1
|
Czapik T, Piasecka J, Kierzek R, Kierzek E. Structural variants and modifications of hammerhead ribozymes targeting influenza A virus conserved structural motifs. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 29:64-74. [PMID: 35784013 PMCID: PMC9217987 DOI: 10.1016/j.omtn.2022.05.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 05/26/2022] [Indexed: 11/16/2022]
Abstract
The naturally occurring structure and biological functions of RNA are correlated, which includes hammerhead ribozymes. We proposed new variants of hammerhead ribozymes targeting conserved structural motifs of segment 5 of influenza A virus (IAV) (+)RNA. The variants carry structural and chemical modifications aiming to improve the RNA cleavage activity of ribozymes. We introduced an additional hairpin motif and attempted to select ribozyme-target pairs with sequence features that enable the potential formation of the trans-Hoogsteen interactions that are present in full-length, highly active hammerhead ribozymes. We placed structurally defined guanosine analogs into the ribozyme catalytic core. Herein, the significantly improved synthesis of 2′-deoxy-2′-fluoroarabinoguanosine derivatives is described. The most potent hammerhead ribozymes were applied to chimeric short hairpin RNA (shRNA)-ribozyme plasmid constructs to improve the antiviral activity of the two components. The modified hammerhead ribozymes showed moderate cleavage activity. Treatment of IAV-infected Madin-Darby canine kidney (MDCK) cells with the plasmid constructs resulted in significant inhibition of virus replication. Real-time PCR analysis revealed a significant (80%–88%) reduction in viral RNA when plasmids carriers were used. A focus formation assay (FFA) for chimeric plasmids showed inhibition of virus replication by 1.6–1.7 log10 units, whereas the use of plasmids carrying ribozymes or shRNAs alone resulted in lower inhibition.
Collapse
|
2
|
Rana AK, Ankri S. Reviving the RNA World: An Insight into the Appearance of RNA Methyltransferases. Front Genet 2016; 7:99. [PMID: 27375676 PMCID: PMC4893491 DOI: 10.3389/fgene.2016.00099] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 05/23/2016] [Indexed: 12/13/2022] Open
Abstract
RNA, the earliest genetic and catalytic molecule, has a relatively delicate and labile chemical structure, when compared to DNA. It is prone to be damaged by alkali, heat, nucleases, or stress conditions. One mechanism to protect RNA or DNA from damage is through site-specific methylation. Here, we propose that RNA methylation began prior to DNA methylation in the early forms of life evolving on Earth. In this article, the biochemical properties of some RNA methyltransferases (MTases), such as 2′-O-MTases (Rlml/RlmN), spOUT MTases and the NSun2 MTases are dissected for the insight they provide on the transition from an RNA world to our present RNA/DNA/protein world.
Collapse
Affiliation(s)
- Ajay K Rana
- Division of Biology, State Forensic Science Laboratory, Ministry of Home Affairs, Government of Jharkhand Ranchi, India
| | - Serge Ankri
- Department of Molecular Microbiology, The Ruth and Bruce Rappaport Faculty of Medicine, Technion Israel Institute of Technology Haifa, Israel
| |
Collapse
|
3
|
Kan LS, Bauman R, Bhan P, Miller PS. Proton Nuclear Magnetic Resonance Measurements of 2′-Aminodeoxyuridylyl-3′,5′-Deoxyuridine. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.199300074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
4
|
5-Fluoro-4-thiouridine phosphoramidite: new synthon for introducing photoaffinity label into oligodeoxynucleotides. Bioorg Med Chem 2011; 19:6098-106. [PMID: 21917468 DOI: 10.1016/j.bmc.2011.08.035] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Revised: 08/09/2011] [Accepted: 08/14/2011] [Indexed: 11/21/2022]
Abstract
The synthesis of phosphoramidite of 5-fluoro-4-thio-2'-O-methyluridine is described. An appropriate set of protecting groups was optimized including the 4-thio function introduced via 4-triazolyl as the 4-(2-cyanoethyl)thio derivative, and the t-butyldimethyl silyl for 2' and 3' hydroxyl protection, enabling efficient synthesis of the phosphoramidite. These protecting groups prevented unwanted side reactions during oligonucleotide synthesis. The utility of the proposed synthetic route was proven by the preparation of several oligonucleotides via automated synthesis. Photochemical experiments confirmed the utility of the synthon.
Collapse
|
5
|
Lam BJ, Joyce GF. An isothermal system that couples ligand-dependent catalysis to ligand-independent exponential amplification. J Am Chem Soc 2011; 133:3191-7. [PMID: 21322594 DOI: 10.1021/ja111136d] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A system was devised that enables quantitative, ligand-dependent exponential amplification for various ligands that can be recognized by an RNA aptamer. The aptamer is linked to an RNA enzyme that catalyzes the joining of two oligonucleotide substrates. The product of this reaction is another RNA enzyme that undergoes self-sustained replication at constant temperature, increasing in copy number exponentially. The concentration of the ligand determines the amount of time required for the replication products to reach a threshold concentration. A standardized plot of time to threshold versus ligand concentration can be used to determine the concentration of ligand in an unknown sample. This system is analogous to quantitative polymerase chain reaction (PCR), linking rare recognition events to subsequent exponential amplification, but unlike PCR can be applied to the quantitative detection of non-nucleic acid ligands.
Collapse
Affiliation(s)
- Bianca J Lam
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | | |
Collapse
|
6
|
Fedoruk-Wyszomirska A, Szymański M, Wyszko E, Barciszewska MZ, Barciszewski J. Highly active low magnesium hammerhead ribozyme. J Biochem 2009; 145:451-9. [PMID: 19124457 DOI: 10.1093/jb/mvn182] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Hammerhead (HH) ribozymes can be used for highly specific inhibition of gene expression through the degradation of target mRNA. In vitro experiments with minimal HH domains demonstrated that the efficiency of catalysis is highly dependent on concentration of magnesium ions. Optimal ion requirements for HH-catalysed RNA cleavage are far from these found in the cell. Recently, it has been proposed that the efficiency of HH ribozymes can be increased at low magnesium concentration through stabilization of a catalytically active conformation by tertiary interactions between helices I and II. We designed a ribozyme stabilized by GAAA tetraloop and its receptor motifs and demonstrated that it can efficiently catalyse target RNA hydrolysis at submillimolar Mg(2+) concentrations in vitro as well as in cultured cells. Both unmodified and locked nucleic acid-modified extended ribozymes proved superior to the minimal core ribozyme and DNAzyme against the same target sequence.
