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Gifford LK, Opalinska JB, Jordan D, Pattanayak V, Greenham P, Kalota A, Robbins M, Vernovsky K, Rodriguez LC, Do BT, Lu P, Gewirtz AM. Identification of antisense nucleic acid hybridization sites in mRNA molecules with self-quenching fluorescent reporter molecules. Nucleic Acids Res 2005; 33:e28. [PMID: 15718294 PMCID: PMC549423 DOI: 10.1093/nar/gni024] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
We describe a physical mRNA mapping strategy employing fluorescent self-quenching reporter molecules (SQRMs) that facilitates the identification of mRNA sequence accessible for hybridization with antisense nucleic acids in vitro and in vivo, real time. SQRMs are 20–30 base oligodeoxynucleotides with 5–6 bp complementary ends to which a 5′ fluorophore and 3′ quenching group are attached. Alone, the SQRM complementary ends form a stem that holds the fluorophore and quencher in contact. When the SQRM forms base pairs with its target, the structure separates the fluorophore from the quencher. This event can be reported by fluorescence emission when the fluorophore is excited. The stem–loop of the SQRM suggests that SQRM be made to target natural stem–loop structures formed during mRNA synthesis. The general utility of this method is demonstrated by SQRM identification of targetable sequence within c-myb and bcl-6 mRNA. Corresponding antisense oligonucleotides reduce these gene products in cells.
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Affiliation(s)
- Lida K. Gifford
- Department of Chemistry, School of Arts and Sciences231 South 34th Street, Philadelphia, PA 19104, USA
| | - Joanna B. Opalinska
- Department of Chemistry, School of Arts and Sciences231 South 34th Street, Philadelphia, PA 19104, USA
| | - David Jordan
- Department of Chemistry, School of Arts and Sciences231 South 34th Street, Philadelphia, PA 19104, USA
| | - Vikram Pattanayak
- Department of Chemistry, School of Arts and Sciences231 South 34th Street, Philadelphia, PA 19104, USA
- Division of Hematology/Oncology, Department of Medicine, School of Medicine, University of PennsylvaniaRoom 713, BRB II/III 421 Curie Boulevard, Philadelphia, PA 19104, USA
| | - Paul Greenham
- Department of Chemistry, School of Arts and Sciences231 South 34th Street, Philadelphia, PA 19104, USA
| | - Anna Kalota
- Department of Chemistry, School of Arts and Sciences231 South 34th Street, Philadelphia, PA 19104, USA
| | - Michelle Robbins
- Department of Chemistry, School of Arts and Sciences231 South 34th Street, Philadelphia, PA 19104, USA
| | - Kathy Vernovsky
- Department of Chemistry, School of Arts and Sciences231 South 34th Street, Philadelphia, PA 19104, USA
| | - Lesbeth C. Rodriguez
- Department of Chemistry, School of Arts and Sciences231 South 34th Street, Philadelphia, PA 19104, USA
| | - Bao T. Do
- Department of Chemistry, School of Arts and Sciences231 South 34th Street, Philadelphia, PA 19104, USA
| | - Ponzy Lu
- Department of Chemistry, School of Arts and Sciences231 South 34th Street, Philadelphia, PA 19104, USA
| | - Alan M. Gewirtz
- Department of Chemistry, School of Arts and Sciences231 South 34th Street, Philadelphia, PA 19104, USA
- To whom correspondence should be addressed. Tel: +1 215 898 4499; Fax: +1 215 573 2078;
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Lundblad EW, Haugen P, Johansen SD. Trans-splicing of a mutated glycosylasparaginase mRNA sequence by a group I ribozyme deficient in hydrolysis. ACTA ACUST UNITED AC 2004; 271:4932-8. [PMID: 15606781 DOI: 10.1111/j.1432-1033.2004.04462.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
RNA reprogramming represents a new concept in correcting genetic defects at the RNA level. However, for the technique to be useful for therapy, the level of reprogramming must be appropriate. To improve the efficiency of group I ribozyme-mediated RNA reprogramming, when using the Tetrahymena ribozyme, regions complementary to the target RNA have previously been extended in length and accessible sites in the target RNAs have been identified. As an alternative to the Tetrahymena model ribozyme, the DiGIR2 group I ribozyme, derived from a mobile group I intron in rDNA of the myxomycete Didymium iridis, represents a new and attractive tool in RNA reprogramming. We reported recently that the deletion of a structural element within the P9 domain of DiGIR2 turns off hydrolysis at the 3' splice site (side reaction) without affecting self-splicing [Haugen, P., Andreassen, M., Birgisdottir, A.B. & Johansen, S.D. (2004) Eur. J. Biochem. 271, 1015-1024]. Here we analyze the potential of the modified ribozyme, deficient in hydrolysis at the 3' splice site, for application in group I ribozyme-mediated trans-splicing of RNA. The improved ribozyme catalyses both cis-splicing and trans-splicing in vitro of a human glycosylasparaginase mRNA sequence with the same efficiency as the original DiGIR2 ribozyme, but without detectable levels of the unwanted hydrolysis.
