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Pelea O, Fulga TA, Sauka-Spengler T. RNA-Responsive gRNAs for Controlling CRISPR Activity: Current Advances, Future Directions, and Potential Applications. CRISPR J 2022; 5:642-659. [PMID: 36206027 PMCID: PMC9618385 DOI: 10.1089/crispr.2022.0052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
CRISPR-Cas9 has emerged as a major genome manipulation tool. As Cas9 can cause off-target effects, several methods for controlling the expression of CRISPR systems were developed. Recent studies have shown that CRISPR activity could be controlled by sensing expression levels of endogenous transcripts. This is particularly interesting, as endogenous RNAs could harbor important information about the cell type, disease state, and environmental challenges cells are facing. Single-guide RNA (sgRNA) engineering played a major role in the development of RNA-responsive CRISPR systems. Following further optimizations, RNA-responsive sgRNAs could enable the development of novel therapeutic and research applications. This review introduces engineering strategies that could be employed to modify Streptococcus pyogenes sgRNAs with a focus on recent advances made toward the development of RNA-responsive sgRNAs. Future directions and potential applications of these technologies are also discussed.
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Affiliation(s)
- Oana Pelea
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; and Kansas City, Missouri, USA.,Address correspondence to: Oana Pelea, Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom,
| | - Tudor A. Fulga
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; and Kansas City, Missouri, USA
| | - Tatjana Sauka-Spengler
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; and Kansas City, Missouri, USA.,Stowers Institute for Medical Research, Kansas City, Missouri, USA.,Address correspondence to: Tatjana Sauka-Spengler, Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom,
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2
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Kirk Field A, Goodchild J. Section Review: Biologicals & Immunologicals: Antisense oligonucleotides: Rational drug design for genetic pharmacology. Expert Opin Investig Drugs 2008. [DOI: 10.1517/13543784.4.9.799] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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3
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Zenkova MA, Karpova GG. Imperfectly matched nucleic acid complexes and their biochemical manifestation. RUSSIAN CHEMICAL REVIEWS 2007. [DOI: 10.1070/rc1993v062n04abeh000023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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4
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Sidahmed AME, Wilkie BN. Control of cytokine gene expression using small RNA interference: blockade of interleukin-10 and interferon-gamma gene expression in pig cells. Vet Immunol Immunopathol 2007; 117:86-94. [PMID: 17368795 DOI: 10.1016/j.vetimm.2007.02.006] [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] [Received: 10/23/2006] [Revised: 02/13/2007] [Accepted: 02/19/2007] [Indexed: 12/26/2022]
Abstract
The ability of small RNA interference (RNAi) to reduce specific gene expression was tested using interleukin-10 (IL-10) and interferon-gamma (IFN-gamma) production by cultured swine blood mononuclear cells stimulated by Escherichia coli lipopolysaccharide or concanavalin A. Antisense (AS) phosphorothioate oligodeoxynucleotides (ODNs) corresponding to a sequence in the region of the AUG initiation codon of swine IL-10 or IFN-gamma mRNA inhibited production of IL-10 (>or=93.5%) and IFN-gamma (>or=99%) mRNAs. Interleukin-10 and IFN-gamma protein production was inhibited more than 95% by the AS ODNs. Scrambled and sense ODNs RNAi used as negative controls did not alter mRNA expression for either cytokine but slightly reduced IL-10 protein production. Cytokine-specific and control RNAi did not inhibit beta(2)-microglobulin mRNA expression in mitogen-stimulated blood mononuclear cells. Thus AS ODNs RNAi specifically inhibit expression of pig IL-10 and IFN-gamma mRNAs by cultured, mitogen-stimulated blood mononuclear cells and may be an attractive alternative method for studying cytokine function.
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Affiliation(s)
- A M E Sidahmed
- Department of Pathobiology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
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5
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Walton SP, Stephanopoulos GN, Yarmush ML, Roth CM. Thermodynamic and kinetic characterization of antisense oligodeoxynucleotide binding to a structured mRNA. Biophys J 2002; 82:366-77. [PMID: 11751323 PMCID: PMC1302476 DOI: 10.1016/s0006-3495(02)75401-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Antisense oligonucleotides act as exogenous inhibitors of gene expression by binding to a complementary sequence on the target mRNA, preventing translation into protein. Antisense technology is being applied successfully as a research tool and as a molecular therapeutic. However, a quantitative understanding of binding energetics between short oligonucleotides and longer mRNA targets is lacking, and selecting a high-affinity antisense oligonucleotide sequence from the many possibilities complementary to a particular RNA is a critical step in designing an effective antisense inhibitor. Here, we report measurements of the thermodynamics and kinetics of hybridization for a number of oligodeoxynucleotides (ODNs) complementary to the rabbit beta-globin (RBG) mRNA using a binding assay that facilitates rapid separation of bound from free species in solution. A wide range of equilibrium dissociation constants were observed, and association rate constants within the measurable range correlated strongly with binding affinity. In addition, a significant correlation was observed of measured binding affinities with binding affinity values predicted using a thermodynamic model involving DNA and RNA unfolding, ODN hybridization, and RNA restructuring to a final free energy minimum. In contrast to the behavior observed for hybridization of short strands, the association rate constant increased with temperature, suggesting that the kinetics of association are related to disrupting the native structure of the target RNA. The rate of cleavage of the RBG mRNA in the presence of ribonuclease H and ODNs of varying association kinetics displayed apparent first-order kinetics, with the rate constant exhibiting binding-limited behavior at low association rates and reaction-limited behavior at higher rates. Implications for the rational design of effective antisense reagents are discussed.