Collapse
|
7
|
Vinayak S, Sharma YD. Inhibition of Plasmodium falciparum ispH (lytB) gene expression by hammerhead ribozyme. Oligonucleotides 2007; 17:189-200. [PMID: 17638523 DOI: 10.1089/oli.2007.0075] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The nonmevalonate pathway of isoprenoid biosynthesis in the apicoplast of the human malaria parasite Plasmodium falciparum is distinct from the mevalonate-dependent pathway of humans and thus a good drug target. We describe here the hammerhead ribozyme based cleavage of the ispH (lytB) gene transcript involved in the last step of this nonmevalonate pathway. Using RNA folding program, three hammerhead ribozymes named as RZ(876), RZ(1260), and RZ(1331) were predicted against ispH (lytB) mRNA. Messenger walk screening (RNaseH) assay confirmed the target accessibility for these ribozymes. All three ribozymes cleaved the target RNA in vitro but RZ(876) exhibited the highest catalytic potential (62.92%). Therefore, RZ(876) was chemically synthesized with appropriate chemical modifications to protect it from nuclease attack while using it for in vitro parasite growth inhibition assay. This ribozyme RZ(876) was able to inhibit 87.36% parasite growth at 30 microM concentration compared to the untreated culture. However, an absolute inhibition of 29.41% was achieved compared to the control ribozyme (RZ(ctrl)). Nonetheless, the growth inhibition effect was found to be sequence-specific as indicated by the decreased level of ispH (lytB) transcript after ribozyme treatment. In conclusion, we have identified the ispH (lytB) as a potential target whose transcript can be cleaved by a ribozyme RZ(876).
Collapse
Affiliation(s)
- Sumiti Vinayak
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi-110029, India
| | | |
Collapse
|
8
|
Ludwig J, Blaschke M, Dunkel M, Beijer B, Ross K, Sproat BS. Structural Requirements at the 15.1–16.1 Position of the Hammerhead Ribozyme. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328319908044774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
9
|
McGee DPC, Zhai Y. REACTION OF ANHYDRONUCLEOSIDES WITH MAGNESIUM ALKOXIDES: REGIOSPECIFIC SYNTHESIS OF 2′-O-ALKYLPYRIMIDINE NUCLEOSIDES. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328319608002733] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
10
|
Gonzalez-Carmona MA, Schüssler S, Serwe M, Alt M, Ludwig J, Sproat BS, Steigerwald R, Hoffmann P, Quasdorff M, Schildgen O, Caselmann WH. Hammerhead ribozymes with cleavage site specificity for NUH and NCH display significant anti-hepatitis C viral effect in vitro and in recombinant HepG2 and CCL13 cells. J Hepatol 2006; 44:1017-25. [PMID: 16469406 DOI: 10.1016/j.jhep.2005.10.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2005] [Revised: 09/30/2005] [Accepted: 10/04/2005] [Indexed: 01/04/2023]
Abstract
BACKGROUND/AIMS Four different ribozymes (Rz) targeting the hepatitis C virus (HCV) 5'-non-coding region (NCR) at nucleotide (nt) positions GUA 165 (Rz1), GUC 270 (Rz2), GUA 330 (Rz3) and GCA 348 (Rz1293) were compared for in vitro cleavage using a 455 nt HCV RNA substrate. The GUA 330 (Rz3) and GCA 348 (Rz1293) ribozymes, both targeting the HCV loop IV region, were found to be the most efficient, and were further analyzed in an in vitro translation system. METHODS For this purpose RNA transcribed from a construct encoding a HCV-5'-NCR-luciferase fusion protein was used. Cleavage-inactive (Rz1426), mismatch (Rz1293m) or unrelated ribozymes (Rz1437) were synthesized as controls for Rz-1293. HCV specificity was analysed by competition experiments using sense and mismatch oligodeoxynucleotides HCVrzCI and HCVrzMM, respectively. RESULTS A chemically modified nuclease-resistant variant of the GCA 348 cleaving ribozyme was selected for cell culture experiments using recombinant HepG2 or CCL13 cell lines stably transfected with a HCV-5'-NCR-luciferase target construct. CONCLUSIONS This ribozyme (Rz1293) showed an inhibitory activity of translation of more than 70% thus verifying that the GCA 348 cleavage site in the HCV loop IV is an accessible target site in vivo and may be suitable for the development of novel optimized hammerhead structures.
Collapse
|
11
|
Boomer RM, Lewis SD, Healy JM, Kurz M, Wilson C, McCauley TG. Conjugation to Polyethylene Glycol Polymer Promotes Aptamer Biodistribution to Healthy and Inflamed Tissues. Oligonucleotides 2005; 15:183-95. [PMID: 16201906 DOI: 10.1089/oli.2005.15.183] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Here, we examine biodistribution of radiolabeled aptamers and assess the relative ability of different stabilized aptamer compositions (mixed 2'-F/2'-O-Me; fully 2'-O-Me modified) to access inflamed tissues in a murine inflammation model. Biodistribution of 3H-labeled aptamers, including pegylated and unpegylated compositions, was assessed 3 hours postadministration using quantitative whole body autoradiography (QWBA). Aptamer penetration of cells in kidney and liver was also examined at a qualitative level by microautoradiography. To evaluate aptamer distribution to diseased tissues, inflammation was induced locally in animal hind limbs by treatment with carrageenan just prior to aptamer dosing. Aptamer compositions examined exhibited significant variation in distribution levels among organs and tissues. Highest concentrations of radioactivity in whole body tissues for all animals were observed in the kidney and urinary bladder contents. Relatively little radioactivity was associated with brain, spinal cord, and adipose tissue. Overall, the total level of radioactivity in whole body tissues was significantly higher for a 20-kDa PEG conjugate than for other aptamers. Comparatively high levels of the 20-kDa conjugate were seen in well-perfused organs and tissues, including liver, lungs, spleen, bone marrow, and myocardium. A fully 2'-O-Me composition aptamer had the lowest level of radioactivity in whole body tissues but distributed to higher concentrations in the gastrointestinal tract contents relative to other aptamers. Interestingly, the 20-kDa PEG-conjugated aptamer showed significantly higher levels of distribution to inflamed paw tissues than did either unconjugated or fully 2'-O-Me-modified aptamers.
Collapse
Affiliation(s)
- Ryan M Boomer
- Archemix Corporation, 1 Hampshire Street, Cambridge, MA 02139, USA
| | | | | | | | | | | |
Collapse
|
12
|
Coppins RL, Silverman SK. Rational modification of a selection strategy leads to deoxyribozymes that create native 3'-5' RNA linkages. J Am Chem Soc 2005; 126:16426-32. [PMID: 15600344 DOI: 10.1021/ja045817x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We previously used in vitro selection to identify several classes of deoxyribozymes that mediate RNA ligation by attack of a hydroxyl group at a 5'-triphosphate. In these reactions, the nucleophilic hydroxyl group is located at an internal 2'-position of an RNA substrate, leading to 2',5'-branched RNA. To obtain deoxyribozymes that instead create linear 3'-5'-linked (native) RNA, here we strategically modified the selection approach by embedding the nascent ligation junction within an RNA:DNA duplex region. This approach should favor formation of linear rather than branched RNA because the two RNA termini are spatially constrained by Watson-Crick base pairing during the ligation reaction. Furthermore, because native 3'-5' linkages are more stable in a duplex than isomeric non-native 2'-5' linkages, this strategy is predicted to favor the formation of 3'-5' linkages. All of the new deoxyribozymes indeed create only linear 3'-5' RNA, confirming the effectiveness of the rational design. The new deoxyribozymes ligate RNA with k(obs) values up to 0.5 h(-1) at 37 degrees C and 40 mM Mg2+, pH 9.0, with up to 41% yield at 3 h incubation. They require several specific RNA nucleotides on either side of the ligation junction, which may limit their practical generality. These RNA ligase deoxyribozymes are the first that create native 3'-5' RNA linkages, which to date have been highly elusive via other selection approaches.
