodified or with 2'-modifications and phosphorothioate groups, and their cleavage activities of the transcript were determined. Their biological activities were assessed in cell culture, using a HIV-1 model assay system where the LTR is a promoter for the expression of the reporter gene luciferase in a transient expression system. Intracellular efficiency of the ribozymes were determined by cotransfection of ribozyme and plasmid DNA, expressing the target RNA. Modified ribozymes, directed against positions 115 and 161, lowered the level of LTR mRNA in the cell resulting in inhibition of expression of the LTR-driven reporter gene luciferase of 87 and 61%, respectively. In the presence of Tat the inhibitions were 43 and 25%. The inactive variants of these ribozymes exhibited a similar inhibitory effect. RNase protection revealed a reduction of RNA which was somewhat stronger for the active than the inactive ribozymes, particularly for ribozyme 115. Unmodified ribozymes showed no inhibition in the cell. The third ribozyme, targeting a GUG-triplet at position 109, possessed only low cleavage activity in vitro and no inhibitory effect in cell culture.

Induction of ribozyme activity by anti-ribozyme oligonucleotides

A new type of hammerhead ribozyme, with cleavage activity enhanced by oligonucleotides, was constructed. Stem II of the ribozyme was substituted with a non complementary loop (loop II). The modified ribozyme exhibited negligible cleavage of a target RNA; however, it was converted to an active molecule in the presence of oligonucleotides which were complementary to loop II. The oligonucleotide compensated for the disabled stem II by binding with the ribozyme. The induction of the cleavage activity was sequence-specific and the oligonucleotides containing a purine base as the 3'-dangling end were able to induce the cleavage activity of the ribozyme most efficiently. A photo-crosslinking experiment proved that a pseudo-half-knot structure was formed in the active molecule. The cleavage of two kinds of substrate RNAs with different sequences was controlled by the corresponding ribozymes activated by specific oligonucleotides.