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Affiliation(s)
- S Patrick Walton
- Center for Engineering in Medicine/Surgical Services, Massachusetts General Hospital, Harvard Medical School and Shriners Burns Hospital, Boston, Massachusetts 02114, USA
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6
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Ding Y, Lawrence CE. Statistical prediction of single-stranded regions in RNA secondary structure and application to predicting effective antisense target sites and beyond. Nucleic Acids Res 2001; 29:1034-46. [PMID: 11222752 PMCID: PMC29728 DOI: 10.1093/nar/29.5.1034] [Citation(s) in RCA: 122] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2001] [Revised: 01/11/2001] [Accepted: 01/11/2001] [Indexed: 11/13/2022] Open
Abstract
Single-stranded regions in RNA secondary structure are important for RNA-RNA and RNA-protein interactions. We present a probability profile approach for the prediction of these regions based on a statistical algorithm for sampling RNA secondary structures. For the prediction of phylogenetically-determined single-stranded regions in secondary structures of representative RNA sequences, the probability profile offers substantial improvement over the minimum free energy structure. In designing antisense oligonucleotides, a practical problem is how to select a secondary structure for the target mRNA from the optimal structure(s) and many suboptimal structures with similar free energies. By summarizing the information from a statistical sample of probable secondary structures in a single plot, the probability profile not only presents a solution to this dilemma, but also reveals 'well-determined' single-stranded regions through the assignment of probabilities as measures of confidence in predictions. In antisense application to the rabbit beta-globin mRNA, a significant correlation between hybridization potential predicted by the probability profile and the degree of inhibition of in vitro translation suggests that the probability profile approach is valuable for the identification of effective antisense target sites. Coupling computational design with DNA-RNA array technique provides a rational, efficient framework for antisense oligonucleotide screening. This framework has the potential for high-throughput applications to functional genomics and drug target validation.
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MESH Headings
- Algorithms
- Animals
- Binding Sites
- Escherichia coli/genetics
- Nucleic Acid Conformation
- Phylogeny
- Probability
- RNA/chemistry
- RNA/genetics
- RNA, Antisense/genetics
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 5S/chemistry
- RNA, Ribosomal, 5S/genetics
- RNA, Transfer, Ala/chemistry
- RNA, Transfer, Ala/genetics
- Rabbits
- Tetrahymena thermophila/genetics
- Xenopus laevis/genetics
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Affiliation(s)
- Y Ding
- Division of Molecular Medicine, Wadsworth Center, New York State Department of Health, Albany, NY 12201-0509, USA.
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7
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Boeve CM, De Ley M. Modulation of human interferon-gamma biosynthesis by antisense oligodeoxynucleotides. Mol Biotechnol 2000; 14:157-63. [PMID: 10872507 DOI: 10.1385/mb:14:2:157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We investigated the inhibition of human interferon-gamma (HuIFN-gamma) production in cultures of lymphocytes with the use of the antisense strategy. Out of a series of antisense oligodeoxynucleotides (ODN) complementary to different regions of the HuIFN-gamma gene, a 16-mer specific for a sequence including the translation initiation codon was the most effective. Here we describe a detailed protocol for the isolation of lymphocytes from buffy coats, the rational design of antisense ODN, and the monitoring of HuIFN-gamma production of the antisense ODN-treated cells.
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Affiliation(s)
- C M Boeve
- Laboratory for Biochemistry, Katholieke Universiteit Leuven, Belgium
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8
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Levin AA. A review of the issues in the pharmacokinetics and toxicology of phosphorothioate antisense oligonucleotides. BIOCHIMICA ET BIOPHYSICA ACTA 1999; 1489:69-84. [PMID: 10806998 DOI: 10.1016/s0167-4781(99)00140-2] [Citation(s) in RCA: 312] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- A A Levin
- Toxicology and Pharmacokinetics, ISIS Pharmaceuticals, Inc., Carlsbad, CA 92008, USA.
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9
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Abstract
Antisense oligonucleotides are widely used as tools to explore the pharmacological effects of inhibiting expression of a selected gene product. In addition, they are being investigated as therapeutic agents for the treatment of viral infections, cancers, and inflammatory disorders. Proof that the pharmacological effects produced by the oligonucleotides are attributable to an antisense mechanism of action requires careful experimentation. Central to this problem is the finding that oligonucleotides are capable of interacting with and modulating function of specific proteins in both a sequence-independent and -dependent manner. Despite these undesired interactions, it has been possible to demonstrate that oligonucleotides are capable of binding to a specific RNA in cultured cells, or within tissues, resulting in selective reduction of the targeted gene product and pharmacological activity. In general, these oligonucleotides were identified after a selection process in which multiple oligonucleotides targeting different regions on the RNA were evaluated for direct inhibition of targeted gene product, resulting in the identification of a potent and selective oligonucleotide. Similar to other drug-receptor interactions, selection of the most potent inhibitor results in an increase in the signal-to-noise ratio, yielding increased confidence that activity observed is the result of a desired effect of the inhibitor. With careful selection, proper controls, and careful dose-response curves it is possible to utilize antisense oligonucleotides as effective research tools and potentially as therapeutic agents.