Collapse
Affiliation(s)
- Rebecca L Coppins
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | | |
Collapse
|
13
|
Abstract
In vitro evolution was previously used to identify a small deoxyribozyme, 7Q10, that ligates RNA with formation of a 2'-5' phosphodiester linkage from a 2',3'-cyclic phosphate and a 5'-hydroxyl group. Ligation occurs in a convenient "binding arms" format analogous to that of the well-known 10-23 and 8-17 RNA-cleaving deoxyribozymes. Here, we report the optimization and generality of 7Q10 as a 2'-5' RNA ligase. By comprehensive mutagenesis of its 16-nucleotide enzyme region, the parent 7Q10 sequence is shown to be optimal for RNA ligation yield, although several mutations are capable of increasing the ligation rate approximately fivefold at the expense of yield. The 7Q10 deoxyribozyme ligates any RNA substrates that form the sequence motif UA GR (arrowhead=ligation site and R=purine), providing at least 30% yield of ligated RNA in approximately 1-2 hours at 37 degrees C and pH 9.0. Comparable yields are obtained in approximately 12-24 hours at pH 7.5, which may be more suitable for larger RNAs that are more sensitive to non-specific degradation. For RNA substrates that form the related ligation junction UA GY (Y=pyrimidine), somewhat lower yields are obtained, but significant ligation activity is still observed. These data establish that 7Q10 is a generally applicable RNA ligase. A plot of log(k(obs)) versus pH from pH 6.9 to 9.0 has a slope of just under 1, suggesting that a single deprotonation occurs during the rate-determining reaction step. The compact 7Q10 deoxyribozyme has both practical utility and the potential for increasing our structural and mechanistic understanding of how nucleic acids can mediate chemical reactions.
Collapse
Affiliation(s)
- Benjamin L Ricca
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | | | | |
Collapse
|
14
|
Blount KF, Grover NL, Mokler V, Beigelman L, Uhlenbeck OC. Steric interference modification of the hammerhead ribozyme. CHEMISTRY & BIOLOGY 2002; 9:1009-16. [PMID: 12323375 DOI: 10.1016/s1074-5521(02)00218-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Although the structure of the hammerhead ribozyme is well characterized, many questions remain about its catalytic mechanism. Extensive evidence suggests the necessity of a conformational change en route to the transition state. We report a steric interference modification approach for investigating this change. By placing large 2' modifications at residues insensitive to structurally conservative 2'-deoxy modifications, we hoped to discover structural effects distal to the site of modification. Of twenty residues tested, six were identified where the addition of 2' bulk inhibits cleavage, even though these bulky modifications could be accommodated in the crystal structure without steric clash. It is proposed that these 2'-modifications inhibit cleavage by preventing formation of the alternate, active conformation. Since these 2' effects are present in both domain I and domain II of the hammerhead, the entire catalytic core must undergo conformational changes during catalysis.
Collapse
Affiliation(s)
- Kenneth F Blount
- Department of Chemistry and Biochemistry, University of Colorado, UCB 215, Boulder, CO 80309, USA
| | | | | | | | | |
Collapse
|
15
|
Matulic-Adamic J, Serebryany V, Haeberli P, Mokler VR, Beigelman L. Synthesis of N-acetyl-D-galactosamine and folic acid conjugated ribozymes. Bioconjug Chem 2002; 13:1071-8. [PMID: 12236789 DOI: 10.1021/bc025525q] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To evaluate potential improvement in tissue specific targeting and cellular uptake of therapeutic ribozymes, we have developed three new phosphoramidite reagents. These reagents can be used in automated solid-phase synthesis to produce oligonucleotide conjugates containing N-acetyl-D-galactosamine (targeting hepatocytes) and folic acid (targeting tumor). N-Acetyl-D-galactosamine was attached through a linker to both 2'-amino-2'-deoxyuridine and D-threoninol scaffolds, and these conjugates were converted to phosphoramidite building blocks. Incorporation of a D-threoninol-based monomer into ribozymes provided multiply labeled ribozyme conjugates. Attachment of the fully protected pteroic acid to the D-threoninol-6-aminocaproyl-L-glutamic acid construct afforded the folic acid conjugate, which was converted into the phosphoramidite and incorporated onto the 5'-end of the ribozyme.
Collapse
Affiliation(s)
- Jasenka Matulic-Adamic
- Department of Chemistry & Biochemistry, Ribozyme Pharmaceuticals, Inc., 2950 Wilderness Place, Boulder, Colorado 80301, USA
| | | | | | | | | |
Collapse
|
16
|
Lyngstadaas SP. Synthetic hammerhead ribozymes as tools in gene expression. CRITICAL REVIEWS IN ORAL BIOLOGY AND MEDICINE : AN OFFICIAL PUBLICATION OF THE AMERICAN ASSOCIATION OF ORAL BIOLOGISTS 2002; 12:469-78. [PMID: 11806517 DOI: 10.1177/10454411010120060201] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
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.
Collapse
Affiliation(s)
- S P Lyngstadaas
- Oral Research Laboratory, Faculty of Dentistry, University of Oslo, Blindern, Norway.
| |
Collapse
|
17
|
Affiliation(s)
- L Wright
- Hematology Research Laboratory, St. Vincent's Hospital, 384 Victoria St., Darlinghurst, New South Wales, 2010 Australia
| | | |
Collapse
|
18
|
2′-C-Methyluridine phosphoramidite: a new building block for the preparation of RNA analogues carrying the 2′-hydroxyl group. Tetrahedron 2001. [DOI: 10.1016/s0040-4020(01)00484-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
19
|
Abstract
The hammerhead ribozyme is an intriguing RNA molecule with the ability to serve as a catalyst to cleave sequence-specifically RNA molecules in an intermolecular reaction. Preferentially Mg(2+) is required for optimal activity by inducing the catalytically competent conformation and by possibly acting as an acid-base catalyst. Even though the three-dimensional structure has been elucidated details of the structure-function relationship and of the mechanism remain unanswered. The hammerhead ribozyme has stimulated the concept of the sequence-specific cleavage of mRNAs intracellularly and thus to inhibit gene expression by preventing translation. This represents an area of considerable interest as it has the potential for the development of drugs.
Collapse
Affiliation(s)
- F Eckstein
- Max-Planck Institut für experimentelle Medizin, Hermann-Rein-Str. 3, D-37075 Göttingen, Germany.
| | | |
Collapse
|
20
|
Hammann C, Norman DG, Lilley DM. Dissection of the ion-induced folding of the hammerhead ribozyme using 19F NMR. Proc Natl Acad Sci U S A 2001; 98:5503-8. [PMID: 11331743 PMCID: PMC33242 DOI: 10.1073/pnas.091097498] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have used (19)F NMR to analyze the metal ion-induced folding of the hammerhead ribozyme by selective incorporation of 5fluorouridine. We have studied the chemical shift and linewidths of (19)F resonances of 5-fluorouridine at the 4 and 7 positions in the ribozyme core as a function of added Mg(2+). The data fit well to a simple two-state model whereby the formation of domain 1 is induced by the noncooperative binding of Mg(2+) with an association constant in the range of 100 to 500 M(-1), depending on the concentration of monovalent ions present. The results are in excellent agreement with data reporting on changes in the global shape of the ribozyme. However, the NMR experiments exploit reporters located in the center of the RNA sections undergoing the folding transitions, thereby allowing the assignment of specific nucleotides to the separate stages. The results define the folding pathway at high resolution and provide a time scale for the first transition in the millisecond range.
