The Effect of Universal Fluorinated Nucleobases on the Catalytic Activity of Ribozymes

Abstract

Four fluoro modified universal nucleobases have been synthesized. The universal nucleobases 1 and 2 , containing a 2,4-difluorobenzene as nucleobase and a 4,6-difluorobenzimidazole, respectively, were chemically incorporated into a selected hammerhead ribozyme sequence which has already been retrovirally expressed as an anti-HIV ribozyme to investigate their effect on the catalytic activity of the ribozymes. The substitution of the natural nucleosides with either 1 or 2 results only in a small decrease of the catalytic activity. The K_m value for the monosubstituted ribozyme with a 2,4-difluorobenzene is 309 nM^?1, the corresponding k_cat is 2.91 · 10^?3 min^?1. A disubstituted hammerhead ribozyme carrying one of each modification has also been synthesized. For a further stabilization of the ribozyme/substrate complex 2′-(β-aminoethoxy) modified fluorinated nucleosides 15 and 16 have been developed.     

Addition of an Extra Substrate Binding Site and Partial Destabilization of Stem Structures in HDV Ribozyme Give Rise to High Sequence-Specificity for its Target RNA

Because the substrate binding site (P1) of HDV ribozyme consists of only seven nucleotides, cleavage of undesired RNA is likely to occur when applied for a specific long RNA target such as mRNA. To overcome this problem, we designed modified trans-acting HDV ribozymes with an extra substrate-binding site (P5) in addition to the original binding site (P1). By inserting an additional seven base-pair stem (P5 stem) into the J1/2 single-stranded region of the ribozyme core system and partial destabilization of the P2 or P4 stem, we succeeded in preparation of new HDV ribozymes that can cleave the target RNA depending on the formation of P5 stem. Moreover, the ribozyme with a six-nucleotide P1 site was able to distinguish the substrate RNA with a complete match from that with a single mismatch in the P1 region. These results suggest that the HDV ribozyme system is useful for the application in vivo.     

Synthesis of 5′-C-Methyl-D-allo- & L-Talo-ribonucleoside 3′-O-Phosphoramidites & Their Incorporation into Hammerhead Ribozymes

Abstract

5′-C-Methyl-D-allo & L-talo-ribonucleoside 3′-O-phosphoramidites were prepared from L-rhamnose in 13 and 15 steps respectively. Incorporation of L-talo residues in the hammerhead ribozyme and the resulting activity and stability of the modified ribozymes is described.     

Amino-Linked Ribozymes: Post-Synthetic Conjugation of Half-Ribozymes

Abstract

A convergent approach, based on the reductive amination of 3′-phospho-glycaldehyde-ribozyme 3 with 5′-aminohexyLribozyme 1 generated an amino-linked ribozyme 4 in good yields. Catalytic activity of the cross-linked ribozyme is discussed.     

Fluorescence Resonance Energy Transfer (Fret) to Follow Ribozyme Reactions In Real Time

Abstract

Fluorescence resonance transfer (FRET) was applied for real time monitoring of ribozyme reactions. Group I ribozyme ligation was followed with two separate, fluorescent-labeled RNA substrates. For hammerhead ribozyme cleavage, a double-fluorescent-labeled substrate was used. For the first time we analyzed multiple turnover conditions. Real time monitoring permits convenient analysis of ribozyme kinetics and the sequence-specific, quantitative detection of RNAs in femtomole amounts.     

Structural Rearrangements Linked to Global Folding Pathways of the Azoarcus Group I Ribozyme

Stable RNAs must fold into specific three-dimensional structures to be biologically active, yet many RNAs form metastable structures that compete with the native state. Our previous time-resolved footprinting experiments showed that Azoarcus group I ribozyme forms its tertiary structure rapidly (τ < 30 ms) without becoming significantly trapped in kinetic intermediates. Here, we use stopped-flow fluorescence spectroscopy to probe the global folding kinetics of a ribozyme containing 2-aminopurine in the loop of P9. The modified ribozyme was catalytically active and exhibited two equilibrium folding transitions centered at 0.3 and 1.6 mM Mg²⁺, consistent with previous results. Stopped-flow fluorescence revealed four kinetic folding transitions with observed rate constants of 100, 34, 1, and 0.1 s^− 1 at 37 °C. From comparison with time-resolved Fe(II)-ethylenediaminetetraacetic acid footprinting of the modified ribozyme under the same conditions, these folding transitions were assigned to formation of the I_C intermediate, tertiary folding and docking of the nicked P9 tetraloop, reorganization of the P3 pseudoknot, and refolding of nonnative conformers, respectively. The footprinting results show that 50-60% of the modified ribozyme folds in less than 30 ms, while the rest of the RNA population undergoes slow structural rearrangements that control the global folding rate. The results show how small perturbations to the structure of the RNA, such as a nick in P9, populate kinetic folding intermediates that are not observed in the natural ribozyme.     