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Affiliation(s)
- C F Bennett
- ISIS Pharmaceuticals, Carlsbad, CA 92008, USA
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10
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Chen TZ, Wu JC, Au LC, Choo KB. Specific inhibition of delta antigen by in vitro system by antisense oligodeoxynucleotide: implications for translation mechanism and treatment. J Virol Methods 1997; 65:183-9. [PMID: 9186941 DOI: 10.1016/s0166-0934(97)02177-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Synthetic antisense oligodeoxynucleotides (ODNs) and a system containing transcription and translation coupled rabbit reticulocyte lysate were used to develop a new model modulating the synthesis of small delta antigen which, in turn, inhibits the replication of HDV (hepatitis D virus). The ODN was stable for at least 50 min in this system at 37 degrees C. Unmodified 15-mer antisense D3 and D4, complementary to translation initiation region and coding region, respectively, inhibit the synthesis of small delta antigen by 95% at a concentration of 5 microM, whereas antisenses complementary to 5' noncoding region, stop codon region and polyadenylation site were less effective. This system also showed a dose-dependent inhibitory effect of antisense D3 on the production of the target protein. However, the synthesis of E6 protein, an internal control, was not affected. These observations imply that this in vitro system is convenient for rapid screening of effective antisense compounds and offers a promising perspective for the investigation of translation mechanisms and for the inhibition of HDV replication by antisense strategy.
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Affiliation(s)
- T Z Chen
- Department of Medicine, Veterans General Hospital-Taipei, Taiwan, R.O.C
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11
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Zenkova M, Ehresmann C, Caillet J, Springer M, Karpova G, Ehresmann B, Romby P. A novel approach to introduce site-directed specific cross-links within RNA-protein complexes. Application to the Escherichia coli threonyl-tRNA synthetase/translational operator complex. EUROPEAN JOURNAL OF BIOCHEMISTRY 1995; 231:726-35. [PMID: 7544283 DOI: 10.1111/j.1432-1033.1995.0726d.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We describe a methodology which allows the introduction of a photoactivatable azido group at specific internal positions of any RNA in order to identify the neighboring elements of an interacting protein. The first step involves site-directed modification of the target RNA with an antisense oligodeoxyribonucleotide bearing, at its 3' or 5' phosphate, a 4-[-N-(2-chloroethyl)-N-methylamino]benzylmethylamino group. Position N7 of a guanine residue located in the close vicinity of the hybrid is the main target for alkylation. The antisense oligodeoxyribonucleotide is then removed by acidic pH treatment and a photoreactive reagent (2,4-dinitro-5-fluorophenylazide) is condensed to the modified nucleotide. This method was used to induce specific cross-links between Escherichia coli threonyl-tRNA synthetase and the leader region of threonyl-tRNA synthetase mRNA, which is involved in translational feedback regulation. Control experiments revealed that the modification affects neither the structure of the mRNA nor the interaction with the enzyme. More than 50% of the modified mRNA complexed with threonyl-tRNA synthetase can be cross-linked to the enzyme, depending on the nucleotide modified.
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Affiliation(s)
- M Zenkova
- Novosibirsk Institute of Bioorganic Chemistry, Siberian Division of Russian Academy of Sciences
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12
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Abstract
To study factors that affect in vivo ribozyme (Rz) activity, a model system has been devised in Saccharomyces cerevisiae based on the inhibition of ADE1 gene expression. This gene was chosen because Rz action can be evaluated visually by the Red phenotype produced when the activity of the gene product is inhibited. Different plasmid constructs allowed the expression of the Rz either in cis or in trans with respect to ADE1. Rz-related inhibition of ADE1 expression was correlated with a Red phenotype and a diminution of ADE1 mRNA levels only when the Rz gene was linked 5' to ADE1. The presence of the expected 3' cleavage fragment was demonstrated using a technique combining RNA ligation and PCR. This yeast system and detection technique are suited to the investigation of general factors affecting Rz-catalyzed inhibition of gene expression under in vivo conditions.
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Affiliation(s)
- G Ferbeyre
- Département de biochimie, Université de Montréal, Québec, Canada
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13
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Johansson HE, Belsham GJ, Sproat BS, Hentze MW. Target-specific arrest of mRNA translation by antisense 2'-O-alkyloligoribonucleotides. Nucleic Acids Res 1994; 22:4591-8. [PMID: 7984406 PMCID: PMC308505 DOI: 10.1093/nar/22.22.4591] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
We describe a novel experimental approach to investigate mRNA translation. Antisense 2'-O-allyl oligoribonucleotides (oligos) efficiently arrest translation of targeted mRNAs in rabbit reticulocyte lysate and wheat germ extract while displaying minimal non-specific effects on translation. Oligo/mRNA-hybrids positioned anywhere within the 5' UTR or the first approximately 20 nucleotides of the open reading frame block cap-dependent translation initiation with high specificity. The thermodynamic stability of hybrids between 2'-O-alkyl oligos and RNA permits translational inhibition with oligos as short as 10 nucleotides. This inhibition is independent of RNase H cleavage or modifications which render the mRNA untranslatable. We show that 2'-O-alkyl oligos can also be employed to interfere with cap-independent internal initiation of translation and to arrest translation elongation. The latter is accomplished by UV-crosslinking of psoralen-tagged 2'-O-methyloligoribonucleotides to the mRNA within the open reading frame. The utility of 2'-O-alkyloligoribonucleotides to arrest translation from defined positions within an mRNA provides new approaches to investigate mRNA translation.