Collapse
Affiliation(s)
- C Hammann
- Cancer Research Campaign Nucleic Acid Structure Research Group, Department of Biochemistry, University of Dundee, Dundee DD1 4HN, United Kingdom
| | | | | |
Collapse
|
21
|
Hovig E, Maelandsmo G, Mellingsaeter T, Fodstad O, Mielewczyk SS, Wolfe J, Goodchild J. Optimization of hammerhead ribozymes for the cleavage of S100A4 (CAPL) mRNA. ANTISENSE & NUCLEIC ACID DRUG DEVELOPMENT 2001; 11:67-75. [PMID: 11334142 DOI: 10.1089/108729001750171272] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Previously, suppression of the S100A4 mRNA by an endogenously expressed ribozyme in osteosarcoma cells was shown to inhibit their metastasis in rats. As a prelude to performing similar studies with exogenous, synthetic ribozymes, we compared a series of hammerhead ribozymes targeted against different sites in the mRNA. The ribozymes differed only in the 7-base flanking sequences complementary to the substrate and were protected against nucleases by chemical modification. Cleavage efficiency varied widely and was not obviously related to the predicted secondary structure of the target RNA. The most active ribozyme of the series was chosen for further optimization. Lengthening its flanking sequences was counterproductive and reduced cleavage even when using excess ribozyme. Using excess substrate (multiple-turnover kinetics), cleavage was fastest with the (6+8) ribozyme having 6 nucleotides (nt) in stem III and 8 nt in stem I. Although these stems strongly influence ribozyme performance, their optimization is still empirical. Faster cleavage was obtained by adding facilitator oligonucleotides to ribozymes with shorter stems of (6+6) and (5+5) nt. Stimulation was particularly strong in the case of the (5+5) ribozyme, which was poorly active by itself. The enhancement caused by different facilitator oligonucleotides paralleled their expected ability to hybridize to RNA as a function of length and chemical modification.
Collapse
Affiliation(s)
- E Hovig
- The Norwegian Radium Hospital, Oslo
| | | | | | | | | | | | | |
Collapse
|
22
|
Pröpsting MJ, Kubicka S, Genschel J, Manns MP, Lochs H, Schmidt HH. Inhibition of transthyretin-met30 expression using Inosine(15.1)-Hammerhead ribozymes in cell culture. Biochem Biophys Res Commun 2000; 279:970-3. [PMID: 11162459 DOI: 10.1006/bbrc.2000.4048] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Hereditary amyloidosis is primarily caused by mutations within the transthyretin gene. More than 75 mutations within transthyretin have been reported in causing amyloidosis. The most common mutation is the val30met mutation in the transthyretin protein (TTR-met30) caused by a mononucleic substitution from G to A (GUC to AUC) in the transthyretin gene resulting in the exchange for the amino acids valine to methionine in the corresponding protein sequence. The aim of this work is the development of a specific cleavage of TTR-met30 mRNA in the cell culture system using hammerhead ribozymes. We showed previously that chemically modified nuclease stable Inosine(15.1)-Hammerhead ribozymes are able to target the TTR-met30 mRNA with high specificity on the RNA level (Biochem. Biophys. Res. Commun. 260, 313-317, 1999). Now we present data confirming our observations on the cellular level. We used the wild-type human normal (hn) TTR expressing cell line HepG2 and the stable transfected cell line 293-TTR-met30 for TTR-met30 experiments. We cleaved the TTR-met30 and hnTTR mRNA with specific nuclease stable chemically modified Inosine(15.1)-Hammerhead ribozymes and analyzed the protein after immunoprecipitation and subsequent Western blotting. We were able to downregulate the TTR concentration by 54.5% (100% = 1.5 mg/l TTR) and also specifically to target the TTR-met30 expression in the cell culture system. The therapeutic effect was improved using cationic liposomes resulting in a total downregulation by 92.1 and 62.7% targeting hnTTR mRNA and TTR-met30 mRNA, respectively. The successful employment of Inosine(15.1)-Hammerhead ribozymes in cell culture is therefore a promising tool for the development of a gene therapeutic strategy for hereditary amyloidosis.
Collapse
Affiliation(s)
- M J Pröpsting
- Medizinische Klinik, Gastroenterologie, Hepatologie und Endokrinologie, Campus Charité Mitte, Berlin, Germany
| | | | | | | | | | | |
Collapse
|
23
|
Synthesis of 2’-Modified Nucleotides. Molecules 2000. [DOI: 10.3390/50500727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
|
24
|
Beaudry A, DeFoe J, Zinnen S, Burgin A, Beigelman L. In vitro selection of a novel nuclease-resistant RNA phosphodiesterase. CHEMISTRY & BIOLOGY 2000; 7:323-34. [PMID: 10801472 DOI: 10.1016/s1074-5521(00)00110-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
BACKGROUND Ribonucleotide-based enzymes (ribozymes) that cleave pathological RNAs are being developed as therapeutic agents. Chemical modification of the hammerhead ribozyme has produced nuclease-resistant catalysts that cleave targeted mRNAs in cell culture and exhibit antitumor activity in animals. Unfortunately, stabilizing modifications usually reduce the catalytic rate in vitro. An alternative to rationally designed chemical modifications of existing ribozymes is to identify novel motifs through in vitro selection of nuclease-stable sequence space. This approach is desirable because the catalysts can be optimized to function under simulated physiological conditions. RESULTS Utilizing in vitro selection, we have identified a nuclease-stable phosphodiesterase that demonstrated optimal activity at simulated physiological conditions. The initial library of 10(14) unique molecules contained 40 randomized nucleotides with all pyrimidines in a nuclease-stabilized 2'-deoxy-2'-amino format. The selection required trans-cleaving activity and base-pairing specificity towards a resin-bound RNA substrate. Initial selective pressure was permissive, with a 30 min reaction time and 25 mM Mg(2+). Stringency of selection pressure was gradually increased until final conditions of 1 mM Mg(2+) and less than 1 min reaction times were achieved. The resulting 61-mer catalyst required the 2'-amino substitutions at selected pyrimidine positions and was stable in human serum (half-life of 16 h). CONCLUSIONS We demonstrated that it is possible to identify completely novel, nuclease-resistant ribozymes capable of trans-cleaving target RNAs at physiologically relevant Mg(2+) concentrations. The new ribozyme motif has minimal substrate requirements, allowing for a wide range of potential RNA targets.