Identification of a Good C-MYC Antisense Oligodeoxynucleotide Target Site and the Inactivity at This Site of Novel NCH Triplet-Targeting Ribozymes

Abstract

A region of c-myc mRNA was identified which permitted very efficient antisense effects to be achieved in living cells using chimeric methylphosphonate-phosphodiester antisense effectors. Novel inosine—containing ribozymes (which cleave after NCH triplets) were directed to an ACA triplet within this region and delivered into living cells. No ribozyme intracellular activity could be identified. Very low ribozyme function was also observed in in vitro assays using a 1700nt substrate RNA.     

Construction of a Modified Hairpin Ribozyme for Investigations of the Structure-Function Relationship

Abstract

We have constructed a new three domain hairpin ribozyme, in which domain II is connected with domain I' by a helix and a nucleotidic linker to enhance the active bent conformation. The insertion of a nucleotide linker into domain I' increased the cleavage activity more than into domain II. Furthermore, Rev responsive elements (RRE) were introduced in the helix connecting domains. The cleavage activities of the hairpin ribozyme containing the RRE were not affected by the presence of the Rev.     

New Structural Motifs for Hammerhead Ribozymes. Catalytic Activity of Abasic Nucleotide Substituted Ribozymes

Abstract

The synthesis of 1-deoxy-D-ribofuranose-3-(2-cyanoethyl N,N-diisopropylphosphoramidite) (6) from D-ribose and its incorporation into a hammerhead ribozyme is described.     

Synthesis of a New Hydroxyamino Linked Thymidine Dimer via a Radical C-C Bond Formation

Abstract

An efficient synthesis of a thymidine nucleoside dimer [T-3′-β-O-N(CH₃)-CH₂-5′-T] has been accomplished via an intermolecular radical coupling reaction. The novel dimer contains an achiral and neutral backbone linkage which may have potential application in constructing backbone modified antisense oligonucleosides.     

Suppression of Human Immunodeficiency Virus Type 1 (HIV-1) Replication by an HIV-1-dependent Double Locked Vector with the Cre/loxP System

We previously demonstrated the function of an HIV-1-dependent ribozyme expression vector, with which the site-specific excision of loxP sequences can be achieved by using the Cre-loxP system (ON/OFF) as a molecular switch in an acute HIV-1 infection. However, this expression system also revealed the lower, non-specific expression of the anti-HIV-1 ribozyme in the absence of tat. To circumvent this problem, we used the more efficient HIV-1-dependent Cre recombinase gene expression vector, encoding the LTR-gag-p17 (extending from the 5′-LTR to the middle of the gag gene (pLTR-gag-p17-Cre)). Comparatively, the pLTR-gag-p17-Cre induces a higher Cre-protein expression level in an HIV-1 infection-dependent manner than the minimal pLTR-Cre. Furthermore, we constructed the ploxP-Rz-U5 and pLTR-gag-p17-Cre plasmids and also combined them into a single vector, pLTR-gag-p17-Cre/loxP-Rz-U5, for a comparison of their anti-HIV-1 activities. The resultant simultaneous expression of the Cre protein and the homologous recombination of the two loxP sequences induced a high level of HIV-1 replication inhibition (95%). Significantly, a high steady-state of ribozyme expression was observed in the RT-PCR analysis. These data imply that targeting the HIV-1 genes with the pLTR-gag-p17-Cre/loxP-Rz-U5 vector, which mediates HIV-1-dependent ribozyme expression, would be a useful tool for HIV-1 gene therapy applications.     

Expression of lexA targeted ribozyme in Escherichia coli BL-21 (DE3) cells

Coding sequences for a hammerhead ribozyme designed to cleave lexA mRNA in a targeted manner was cloned under phage T7 promoter and expressed in E. coli strain BL-21 (DE3) expressing T7 RNA polymerase under the control of IPTG-inducible lac UV-5 promoter. Ribozyme expression in vivo was demonstrated by RNase protection assay. Also, total RNA extracted from these transformed cells following induction by IPTG, displays site-specific cleavage of labeled lexA RNA in an In vitro reaction. The result demonstrates the active ribozyme in extracts of cell transformed with a recombinant cassette and goes beyond the earlier demonstration of the stability of In vitro synthesized ribozyme in cell extracts. The observed rise in lexA mRNA rules out any role for protease activity or resulting fragments of lexA protein in de-repression of RNA. (Mol Cell Biochem 271: 197–203, 2005)     

Cleavage of Short RNAs Containing Higher Ordered Structures by Hammerhead Ribozymes

Abstract

Cleavage of two types of secondary structure-forming substrates by their cognate hammerhead ribozymes were studied by measuring their kinetic parameters. A substrate with a self-complementary structure (GGUCCUAGGA, CL-3) was slowly cleaved by a two-stranded ribozyme. An isomer having no complementary sequence (GGUCGUAGCA, CL-3N) was cleaved more than 10 times faster than the self-complementary substrate. A newly designed ribozyme which contained a stable loop and stem cleaved the self-complementary decamer 40 times faster than the two-stranded ribozyme. A 15 mer which derived from a ras mRNA was found to have an intermolecular base pairs and was used to design more efficient ribozymes. Gel mobility shift assay was employed to investigate the binding properties of substrates to ribozymes. Investigations of the thermodynamic stability of the ribozyme-substrate complex are essential in the design of ribozymes that efficiently cleave RNA.