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Affiliation(s)
- Eirik W Lundblad
- Department of Molecular Biotechnology, RNA Research group, Institute of Medical Biology, University of Tromsø, Norway
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Scherer LJ, Rossi JJ. Approaches for the sequence-specific knockdown of mRNA. Nat Biotechnol 2004; 21:1457-65. [PMID: 14647331 DOI: 10.1038/nbt915] [Citation(s) in RCA: 330] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Over the past 25 years there have been thousands of published reports describing applications of antisense nucleic acid derivatives for targeted inhibition of gene function. The major classes of antisense agents currently used by investigators for sequence-specific mRNA knockdowns are antisense oligonucleotides (ODNs), ribozymes, DNAzymes and RNA interference (RNAi). Whatever the method, the problems for effective application are remarkably similar: efficient delivery, enhanced stability, minimization of off-target effects and identification of sensitive sites in the target RNAs. These challenges have been in existence from the first attempts to use antisense research tools, and need to be met before any antisense molecule can become widely accepted as a therapeutic agent.
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Affiliation(s)
- Lisa J Scherer
- Division of Molecular Biology, Beckman Research Institute of the City of Hope, Duarte, California 91010, USA
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Abstract
With the advent of functional genomics and the shift of interest towards sequence-based therapeutics, the past decades have witnessed intense research efforts on nucleic acid-mediated gene regulation technologies. Today, RNA interference is emerging as a groundbreaking discovery, holding promise for development of genetic modulators of unprecedented potency. Twenty-five years after the discovery of antisense RNA and ribozymes, gene control therapeutics are still facing developmental difficulties, with only one US FDA-approved antisense drug currently available in the clinic. Limited predictability of target site selection models is recognized as one major stumbling block that is shared by all of the so-called complementary technologies, slowing the progress towards a commercial product. Currently employed in vitro systems for target site selection include RNAse H-based mapping, antisense oligonucleotide microarrays, and functional screening approaches using libraries of catalysts with randomized target-binding arms to identify optimal ribozyme/DNAzyme cleavage sites. Individually, each strategy has its drawbacks from a drug development perspective. Utilization of message-modulating sequences as therapeutic agents requires that their action on a given target transcript meets criteria of potency and selectivity in the natural physiological environment. In addition to sequence-dependent characteristics, other factors will influence annealing reactions and duplex stability, as well as nucleic acid-mediated catalysis. Parallel consideration of physiological selection systems thus appears essential for screening for nucleic acid compounds proposed for therapeutic applications. Cellular message-targeting studies face issues relating to efficient nucleic acid delivery and appropriate analysis of response. For reliability and simplicity, prokaryotic systems can provide a rapid and cost-effective means of studying message targeting under pseudo-cellular conditions, but such approaches also have limitations. To streamline nucleic acid drug discovery, we propose a multi-model strategy integrating high-throughput-adapted bacterial screening, followed by reporter-based and/or natural cellular models and potentially also in vitro assays for characterization of the most promising candidate sequences, before final in vivo testing.
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Affiliation(s)
- Isabelle Gautherot
- Virology Platform, Industrialization and Process Development, AVENTIS PASTEUR, Marcy l'Etoile, France.