Collapse
Affiliation(s)
- A Beaudry
- Department of Biochemistry, Ribozyme Pharmaceuticals, Boulder, CO 80301, USA
| | | | | | | | | |
Collapse
|
25
|
Salmi P, Sproat BS, Ludwig J, Hale R, Avery N, Kela J, Wahlestedt C. Dopamine D(2) receptor ribozyme inhibits quinpirole-induced stereotypy in rats. Eur J Pharmacol 2000; 388:R1-2. [PMID: 10657555 DOI: 10.1016/s0014-2999(99)00866-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The injection of a dopamine D(2) receptor hammerhead ribozyme (20 microg) once daily for 5 days into the nucleus accumbens of rats resulted in an inhibition of stereotyped sniffing and locomotor activation produced by the selective dopamine D(2) receptor agonist, quinpirole (0.4 mg kg(-1) s.c.). The results suggest that ribozymes may be useful in the study of in vivo gene function in the brain.
Collapse
Affiliation(s)
- P Salmi
- Center for Genomics Research, Karolinska Institutet, 171 77, Stockholm, Sweden
| | | | | | | | | | | | | |
Collapse
|
26
|
Muotri AR, da Veiga Pereira L, dos Reis Vasques L, Menck CF. Ribozymes and the anti-gene therapy: how a catalytic RNA can be used to inhibit gene function. Gene 1999; 237:303-10. [PMID: 10521654 DOI: 10.1016/s0378-1119(99)00334-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ribozymes are RNA molecules that possess the dual properties of RNA sequence-specific recognition and site-specific cleavage of other RNA molecules. These properties provide powerful tools for studies requiring gene inhibition, when the DNA sequence is known. The use of these molecules goes beyond basic research, with a potential impact in therapeutical practice in medicine in the near future. In this review, we briefly describe the progress towards developing this class of molecules and its applications for the control of gene expression.
Collapse
Affiliation(s)
- A R Muotri
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil.
| | | | | | | |
Collapse
|
27
|
Pröpsting MJ, Blaschke M, Haas RE, Genschel J, Hedrich HJ, Manns MP, Schmidt HH. Inosine(15.1) hammerhead ribozymes for targeting the transthyretin-30 mutation. Biochem Biophys Res Commun 1999; 260:313-7. [PMID: 10403767 DOI: 10.1006/bbrc.1999.0906] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The most common cause of hereditary amyloidosis (HA) is the val30met mutation in the transthyretin protein (TTR-met30). The mutation is caused by a mononucleic substitution from G to A (GUC to AUC) in the transthyretin gene resulting in the exchange for the amino acids valine to methionine in the corresponding protein sequence. The aim of our work was the development of a specific cleavage of TTR-30 mRNA using hammerhead ribozymes. We chemically modified nuclease stable hammerhead ribozymes to target the TTR-30 mRNA with high specificity. The exchange of adenosine(15.1) with inosine(15.1) in the catalytic core of the hammerhead ribozyme resulted in a change of the cleavable target sequence from N(16.2)U(16.1)H(17) to N(16. 2)C(16.1)H(17) without loss in ribozymal activity (Nucleic Acids Res. 26, 2279-2285, 1998). This modification allowed a specific cleavage of the TTR-30 mutation ("gCC Gug" to "gCC Aug"). In vitro experiments with TTR-30 mRNA demonstrated that the RNase stable inosine(15.1) hammerhead ribozyme cleaved the TTR-30 mRNA with 100% specificity and with a velocity of 0.23 min(-1), whereas no cleavage occured in the wildtype mRNA of TTR. In conclusion, the development of this NCH specific hammerhead ribozyme represents a promising tool for future in vivo therapeutic application for TTR-met30 induced hereditary amyloidosis.
Collapse
Affiliation(s)
- M J Pröpsting
- Department of Gastroenterologie and Hepatologie, Medical School Hannover, Hannover, D-30623, Germany
| | | | | | | | | | | | | |
Collapse
|
28
|
Giannini CD, Roth WK, Piiper A, Zeuzem S. Enzymatic and antisense effects of a specific anti-Ki-ras ribozyme in vitro and in cell culture. Nucleic Acids Res 1999; 27:2737-44. [PMID: 10373591 PMCID: PMC148483 DOI: 10.1093/nar/27.13.2737] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Due to their mode of action, ribozymes show antisense effects in addition to their specific cleavage activity. In the present study we investigated whether a hammerhead ribozyme is capable of cleaving mutated Ki-ras mRNA in a pancreatic carcinoma cell line and whether antisense effects contribute to the activity of the ribozyme. A 2[prime]-O-allyl modified hammerhead ribozyme was designed to cleave specifically the mutated form of the Ki- ras mRNA (GUU motif in codon 12). The activity was monitored by RT-PCR on Ki- ras RNA expression by determination of the relative amount of wild type to mutant Ki-ras mRNA, by 5-bromo-2[prime]-deoxy-uridine incorporation on cell proliferation and by colony formation in soft agar on malignancy in the human pancreatic adenocarcinoma cell line CFPAC-1, which is heterozygous for the Ki-ras mutation. A catalytically inactive ribozyme was used as control to differentiate between antisense and cleavage activity and a ribozyme with random guide sequences as negative control. The catalytically active anti-Ki-ras ribozyme was at least 2-fold more potent in decreasing cellular Ki-ras mRNA levels, inhibiting cell proliferation and colony formation in soft agar than the catalytically inactive ribozyme. The catalytically active anti-Ki-ras ribozyme, but not the catalytically inactive or random ribozyme, increased the ratio of wild type to mutated Ki-ras mRNA in CFPAC-1 cells. In conclusion, both cleavage activity and antisense effects contribute to the activity of the catalytically active anti-Ki-ras hammerhead ribozyme. Specific ribozymes might be useful in the treatment of pancreatic carcinomas containing an oncogenic GTT mutation in codon 12 of the Ki-ras gene.
Collapse
Affiliation(s)
- C D Giannini
- Medizinische Klinik II, Universitätsklinikum, Theodor-Stern-Kai 7, D-60590 Frankfurt am Main, Germany
| | | | | | | |
Collapse
|
29
|
Bevers S, Ha SB, McLaughlin LW. Critical nature of a specific uridine O2-carbonyl for cleavage by the hammerhead ribozyme. Biochemistry 1999; 38:7710-8. [PMID: 10387010 DOI: 10.1021/bi982977a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Three modified hammerhead ribozyme/substrate complexes have been prepared in which individual uridine O2-carbonyls have been eliminated. The modified complexes were chemically synthesized with the substitution of a single 2-pyridone (2P) base analogue for residues U4, U7, and U16.1. Steady-state kinetic analyses indicate that the cleavage efficiencies for the U7 and U16.1 complexes were not significantly reduced relative to the native complex as measured by kcat/KM. The cleavage efficiency for the 2P4 complex, with the analogue present within the uridine loop, was reduced by greater than 2 orders of magnitude. This significant reduction in catalytic efficiency was due primarily to a decrease in kcat. The pH vs cleavage rate profile suggests that the O2-carbonyl of the U4 residue of the hammerhead complex is critical for transition state stabilization and efficient cleavage activity. The results of a Mg2+ rescue assay do not implicate the O2-carbonyl of U4 in an interaction with a divalent metal ion. In addition, the results of a ribozyme folding assay suggest that the presence of the 2P4 within the uridine loop does not alter the folding pathway (relative to the native sequence) both in the absence and in the presence of Mg2+. The O2-carbonyl of U4 appears oriented toward the interior of the catalytic pocket where it may be involved in a critical hydrogen bonding interaction necessary for transition state stabilization.