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Affiliation(s)
- H E Johansson
- Gene Expression Programme, European Molecular Biology Laboratory, Heidelberg, Germany
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14
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Lledo PM, Mason WT, Zorec R. Study of stimulus-secretion coupling in single cells using antisense oligodeoxynucleotides and patch-clamp techniques to inhibit specific protein expression. Cell Mol Neurobiol 1994; 14:539-56. [PMID: 7621512 DOI: 10.1007/bf02088836] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- P M Lledo
- C.N.R.S. Institut Alfred Fessard, Gif-sur-Yvette, France
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15
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Pantopoulos K, Johansson HE, Hentze MW. The role of the 5' untranslated region of eukaryotic messenger RNAs in translation and its investigation using antisense technologies. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1994; 48:181-238. [PMID: 7938549 PMCID: PMC7133200 DOI: 10.1016/s0079-6603(08)60856-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
This chapter discusses the recent advances in the field of translational control and the possibility of applying the powerful antisense technology to investigate some of the unanswered questions, especially those pertaining to the role of the 5’untranslated region ( UTR) on translation initiation. Translational regulation is predominantly exerted during the initiation phase that is considered to be the rate-limiting step. Two types of translational regulation can be distinguished: global, in which the initiation rate of (nearly) all cellular messenger RNA (mRNA) is controlled and selective, in which the translation rate of specific mRNAs varies in response to the biological stimuli. In most cases of global regulation, control is exerted via the phosphorylation state of certain initiation factors, whereas only a few examples of selective regulation have been characterized well enough to define the underlying molecular events. Interestingly, cis-acting regulatory sequences, affecting translation initiation, have been found not only in the 5’UTRs of selectively regulated mRNAs, but also in the 3’UTRs. Thus, in addition to the protein encoding open reading frames, both the 5’ and 3’UTRs of mRNAs must be considered for their effect on translation.
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Key Words
- alas, 5-aminolevulinate synthase
- bfgf, basic fibroblast growth factor
- bip, immunoglobulin-binding protein
- cat, chloramphenicol acetyltransferase
- dai, double-stranded rna-activated inhibitor
- ealas, erythroid-specific form of alas
- frp, ferritin repressor protein
- gcd, general control derepressible
- gcn, general control nonderepressible
- gef, guanine-nucleotide exchange factor
- grp, glucose-regulated protein
- hgh, human growth hormone
- icam, intracellular adhesion molecule
- ire, iron-responsive element
- ire-bp, iron-responsive element-binding protein
- ires, internal ribosomal entry site
- irf, iron regulatory factor
- irp, iron regulatory protein
- la, lupus erythematosus antigen
- lap, liver-enriched activating protein
- lip, liver-enriched inhibitory protein
- mep, methyl phosphonate
- pa, phosphoramidate
- pdgf, platelet-derived growth factor
- pest, phosphotriester
- pll, poly(1-lysine)
- po, phosphodiester
- ps, phosphorothioate
- ps2, phosphorodithioate
- ssl, suppressor of stem-loop
- tce, translational control element
- tgf, transforming growth factor
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Affiliation(s)
- K Pantopoulos
- Gene Expression Programme, European Molecular Biology Laboratory, Heidelberg, Germany
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16
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Affiliation(s)
- G Carter
- ICRF Oncology Group, Royal Postgraduate Medical School, Hammersmith Hospital, London, UK
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17
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Jaroszewski JW, Syi JL, Ghosh M, Ghosh K, Cohen JS. Targeting of antisense DNA: comparison of activity of anti-rabbit beta-globin oligodeoxyribonucleoside phosphorothioates with computer predictions of mRNA folding. ANTISENSE RESEARCH AND DEVELOPMENT 1993; 3:339-48. [PMID: 8155975 DOI: 10.1089/ard.1993.3.339] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
To assess the usefulness of computer-assisted modeling of mRNA as an aid in design of antisense DNA, the efficiency of inhibition of translation of rabbit beta-globin mRNA by various antisense sequences was compared with calculated structures of the mRNA. The model obtained by consideration of 30 lowest-energy computer-simulated structures is consistent with the high accessibility of the AUG initiation codon region known from digestion with nucleases and with previous antisense inhibition studies reported in the literature. Additional antisense inhibition data were obtained with 20-mer phosphorothioate oligonucleotides, targeted to regions of beta-globin mRNA differing moderately in their degree of participation in intramolecular folding. The efficiency of translation arrest by the oligonucleotides in cell-free expression systems (wheat germ extract and rabbit reticulocyte lysate) was obtained by measuring incorporation of [35S]methionine into total protein, and corrected for sequence-nonspecific inhibition using brome mosaic virus mRNA. In the presence of RNase H (wheat germ system), the inhibitory activity of the oligonucleotides showed correlation with the calculated secondary structure of mRNA, in particular at low oligonucleotide-to-mRNA ratios (correlation coefficient, 0.95). No correlation was observed in the reticulocyte lysate system, in which the inhibition is mediated by translational arrest.