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Long MB, Jones J, Sullenger BA, Byun J. Ribozyme-mediated revision of RNA and DNA. J Clin Invest 2003. [DOI: 10.1172/jci200319386] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Long MB, Jones JP, Sullenger BA, Byun J. Ribozyme-mediated revision of RNA and DNA. J Clin Invest 2003; 112:312-8. [PMID: 12897196 PMCID: PMC166303 DOI: 10.1172/jci19386] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Meredith B Long
- Department of Surgery, Duke University Medical Center, Box 2601, Durham, North Carolina 27710, USA.
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Affiliation(s)
- L Wright
- Hematology Research Laboratory, St. Vincent's Hospital, 384 Victoria St., Darlinghurst, New South Wales, 2010 Australia
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Giordano V, Jin DY, Rekosh D, Jeang KT. Intravirion targeting of a functional anti-human immunodeficiency virus ribozyme directed to pol. Virology 2000; 267:174-84. [PMID: 10662613 DOI: 10.1006/viro.1999.0112] [Citation(s) in RCA: 13] [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
Ribozymes are catalytic RNAs that offer several advantages as specific therapeutic genes against human immunodeficiency virus type 1 (HIV-1). Significant challenges in antiviral uses of ribozymes include (1) how best to express and to deliver this agent and (2) what is the best locale to target ribozymes against HIV-1 RNA. To explore the former, we have previously characterized several vector systems for efficient expression/delivery of anti-HIV-1 ribozymes (Dropulic et al., 1992; Dropulic and Jeang, 1994a; Smith et al., 1997). Here, to investigate an optimal locale for ribozyme-targeting, we asked whether it might be advantageous to direct ribozymes into HIV-1 virions as opposed to the more conventional approach of targeting ribozymes into infected cells. Two series of experiments were performed. First, we demonstrated that anti-HIV-1 ribozymes could indeed be packaged specifically and efficiently into virions. Second, we compared the virus suppressing activity of a packageable ribozyme with its counterpart, which cannot be packaged into HIV-1 virions. Our results showed that although both ribozymes cleaved HIV-1 genomic RNA in vitro with equivalent efficiencies, the former ribozyme demonstrated significantly higher virus-suppressing activity than the latter. These findings provide proof-of-principle that to combat productive HIV-1 replication, intravirion targeting is more effective than intracellular targeting of ribozymes.
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Affiliation(s)
- V Giordano
- Molecular Virology Section, Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, 9000 Rockville Pike, Bethesda, Maryland 20892-0460, USA
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Abstract
For the past several years, we have been engaged in developing a therapeutically effective strategy for disrupting gene function with reverse complementary, or so called 'antisense', oligodeoxynucleotides (ODN). This pursuit has focused on finding appropriate diseases in which to apply this approach, and suitable gene targets. Of the genes that we have targeted for disruption using the antisense ODN strategy (Clevenger et al., 1995; Gewirtz and Calabretta, 1988; Ratajczak et al., 1992c; Small et al., 1994) one that has been of particular interest, and one where therapeutically motivated disruptions are now in clinical trial, is the myb gene (reviewed in Lyon et al., 1994). These trials involve treatment of human leukemias. These diseases are a logical choice for developing oncogene targeted therapies because of easy access to tissues, and the abundance of knowledge about the cell and molecular biology of these diseases. Nevertheless, as will be touched on below, other malignancies have also been examined as models for Myb targeted therapy with some surprisingly encouraging results. Finally, while we have focused our efforts on the ODN strategy, I will allude briefly to other strategies for disrupting Myb function with therapeutic intent.
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Affiliation(s)
- A M Gewirtz
- Department of Internal Medicine, Institute for Human Gene Therapy, University of Pennsylvania School of Medicine, Philadelphia 19104, USA
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Abstract
The ability of certain enzymatic RNA molecules, or ribozymes, to site-specifically cleave other RNA molecules opens new vistas in gene therapy. Ribozymes can be designed to target specifically a particular mRNA and inhibit protein expression, permitting 'anti-gene' therapy. Here, we describe the progress towards developing ribozymes for use in gene therapy applications. Significant advances have been made in understanding ribozyme transcription unit design and the first clinical tests of ribozyme safety in humans are soon to be initiated.
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Affiliation(s)
- L A Couture
- Ribozyme Pharmaceuticals, Inc, Bouldar, CO 80301, USA
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