Collapse
Affiliation(s)
- S Bevers
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, USA
| | | | | |
Collapse
|
30
|
|
31
|
Wang FS, Kobayashi H, Liang KW, Holland JF, Ohnuma T. Retrovirus-mediated transfer of anti-MDR1 ribozymes fully restores chemosensitivity of P-glycoprotein-expressing human lymphoma cells. Hum Gene Ther 1999; 10:1185-95. [PMID: 10340550 DOI: 10.1089/10430349950018175] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Development of multidrug resistance (MDR) is the major obstacle to successful cancer chemotherapy. We have developed Daudi human lymphoma cells that are 20-fold more resistant than the parent cell line to vincristine (VCR) by infecting cells with pHaMDR1/A retroviral vector (Daudi/MDR20). Three DNA sequences of anti-MDR1 hammerhead ribozymes (Rzs), one cleaving codon 196 of MDR1 mRNA (196MDR1-Rz), the second a stem II base-modified (U9-->Gg, U13-->A13, G14-->A14, A18-->C18) Rz against codon 196 (196MDR1-sRz), and the third a stem II base-modified Rz directed against the -6 approximately -4 GUC sequence of the translation initiation site of the MDR1 mRNA (iMDR1-sRz), were synthesized and cloned into the retroviral vector N2A+tRNAiMet downstream of the RNA polymerase III promoter and adjacent to a tRNA gene sequence, forming the constructs N2A+tRNAiMet-196MDR1-Rz, N2A+tRNAiMet-196MDR1-sRz, and N2A+tRNAiMet-iMDR1-sRz. The three constructs were transfected into GP+envAM 12 cells for packaging the retroviral vectors. The supernatants containing the packaged retrovirus in high titers (1.1-2.5 X 10(5) CFU/ml as determined by infection of NIH 3T3 cells) were used to infect Daudi/MDR20 cells. The iMDR1-sRz- and 196MDR1-sRz-transduced Daudi/MDR20 cells completely restored chemosensitivity to VCR and doxorubicin, and were accompanied by blocked expression of MDR1 mRNA and P-glycoprotein as well as overexpression of anti-MDR1 Rz. In a cell-free system, the chimeric tRNA-sRz molecules were more stable and had more efficient catalytic activities than the corresponding naked Rz molecules. The stem II base-modified Rz were also more stable and efficient in catalytic activities than the unmodified Rz molecules. The base modification in the Rz stem II structure and the development of chimeric tRNA-Rz molecules were identified to enhance the cleavage efficacy. The combination of these two factors, together with the use of a retroviral vector, appear to have contributed to the complete reversal of MDR.
Collapse
Affiliation(s)
- F S Wang
- Samuel Bronfman Department of Medicine, Mount Sinai School of Medicine, New York, NY 10029-6574, USA
| | | | | | | | | |
Collapse
|
32
|
Citti L, Eckstein F, Capecchi B, Mariani L, Nevischi S, Poggi A, Rainaldi G. Transient transfection of a synthetic hammerhead ribozyme targeted against human MGMT gene to cells in culture potentiates the genotoxicity of the alkylation damage induced by mitozolomide. ANTISENSE & NUCLEIC ACID DRUG DEVELOPMENT 1999; 9:125-33. [PMID: 10355819 DOI: 10.1089/oli.1.1999.9.125] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Unmodified and chemically modified forms of a synthetic hammerhead ribozyme with the mRNA of methylguanine-DNA methyltransferase (MGMT) gene as substrate were characterized for their in vitro and in vivo activities. The unmodified ribozyme efficiently cleaved in vitro a short synthetic substrate, and it was rapidly degraded in fetal bovine serum (FBS). The introduction of phosphorothioates and the substitution of uridine with thymidine at probable nuclease-sensitive sites slightly increased the nuclease resistance of the ribozyme. Conversely, pyrimidine nucleoside substitution with 2'NH2 and 2'F nucleosides strongly enhanced nuclease resistance. The in vivo activity was determined by measuring the genotoxicity induced by the alkylating drug mitozolomide, the damage of which is repaired by MGMT enzyme. CHO/47 cells, temporarily depleted of the MGMT protein, were first transfected with the various synthetic ribozymes and subsequently treated with mitozolomide. At equivalent concentration of the drug, the induction of sister chromatid exchanges was higher in ribozyme-transfected than in untransfected cells, indicating that the synthetic ribozymes potentiated the genotoxicity of mitozolomide. Moreover, the concomitant occurrence of messenger RNA reduction in ribozyme-transfected cells indicated that the inhibition of MGMT resynthesis was the basis of the enhanced genotoxicity.
Collapse
Affiliation(s)
- L Citti
- Genetica e Biochimica Tossicologica, Istituto di Mutagenesi e Differenziamento, CNR, Pisa, Italy
| | | | | | | | | | | | | |
Collapse
|
33
|
Dunkel M, Reither V. Synthesis of 2'-C-alpha-difluoromethylarauridine and its 3'-O-phosphoramidite incorporation into a hammerhead ribozyme. Bioorg Med Chem Lett 1999; 9:787-92. [PMID: 10201848 DOI: 10.1016/s0960-894x(99)00063-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The 2'-C-difluoromethylated nucleoside 4 was synthesized starting from uridine. 4 was then converted to the 3'-O-phosphoramidite derivative 5 and was incorporated into a hammerhead ribozyme (7). The cleavage characteristics of the modified oligonucleotide have been analysed.
Collapse
|
34
|
Matulic-Adamic J, Daniher AT, Gonzalez C, Beigelman L. Nuclease resistant hammerhead motif: from '5-ribo' to '3-ribo' model. Bioorg Med Chem Lett 1999; 9:157-60. [PMID: 10021919 DOI: 10.1016/s0960-894x(98)00706-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Previously developed '5-ribo' nuclease stabilized hammerhead motif was further refined by systematic incorporation of 1-(beta-D-xylofuranosyl) adenine (xA) and 1-(beta-D-xylofuranosyl) guanine (xG) in the place of conserved ribopurine residues of the catalytic core. Modified ribozymes substituted with xA at positions A15.1 and A6 demonstrated catalytic activity close to the parent stabilized ribozyme. Analogous guanosine substitutions at positions G5, G8, and G12 substantially lowered catalytic rates.