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Affiliation(s)
- J W Jaroszewski
- Department of Organic Chemistry, Royal Danish School of Pharmacy, Copenhagen
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18
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Madhubala R, Pegg AE. Inhibition of ornithine decarboxylase and S-adenosylmethionine decarboxylase synthesis by antisense oligodeoxynucleotides. Mol Cell Biochem 1992; 118:191-5. [PMID: 1338119 DOI: 10.1007/bf00299398] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Oligodeoxynucleotides 18 nucleotides in length having sequences complementary to regions spanning the initiation codon regions of ornithine decarboxylase or S-adenosylmethionine decarboxylase mRNAs were tested for their ability to inhibit translation of these mRNAs. In reticulocyte lysates, a strong and dose dependent reduction of ornithine decarboxylase synthesis in response to mRNA from D-R L1210 cells was brought about by 5'-AAAGCTGCTCATGGTTCT-3' which is complementary to the sequence from -6 to +12 of the mRNA sequence but there was no inhibition by 5'-TGCAGCTTCCATCACCGT-3'. Conversely, the latter oligodeoxynucleotide which is complementary to the sequence from -6 to +12 of the mRNA of S-adenosyl methionine decarboxylase was a strong inhibitor of the synthesis of this enzyme in response to rat prostate mRNA and the antisense sequence from ornithine decarboxylase had no effect. The translation of ornithine decarboxylase mRNA in a wheat germ system was inhibited by the antisense oligodeoxynucleotide at much lower concentration than those needed in the reticulocyte lysate suggesting that degradation of the hybrid by ribonuclease H may be an important factor in this inhibition. These results indicate that such oligonucleotides may be useful to regulate cellular polyamine levels and as probes to study control of mRNA translation.
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Affiliation(s)
- R Madhubala
- Department of Cellular and Molecular Physiology, Pennsylvania State University College of Medicine, Milton S. Hershey Medical Centre, Hershey 17033
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19
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Krieg AM. Applications of antisense oligodeoxynucleotides in immunology and autoimmunity research. ACTA ACUST UNITED AC 1992. [DOI: 10.1016/s1058-6687(05)80016-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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20
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Ricker RD, Kaji A. Studies on antisense inhibition of translation in vitro. Anomalies and re-evaluation. FEBS Lett 1992; 309:363-70. [PMID: 1516711 DOI: 10.1016/0014-5793(92)80808-t] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Experiments were carried out to better characterize antisense control of translation. Results in an E. coli system confirmed specific inhibition of poly(U) translation. At low concentrations, certain homopolymers (including poly(rA)) stimulated translation. Oligo(dA(n)) was inhibitory at n less than or equal to 8. Translation of globin mRNA in reticulocyte lysates indicated that ssDNA 15-mers targeted at beta-globin mRNA inhibited both alpha- and beta-globin production. Sequences targeted immediately downstream of the AUG were the least effective in inhibition. These and other anomalies are discussed here in relation to those of others, emphasizing caution in performing antisense experiments.
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Affiliation(s)
- R D Ricker
- Department of Microbiology, University of Pennsylvania, School of Medicine, Philadelphia 19104-6076
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21
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Goodchild J. Enhancement of ribozyme catalytic activity by a contiguous oligodeoxynucleotide (facilitator) and by 2'-O-methylation. Nucleic Acids Res 1992; 20:4607-12. [PMID: 1383929 PMCID: PMC334191 DOI: 10.1093/nar/20.17.4607] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
RNA catalysts (ribozymes) designed to cleave sequences unique to viral RNA's might be developed as therapeutics. For this purpose, they would require high catalytic efficiency and resistance to nucleases. Reported here are two approaches that can be used in combination to improve these properties. First, catalytic efficiency can be improved by oligonucleotides (facilitators) that bind to the substrate contiguously with the 3'-end of the ribozyme. Second, 2'-O-methylation of flanking sequences of the ribozyme increases catalytic activity as well as resistance to nucleases. In combination with a facilitator oligodeoxynucleotide, the cleavage rate was increased 20 fold over that of the unmodified ribozyme.
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Affiliation(s)
- J Goodchild
- Worcester Foundation for Experimental Biology, Shrewsbury, MA 01545
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22
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Stull RA, Taylor LA, Szoka FC. Predicting antisense oligonucleotide inhibitory efficacy: a computational approach using histograms and thermodynamic indices. Nucleic Acids Res 1992; 20:3501-8. [PMID: 1352874 PMCID: PMC312508 DOI: 10.1093/nar/20.13.3501] [Citation(s) in RCA: 76] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Antisense oligonucleotides (ASOs) are designed to bind to a specific mRNA and selectively suppress its translation. To facilitate selection of optimal ASO targets, we have developed three thermodynamic indices to evaluate putative structural complexes important in ASO action. These indices are: a secondary structure score (Sscore), which estimates the strength of local mRNA secondary structures at the ASO target site; a duplex score (Dscore), which estimates the delta Gformation for the ASO:mRNA target sequence duplex; and a competition score (Cscore), which is the difference between the Dscore and the Sscore. We also present two histograms to graphically display these indices from different regions of the mRNA. The indices are compared to the inhibition reported in five studies of ASO-mediated suppression of gene expression. The Dscore is the most consistent predictor of ASO efficacy in four of the five studies (r2 from 0.44 to 0.99), while the results of the fifth study could not be predicted by any thermodynamic or physical index. Thus the Dscores and their histogram may prove useful in selection of ASO targets.