     

Ribozyme mediated trans insertion-splicing of modified oligonucleotides into RNA

The trans insertion-splicing reaction, catalyzed by a group I intron-derived from Pneumocystis carinii, was recently developed for the site-specific insertion of a segment of RNA into a separate RNA substrate. The molecular determinants of this reaction for binding and catalysis are reasonably well understood, making them easily and highly modifiable for altering substrate specificity. To demonstrate proof-of-concept, we now report that the P. carinii ribozyme can except modified oligonucleotides as substrates for catalyzing the trans insertion-splicing reaction. Oligonucleotides that contain one or more sugar modifications (deoxy or methoxy substitution), a backbone modification (phosphorothioate substitution), or a base modification (2-aminopurine or 4-thiouridine) are effective substrates in this reaction. Apparently, trans insertion-splicing is a unique and viable reaction for the site-specific incorporation of modified oligonucleotides into RNAs. This is the first report of a group I intron-derived ribozyme being capable of catalyzing the insertion of a modified oligonucleotide into RNA.     

The role of phosphate groups in the VS ribozyme-substrate interaction

The VS ribozyme trans-cleavage substrate interacts with the catalytic RNA via tertiary interactions. To study the role of phosphate groups in the ribozyme–substrate interaction, 18 modified substrates were synthesized, where an epimeric phosphorothioate replaces one of the phosphate diester linkages. Sites in the stem–loop substrate where phosphorothioate substitution impaired reaction cluster in two regions. The first site is the scissile phosphate diester linkage and nucleotides downstream of this and the second site is within the loop region. The addition of manganese ions caused recovery of the rate of reaction for phosphorothioate substitutions between A621 and A622 and U631 and C632, suggesting that these two phosphate groups may serve as ligands for two metal ions. In contrast, significant manganese rescue was not observed for the scissile phosphate diester linkage implying that electrophilic catalysis by metal ions is unlikely to contribute to VS ribozyme catalysis. In addition, an increase in the reaction rate of the unmodified VS ribozyme was observed when a mixture of magnesium and manganese ions acted as the cofactor. One possible explanation for this effect is that the cleavage reaction of the VS ribozyme is rate limited by a metal dependent docking of the substrate on the ribozyme.     

Inducible Knockdown of Plasmodium Gene Expression Using the glmS Ribozyme

Conventional reverse genetic approaches for study of Plasmodium malaria parasite gene function are limited, or not applicable. Hence, new inducible systems are needed. Here we describe a method to control P. falciparum gene expression in which target genes bearing a glmS ribozyme in the 3′ untranslated region are efficiently knocked down in transgenic P. falciparum parasites in response to glucosamine inducer. Using reporter genes, we show that the glmS ribozyme cleaves reporter mRNA in vivo leading to reduction in mRNA expression following glucosamine treatment. Glucosamine-induced ribozyme activation led to efficient reduction of reporter protein, which could be rapidly reversed by removing the inducer. The glmS ribozyme was validated as a reverse-genetic tool by integration into the essential gene and antifolate drug target dihydrofolate reductase-thymidylate synthase (PfDHFR-TS). Glucosamine treatment of transgenic parasites led to rapid and efficient knockdown of PfDHFR-TS mRNA and protein. PfDHFR-TS knockdown led to a growth/arrest mutant phenotype and hypersensitivity to pyrimethamine. The glmS ribozyme may thus be a tool for study of essential genes in P. falciparum and other parasite species amenable to transfection.     

Metal ion specificities for folding and cleavage activity in the Schistosoma hammerhead ribozyme

The effects of various metal ions on cleavage activity and global folding have been studied in the extended Schistosoma hammerhead ribozyme. Fluorescence resonance energy transfer was used to probe global folding as a function of various monovalent and divalent metal ions in this ribozyme. The divalent metals ions Ca²⁺, Mg²⁺, Mn²⁺, and Sr²⁺ have a relatively small variation (less than sixfold) in their ability to globally fold the hammerhead ribozyme, which contrasts with the very large difference (>10,000-fold) in apparent rate constants for cleavage for these divalent metal ions in single-turnover kinetic experiments. There is still a very large range (>4600-fold) in the apparent rate constants for cleavage for these divalent metal ions measured in high salt (2 M NaCl) conditions where the ribozyme is globally folded. These results demonstrate that the identity of the divalent metal ion has little effect on global folding of the Schistosoma hammerhead ribozyme, whereas it has a very large effect on the cleavage kinetics. Mechanisms by which the identity of the divalent metal ion can have such a large effect on cleavage activity in the Schistosoma hammerhead ribozyme are discussed.