Collapse
Affiliation(s)
- J Matulic-Adamic
- Department of Chemistry & Biochemistry, Ribozyme Pharmaceuticals, Inc., Boulder, CO 80301, USA
| | | | | | | |
Collapse
|
35
|
Abstract
Synthetic oligonucleotide analogs have greatly aided our understanding of several biochemical processes. Efficient solid-phase and enzyme-assisted synthetic methods and the availability of modified base analogs have added to the utility of such oligonucleotides. In this review, we discuss the applications of synthetic oligonucleotides that contain backbone, base, and sugar modifications to investigate the mechanism and stereochemical aspects of biochemical reactions. We also discuss interference mapping of nucleic acid-protein interactions; spectroscopic analysis of biochemical reactions and nucleic acid structures; and nucleic acid cross-linking studies. The automation of oligonucleotide synthesis, the development of versatile phosphoramidite reagents, and efficient scale-up have expanded the application of modified oligonucleotides to diverse areas of fundamental and applied biological research. Numerous reports have covered oligonucleotides for which modifications have been made of the phosphodiester backbone, of the purine and pyrimidine heterocyclic bases, and of the sugar moiety; these modifications serve as structural and mechanistic probes. In this chapter, we review the range, scope, and practical utility of such chemically modified oligonucleotides. Because of space limitations, we discuss only those oligonucleotides that contain phosphate and phosphate analogs as internucleotidic linkages.
Collapse
Affiliation(s)
- S Verma
- Max-Planck-Institut für Experimentelle Medizin, Göttingen, Germany
| | | |
Collapse
|
36
|
Ma MY, Jacob-Samuel B, Dignam JC, Pace U, Goldberg AR, George ST. Nuclease-resistant external guide sequence-induced cleavage of target RNA by human ribonuclease P. ANTISENSE & NUCLEIC ACID DRUG DEVELOPMENT 1998; 8:415-26. [PMID: 9826268 DOI: 10.1089/oli.1.1998.8.415] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
External guide sequences (EGSs) are short oligoribonucleotides, which are designed to bind to a given RNA target and form a precursor tRNA-like complex. This complex can be recognized by ribonuclease P (RNase P), resulting in specific cleavage of the RNA target. To explore the potential of this class of compounds as therapeutic agents and valuable tools for gene function analysis, various chemical modifications were introduced into an all-RNA EGS molecule to confer nuclease resistance. In particular, 2'-O-methyl substitutions were incorporated into the entire sequence (i.e., A-stem, D-stem, and T-stem) except the T-loop region without loss of cleavage-inducing activity. Replacement of rU (position 54) and rC (position 56) in the T-loop with their 2'-O-methyl counterparts caused pronounced decrease in activity. Moreover, phosphorothioate backbone modification of the T-loop did not provide sufficient protection against endonucleolytic attack at the ribopyrimidine residues. Systematic modification of the T-loop with a variety of modified nucleosides and the addition of a 3'-3' inverted T at the 3'-end have generated several lead EGS prototypes, which not only exhibit wild-type activity in inducing RNase P-mediated target cleavage as compared with the all-RNA control but also remain intact in human serum for more than 24 hours. These results should provide useful insights into the design and development of oligonucleotide-based EGSs as potential regulators of gene expression.
Collapse
Affiliation(s)
- M Y Ma
- Innovir Laboratories, Inc., New York, NY 10021, USA
| | | | | | | | | | | |
Collapse
|
37
|
Hartmann RK, Krupp G, Hardt WD. Towards a new concept of gene inactivation: specific RNA cleavage by endogenous ribonuclease P. BIOTECHNOLOGY ANNUAL REVIEW 1998; 1:215-65. [PMID: 9704090 DOI: 10.1016/s1387-2656(08)70053-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In the first part of this chapter, general concepts for gene inactivation, antisense techniques and catalytic RNAs (ribozymes) are presented. The requirements for modified oligonucleotides are discussed with their effects on the stability of base-paired hybrids and on resistance against nuclease attack. This also includes the problems in the choice of an optimal target sequence within the inactivated RNA and the options of cellular delivery systems. The second part describes the recently introduced antisense concept based on the ubiquitous cellular enzyme ribonuclease P. This system is unique, since the substrate recognition requires the proper tertiary structure of the cleaved RNA. General properties and possible advantages of this approach are discussed.
Collapse
Affiliation(s)
- R K Hartmann
- Institut für Biochemie, Freie Universität Berlin, Germany
| | | | | |
Collapse
|
38
|
Affiliation(s)
- T K Stage-Zimmermann
- Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309-0215, USA
| | | |
Collapse
|
39
|
Asahina Y, Ito Y, Wu CH, Wu GY. DNA ribonucleases that are active against intracellular hepatitis B viral RNA targets. Hepatology 1998; 28:547-54. [PMID: 9696023 DOI: 10.1002/hep.510280236] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
DNA ribonucleases directed against direct repeat 1 (DR1) and polyadenylation signal regions of hepatitis B virus (HBV) messages were prepared with phosphorothioate modifications and varying arm lengths. DNA ribonucleases modified throughout the entire molecule and in the target binding arms were completely protected from degradation after incubation with serum. DNA ribonuclease modified only at the 5' and 3' termini remained 92.9% intact after incubation. Molecules with no modification were degraded to 67.6% under the same conditions. However, modification of the entire molecule and in the recognition arms resulted in 99.8% and 98.4% inactivation of cleavage activity, respectively. Modification of only the termini resulted in retention of 20% to 40% of original activity. Lengthening each terminally modified arm from 9 to 11 nucleotides increased cleavage efficiency almost 10-fold. In Huh 7 cells, DR1-directed DNA ribonucleases with terminal modifications significantly suppressed HBV-luciferase fusion gene expression up to 48% of control. In contrast, DNA ribonucleases had no effect on a control construct lacking any HBV target sequences. Moreover, inactivated mutant and HCV-directed DNA ribonucleases had no significant effects on the HBV target. We conclude that resistance of DNA ribonucleases to degradation can be enhanced through phosphorothioate modification. Cleavage activity can be retained by limiting modification to the termini and lengthening the recognition arms. Such DNA ribonucleases can be made to specifically cleave target HBV RNA and substantially inhibit intracellular viral gene expression.
Collapse
Affiliation(s)
- Y Asahina
- Department of Medicine, University of Connecticut Health Center, Farmington 06030, USA
| | | | | | | |
Collapse
|
40
|
Ludwig J, Blaschke M, Sproat BS. Extending the cleavage rules for the hammerhead ribozyme: mutating adenosine15.1 to inosine15.1 changes the cleavage site specificity from N16.2U16.1H17 to N16.2C16.1H17. Nucleic Acids Res 1998; 26:2279-85. [PMID: 9580675 PMCID: PMC147568 DOI: 10.1093/nar/26.10.2279] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
In this paper, we show that an adenosine to inosine mutation at position 15.1 changes the substrate specificity of the hammerhead ribozyme from N16.2U16.1H17to N16.2C16.1H17(H represents A, C or U). This result extends the hammerhead cleavage triplet definition from N16.2U16.1H17to the more general N16.2Y16.1H17. Comparison of cleavage rates using I15.1ribozymes for NCH triplets and standard A15.1 ribozymes for NUH triplets under single turnover conditions shows similar or slightly enhanced levels of reactivity for the I15. 1-containing structures. The effect of I15.1 substitution was also tested in nuclease-resistant 2'- O -alkyl substituted derivatives (oligozymes), showing a similar level of activity for the NUH and NCH cleaving structures. The availability of NCH triplets that can be targeted without loss of efficiency increases the flexibility of ribozyme targeting strategies. This was demonstrated by an efficient cleavage of an HCV transcript at a previously inaccessible GCA site in codon 2.