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Affiliation(s)
- R A Stull
- Department of Pharmacy, University of California, San Francisco 94143-0446
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23
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Porumb H, Bertrand JR, Paoletti J, Vasseur JJ, Rayner B, Imbach JL, Malvy C. 9-Aminoellipticine-derivatized alpha- and beta-oligodeoxyribonucleotides targeted to the cap of beta-globin mRNA: hybridization to natural and engineered mRNA, inhibition of translation, and improved effect of tandem chains. ANTISENSE RESEARCH AND DEVELOPMENT 1992; 2:279-92. [PMID: 1292777 DOI: 10.1089/ard.1992.2.279] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We studied the duplex stability and the antimessenger activity of 9-aminoellipticine-5'-functionalized alpha- and beta-anomeric DNA sequences complementary to the first 14 nucleotides of the rabbit beta-globin mRNA. The duplex formed by the beta-conjugate with the natural mRNA target possessed a marginally better stability to that of the duplex formed by the unfunctionalized compound, as measured by the thermal elution. The alpha-conjugate did not anneal to native mRNA, possibly due to the interference of the 9-aminoellipticine with the cap structure and, unlike the beta-adduct, was practically inactive as inhibitor of translation in a cell-free system. However, it did hybridize to an RNA construction containing the beta-globin mRNA plus an additional 50 bases in 5'. Surprisingly, translation from this construction was inhibited by the alpha-species in spite of the nonvicinity of the target to the cap. Both alpha and beta conjugates hybridized to a DNA 14-mer of the same sequence as that targeted onto the mRNA. Thermal denaturation and fluorescence spectroscopy showed that the drug brought no considerable stabilization to the duplex, the linker presumably being unfavorable to intercalation. An increased stability of the complex and a higher inhibitory effect on cell-free beta-globin translation were obtained with two contiguous beta-oligomers of which one was functionalized.
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Affiliation(s)
- H Porumb
- Laboratoire de Biochimie-Enzymologie et de Physicochimie Macromoléculaire, CNRS URA 147, Institut Gustave Roussy, Villejuif, France
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24
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Schwemmle M, Schickinger J, Bader M, Sarre TF, Hilse K. A 60-kDa protein from rabbit reticulocytes specifically recognizes the capped 5' end of beta-globin mRNA. EUROPEAN JOURNAL OF BIOCHEMISTRY 1991; 201:139-45. [PMID: 1915356 DOI: 10.1111/j.1432-1033.1991.tb16266.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The binding of proteins from rabbit reticulocyte lysate to in-vitro-generated beta-globin mRNA and its defined segments was investigated using ultraviolet-cross-linking experiments as well as gel-retardation assays. Under stringent conditions, only three proteins (72, 60 and 50 kDa) were found associated with full-length beta-globin mRNA at different positions. The 72-kDa protein is most likely the poly(A)-binding protein and binds, as expected, to the poly(A) tail, whereas the 50-kDa protein exhibits affinity for the trailer region of beta-globin mRNA. The binding region of the 60-kDa protein is located at the 5' end of beta-globin mRNA. The interaction of this protein is dependent on the presence of the 5' cap structure, as indicated by competition experiments using an uncapped beta-globin-mRNA leader segment. Further competition experiments with beta-globin mRNA, deleted in part in the leader region, suggest that, besides the cap structure, certain sequence elements are necessary for the interaction of the 60-kDa protein and the beta-globin mRNA leader.
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Affiliation(s)
- M Schwemmle
- Institute for Biology III, University of Freiburg, Federal Republic of Germany
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25
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Byrn S, Carlson D, Chen J, Cushman M, Goldman M, Ma W, Pidgeon C, Ray K, Stowell J, Weith H. Drug-oligonucleotide conjugates. Adv Drug Deliv Rev 1991. [DOI: 10.1016/0169-409x(91)90022-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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26
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Sartorius C, Franklin RM. Hybridization arrest of cell-free translation of the malarial dihydrofolate reductase/thymidylate synthase mRNA by anti-sense oligodeoxyribonucleotides. Nucleic Acids Res 1991; 19:1613-8. [PMID: 2027768 PMCID: PMC333923 DOI: 10.1093/nar/19.7.1613] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
In order to inhibit the in vitro translation of Plasmodium falciparum mRNA coding for the bifunctional enzyme dihydrofolate reductase-thymidylate synthase (DHFR-TS), oligodeoxynucleotides (ODNs) were directed against the translation initiation site or a site in the TS-coding region. In both cases considerable hybridization arrest, i.e. greater than 50% inhibition, was only achieved if the lengths of the ODNs to the two regions were 30 and 39 nucleotides, respectively, or longer. The ODN with the highest efficiency was a 49-mer directed against the TS-coding region (OTS49); 45 microM was sufficient to inhibit the expression of DHFR-TS by almost 90%. In this case the synthesis of DHFR-TS was interrupted at the binding site of OTS49 by a RNase H-independent mechanism. The resulting polypeptide was smaller (55 kDa) than one subunit of the native protein (71 kDa) and lacked TS activity.