Collapse
Affiliation(s)
- J Ludwig
- Innovir GmbH, Olenhuser Landstrasse 20b, D-37124 Rosdorf, Germany.
| | | | | |
Collapse
|
41
|
Zhou DM, Taira K. The Hydrolysis of RNA: From Theoretical Calculations to the Hammerhead Ribozyme-Mediated Cleavage of RNA. Chem Rev 1998; 98:991-1026. [PMID: 11848922 DOI: 10.1021/cr9604292] [Citation(s) in RCA: 158] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- De-Min Zhou
- Institute of Applied Biochemistry, University of Tsukuba, Tennoudai 1-1-1, Tsukuba Science City 305-8572, Japan, National Institute for Advanced Interdisciplinary Research, 1-1-4 Higashi, Tsukuba Science City 305-8562, Japan, and National Institute of Bioscience & Human Technology, 1-1 Higashi, Tsukuba Science City 305-8566, Japan
| | | |
Collapse
|
42
|
Eckstein F. Exogenous application of ribozymes for inhibiting gene expression. CIBA FOUNDATION SYMPOSIUM 1998; 209:207-12; discussion 212-7. [PMID: 9383578 DOI: 10.1002/9780470515396.ch15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Sequence-specific inhibition of gene expression is an attractive concept for the development of a new generation of therapeutics. Two alternatives can be envisaged for the introduction of ribozymes into cells: endogenous or exogenous delivery. In the latter, the ribozyme is prepared by chemical synthesis or transcription and delivered to the cell either unaided or with the help of liposomes. A problem with this approach is the abundance of RNases in the serum, and thus the stabilization of the ribozyme is necessary but without the impairment of catalytic efficiency. This has been achieved by several groups by 2'-modification of the pyrimidine nucleosides and the introduction of a few phosphorothioates at the termini. The selection of ribozyme-accessible sites on the target and the attachment of cholesterol and peptides to the ribozymes will be discussed. Examples of the application of these modified ribozymes in cell cultures will be presented, including the inhibition of expression of the multiple drug resistance gene, after unaided as well as liposome-aided delivery, and studies of animal models demonstrating the potential of this particular application strategy.
Collapse
Affiliation(s)
- F Eckstein
- Max-Planck Institute of Experimental Medicine, Göttingen, Germany
| |
Collapse
|
43
|
Abstract
AbstractRibozymes are catalytic RNA molecules that recognize their target RNA in a highly sequence-specific manner. They can therefore be used to inhibit deleterious gene expression (by cleavage of the target mRNA) or even repair mutant cellular RNAs. Targets such as the mRNAs of oncogenes (resulting from base mutations or chromosome translocations, eg, ras or bcr-abl) and viral genomes and transcripts (human immunodeficiency virus–type 1 [HIV-1]) are ideal targets for such sequence-specific agents. The aim of this review is therefore to introduce the different classes of ribozymes, highlighting some of the chemistry of the reactions they catalyze, to address the specific inhibition of genes by ribozymes, the problems yet to be resolved, and how new developments in the field give hope to the future for ribozymes in the therapeutic field.
Collapse
|
44
|
Abstract
Ribozymes are catalytic RNA molecules that recognize their target RNA in a highly sequence-specific manner. They can therefore be used to inhibit deleterious gene expression (by cleavage of the target mRNA) or even repair mutant cellular RNAs. Targets such as the mRNAs of oncogenes (resulting from base mutations or chromosome translocations, eg, ras or bcr-abl) and viral genomes and transcripts (human immunodeficiency virus–type 1 [HIV-1]) are ideal targets for such sequence-specific agents. The aim of this review is therefore to introduce the different classes of ribozymes, highlighting some of the chemistry of the reactions they catalyze, to address the specific inhibition of genes by ribozymes, the problems yet to be resolved, and how new developments in the field give hope to the future for ribozymes in the therapeutic field.
Collapse
|
45
|
|
46
|
Greiner B, Pfleiderer W. Nucleotides. Part LVII.. Synthesis of phosphoramidite building blocks of 2?-amino-2?-deoxyribonucleosides: New compounds for oligonucleotide synthesis. Helv Chim Acta 1998. [DOI: 10.1002/hlca.19980810556] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
47
|
Ribozymes as Biotherapeutic Tools for the Modulation of Gene Expression. Gene Ther 1998. [DOI: 10.1007/978-3-662-03577-1_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
48
|
Burlina F, Favre A, Fourrey JL. Chemical engineering of RNase resistant and catalytically active hammerhead ribozymes. Bioorg Med Chem 1997; 5:1999-2010. [PMID: 9416417 DOI: 10.1016/s0968-0896(97)00144-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- F Burlina
- Institut de Chimie des Substances Naturelles, CNRS, Gif-sur-Yvette, France
| | | | | |
Collapse
|
49
|
Scherr M, Grez M, Ganser A, Engels JW. Specific hammerhead ribozyme-mediated cleavage of mutant N-ras mRNA in vitro and ex vivo. Oligoribonucleotides as therapeutic agents. J Biol Chem 1997; 272:14304-13. [PMID: 9162065 DOI: 10.1074/jbc.272.22.14304] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Two hammerhead ribozymes targeted to point mutations in codon 13 of the N-ras oncogene were synthesized and their catalytic activity and substrate specificity evaluated in vitro and ex vivo. In vitro studies showed that these ribozymes were specific for the oncogenic form of N-ras, since cleavage was observed only in a 849-nucleotide-long transcript containing mutant but not wild-type N-ras sequences. For the ex vivo studies, the ribozymes were 2'-modified to protect them against degradation by nucleases. 2'-Fluoro-2'-deoxyuridine/cytidine-substituted ribozymes were nearly as active as their unmodified counterparts, but had a prolonged stability in cell culture supernatant containing fetal calf serum. The stability of the modified ribozymes increased by introduction of terminal phosphorothioates groups without significant influence in their catalytic efficiency. A sensitive assay based on the use of N-ras/luciferase fusion genes as a reporter system was established to detect ribozyme-mediated cleavage in HeLa cells. A reduction of nearly 60% in luciferase activity was observed in cells expressing mutant but not wild-type N-ras/luciferase fusion transcripts. Moreover, cleavage of N-ras transcripts in HeLa cells was directly confirmed by a semi-quantitative RT-PCR assay.
Collapse
Affiliation(s)
- M Scherr
- Institut für Organische Chemie, Johann Wolfgang Goethe-Universität, D-60439 Frankfurt am Main, Germany
| | | | | | | |
Collapse
|
50
|
Ning J, Kong F. Synthesis and glycosidic coupling reaction of substituted 2,6-dioxabicyclo[3.1.0]hexanes: 1,2-anhydro-3,5-di-O-benzyl-alpha-D-ribofuranose. Carbohydr Res 1997; 300:355-60. [PMID: 9210301 DOI: 10.1016/s0008-6215(97)00060-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- J Ning
- Research Center for Eco-Environmental Sciences, Academia Sinica, Beijing, PR China
| | | |
Collapse
|