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Affiliation(s)
- C Sartorius
- Biocenter, Department Structural Biology, Basel, Switzerland
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27
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Boiziau C, Kurfurst R, Cazenave C, Roig V, Thuong NT, Toulmé JJ. Inhibition of translation initiation by antisense oligonucleotides via an RNase-H independent mechanism. Nucleic Acids Res 1991; 19:1113-9. [PMID: 1850511 PMCID: PMC333789 DOI: 10.1093/nar/19.5.1113] [Citation(s) in RCA: 112] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
We have used alpha-oligomers as antisense oligonucleotides complementary to three different sequences of the rabbit beta-globin mRNA: a region adjacent to the cap site, a region spanning the AUG initiation codon or a sequence in the coding region. These alpha-oligonucleotides were synthesized either with a free 5' OH group or linked to an acridine derivative. The effect of these oligonucleotides on mRNA translation was investigated in cell-free extracts and in Xenopus oocytes. In rabbit reticulocyte lysate and in wheat germ extracts oligomers targeted to the cap site and the initiation codon reduced beta-globin synthesis in a dose-dependent manner, whereas the target mRNA remained intact. The anti-cap alpha-oligomer was even more efficient that its beta-counterpart in rabbit reticulocyte lysate. In contrast, only the alpha-oligomer, linked to the acridine derivative, complementary to the cap region displayed significant antisense properties in Xenopus oocytes. Therefore initiation of translation can be arrested by oligonucleotide/RNA hybrids which are not substrates for RNase-H.
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Affiliation(s)
- C Boiziau
- Laboratoire de Biophysique, Muséum National d'Histoire Naturelle, Paris, France
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28
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Sartorius C, Franklin RM. The use of antisense oligonucleotides as chemotherapeutic agents for parasites. ACTA ACUST UNITED AC 1991; 7:90-3. [PMID: 15463454 DOI: 10.1016/0169-4758(91)90204-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Although several approaches to the control of human parasites are possible, the prevention and therapy of the corresponding diseases still remain a difficult task. The development of vaccines has been hampered by the poor immunological response to or the high variability of parasitic antigens. Problems also arise for chemotherapy where differences in the biochemistry of host and parasite must be exploited. The increasingly difficult search for new drugs is always challenged by the appearance of resistance.
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Affiliation(s)
- C Sartorius
- Biocenter, Department of Structural Biology, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
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29
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30
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Abstract
The antiviral use of antisense oligonucleotides is described with particular reference to our own work on the inhibition of HIV-1. Subjects include the design, metabolism, and modification of these agents and the possible future use of ribozymes.
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Affiliation(s)
- J Goodchild
- Worcester Foundation for Experimental Biology, Shrewsbury, Massachusetts
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31
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Hélène C, Toulmé JJ. Specific regulation of gene expression by antisense, sense and antigene nucleic acids. BIOCHIMICA ET BIOPHYSICA ACTA 1990; 1049:99-125. [PMID: 1694695 DOI: 10.1016/0167-4781(90)90031-v] [Citation(s) in RCA: 624] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- C Hélène
- Muséum National d'Histoire Naturelle, INSERM U201-CNRS UA.481, Paris, France
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32
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Agrawal S, Mayrand SH, Zamecnik PC, Pederson T. Site-specific excision from RNA by RNase H and mixed-phosphate-backbone oligodeoxynucleotides. Proc Natl Acad Sci U S A 1990; 87:1401-5. [PMID: 2154746 PMCID: PMC53483 DOI: 10.1073/pnas.87.4.1401] [Citation(s) in RCA: 119] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Oligodeoxynucleotides containing phosphodiester or modified internucleoside linkages were investigated with respect to their ability to be acted on by ribonuclease H activities present in a HeLa cell nuclear extract after hybridization with complementary sequences in RNA. Oligodeoxynucleotides complementary to nucleotides 2-14 of human U1 small nuclear RNA were investigated. Extensive cleavage of U1 RNA was observed with the unmodified oligodeoxynucleotide and with the phosphorothioate analogue but not with U1-complementary oligodeoxynucleotides containing methylphosphonate, phosphoro-N-morpholidate, or phosphoro-N-butylamidate internucleoside linkages. Additional experiments using a 514-nucleotide-long RNA substrate demonstrated the capacity of complementary phosphodiester- and phosphorothioate-linked oligodeoxynucleotides (but not ones containing methylphosphonate, phosphoro-N-morpholidate, or phosphoro-N-butylamidate linkages) to serve as RNase H targets when hybridized to an internal RNA site. Detailed comparisons revealed phosphodiester-linked oligodeoxynucleotides to be more efficient than the comparable phosphorothioate-linked oligomers with respect to RNase H action. Various pentadecamer oligodeoxynucleotides complementary to the 514-nucleotide-long test RNA and containing 2-6 consecutive phosphodiester- or phosphorothioate-linked nucleotides flanked by RNase H-resistant methylphosphonate linkages afforded precise "site-directed" RNase H excision within the DNA.RNA hybrid. These results serve to assort modified oligodeoxynucleotide-containing hybrids into RNase H-sensitive and -resistant classes and also provide clues as to how RNase H makes contact with the DNA strand in a DNA.RNA hybrid.
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Affiliation(s)
- S Agrawal
- Cell Biology Group, Worcester Foundation for Experimental Biology, Shrewsbury, MA 01545
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Degols G, Leonetti JP, Gagnor C, Lemaitre M, Lebleu B. Antiviral activity and possible mechanisms of action of oligonucleotides-poly(L-lysine) conjugates targeted to vesicular stomatitis virus mRNA and genomic RNA. Nucleic Acids Res 1989; 17:9341-50. [PMID: 2479915 PMCID: PMC335136 DOI: 10.1093/nar/17.22.9341] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Synthetic oligonucleotides (oligomers) complementary to vesicular stomatitis virus (VSV) N protein mRNA have specific antiviral properties at concentrations lower than 1 microM when they are covalently linked to poly(L-lysine) (PLL). Since it is generally postulated that antisense oligomers act at the translational level, oligomers with potential targets on VSV viral mRNA and/or genomic RNA have been tested here. In vitro translation experiments in reticulocyte lysates, in vitro transcription experiments with permeabilized viruses, measurement of viral RNA transcription and accumulation in VSV infected cells, and antiviral experiments demonstrate in our model that antisense oligomers probably also act at other levels. Difficulties in the choice of the most effective antisense oligomer targets are also discussed.
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Affiliation(s)
- G Degols
- Laboratoire de Biochimie des Proteines, UA CNRS 1191, Université des Sciences et Techniques du Languedoc, Montpellier, France
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34
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Cazenave C, Stein CA, Loreau N, Thuong NT, Neckers LM, Subasinghe C, Hélène C, Cohen JS, Toulmé JJ. Comparative inhibition of rabbit globin mRNA translation by modified antisense oligodeoxynucleotides. Nucleic Acids Res 1989; 17:4255-73. [PMID: 2472605 PMCID: PMC317933 DOI: 10.1093/nar/17.11.4255] [Citation(s) in RCA: 203] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
We have studied the translation of rabbit globin mRNA in cell free systems (reticulocyte lysate and wheat germ extract) and in microinjected Xenopus oocytes in the presence of anti-sense oligodeoxynucleotides. Results obtained with the unmodified all-oxygen compounds were compared with those obtained when phosphorothioate or alpha-DNA was used. In the wheat germ system a 17-mer sequence targeted to the coding region of beta-globin mRNA was specifically inhibitory when either the unmodified phosphodiester oligonucleotide or its phosphorothioate analogue were used. In contrast no effect was observed with the alpha-oligomer. These results were ascribed to the fact that phosphorothioate oligomers elicit an RNase-H activity comparable to the all-oxygen congeners, while alpha-DNA/mRNA hybrids were a poor substrate. Microinjected Xenopus oocytes followed a similar pattern. The phosphorothioate oligomer was more efficient to prevent translation than the unmodified 17-mer. Inhibition of beta-globin synthesis was observed in the nanomolar concentration range. This result can be ascribed to the nuclease resistance of phosphorothioates as compared to natural phosphodiester linkages, alpha-oligomers were devoid of any inhibitory effect up to 30 microM. Phosphorothioate oligodeoxyribonucleotides were shown to be non-specific inhibitors of protein translation, at concentrations in the micromolar range, in both cell-free systems and oocytes. Non-specific inhibition of translation was dependent on the length of the phosphorothioate oligomer. These non-specific effects were not observed with the unmodified or the alpha-oligonucleotides.
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Affiliation(s)
- C Cazenave
- Laboratoire de Biophysique, INSERM U201, Paris, France
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35
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Goodchild J, Agrawal S, Civeira MP, Sarin PS, Sun D, Zamecnik PC. Inhibition of human immunodeficiency virus replication by antisense oligodeoxynucleotides. Proc Natl Acad Sci U S A 1988; 85:5507-11. [PMID: 3041414 PMCID: PMC281786 DOI: 10.1073/pnas.85.15.5507] [Citation(s) in RCA: 182] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Twenty different target sites within human immunodeficiency virus (HIV) RNA were selected for studies of inhibition of HIV replication by antisense oligonucleotides. Target sites were selected based on their potential capacity to block recognition functions during viral replication. Antisense oligomers complementary to sites within or near the sequence repeated at the ends of retrovirus RNA (R region) and to certain splice sites were most effective. The effect of antisense oligomer length on inhibiting virus replication was also investigated, and preliminary toxicity studies in mice show that these compounds are toxic only at high levels. The results indicate potential usefulness for these oligomers in the treatment of patients with acquired immunodeficiency syndrome (AIDS) and AIDS-related complex either alone or in combination with other drugs.
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Affiliation(s)
- J Goodchild
- Worcester Foundation for Experimental Biology, Shrewsbury, MA 01545
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