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Aslan Y, Tadjuidje E, Zorn AM, Cha SW. High-efficiency non-mosaic CRISPR-mediated knock-in and indel mutation in F0 Xenopus. Development 2017; 144:2852-2858. [PMID: 28694259 DOI: 10.1242/dev.152967] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 06/28/2017] [Indexed: 01/03/2023]
Abstract
The revolution in CRISPR-mediated genome editing has enabled the mutation and insertion of virtually any DNA sequence, particularly in cell culture where selection can be used to recover relatively rare homologous recombination events. The efficient use of this technology in animal models still presents a number of challenges, including the time to establish mutant lines, mosaic gene editing in founder animals, and low homologous recombination rates. Here we report a method for CRISPR-mediated genome editing in Xenopus oocytes with homology-directed repair (HDR) that provides efficient non-mosaic targeted insertion of small DNA fragments (40-50 nucleotides) in 4.4-25.7% of F0 tadpoles, with germline transmission. For both CRISPR/Cas9-mediated HDR gene editing and indel mutation, the gene-edited F0 embryos are uniformly heterozygous, consistent with a mutation in only the maternal genome. In addition to efficient tagging of proteins in vivo, this HDR methodology will allow researchers to create patient-specific mutations for human disease modeling in Xenopus.
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Affiliation(s)
- Yetki Aslan
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Emmanuel Tadjuidje
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Aaron M Zorn
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Sang-Wook Cha
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
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Abstract
The ability to manipulate gene expression in Xenopus oocytes and then generate fertilized embryos by transfer into host females has made it possible to rapidly characterize maternal signaling pathways in vertebrate development. Maternal mRNAs in particular can be efficiently depleted using antisense deoxyoligonucleotides (oligos), mediated by endogenous RNase-H activity. Since the microinjection of antisense reagents or mRNAs into eggs after fertilization often fails to affect maternal signaling pathways, mRNA depletion in the Xenopus oocyte is uniquely suited to assessing maternal functions. In this review, we highlight the advantages of using antisense in Xenopus oocytes and describe basic methods for designing and choosing effective oligos. We also summarize the procedures for fertilizing cultured oocytes by host-transfer and interpreting the specificity of antisense effects. Although these methods can be technically demanding, the use of antisense in oocytes can be used to address biological questions that are intractable in other experimental settings.
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Affiliation(s)
- Alissa M Hulstrand
- The University of Iowa, Department of Biology, 257 BB, Iowa City, IA 52242-1324, USA
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Abstract
This review examines the role that antisense oligonucleotides play in the treatment of superficial and muscle-invasive bladder cancer. The unique environment of the urinary bladder allows intravesical instillation of antisense oligonucleotides, and researchers have already demonstrated uptake of antisense oligonucleotides in models of bladder cancer. Second, proof of principle has been established by demonstrating downregulation of the antisense target mRNA and protein. Third, and most importantly from a therapeutic perspective, synergy between chemotherapy and antisense oligonucleotides has been shown in bladder cancer models in vitro and in vivo. The collective evidence points to a role for antisense oligonucleotides in the treatment of superficial and muscle-invasive bladder cancer in combination with existing treatment modalities.
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Affiliation(s)
- Anthony J Glackin
- Queen's University Belfast, Uro-oncology Group, Institute of Pathology, Grosvenor Road, Belfast, BT12 6BN, Northern Ireland.
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Kozu T, Sugio Y, Fukuyama T, Sueoka E, Otsuka T, Akagi K. Ribonuclease H attack of leukaemic fused transcripts AML1-MTG8 (ETO) by DNA/RNA chimeric hammerhead ribozymes. Genes Cells 2000; 5:637-47. [PMID: 10947849 DOI: 10.1046/j.1365-2443.2000.00353.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
BACKGROUND Catalytic anti-sense oligonucleotides might be useful tools for controlling specific gene expression. However, to obtain effective oligonucleotides of the desired function in vivo is still a difficult task. RESULTS To evaluate the usefulness of synthesized DNA/RNA hammerhead ribozymes targeting AML1-MTG8 (ETO) leukaemic fusion transcripts in vivo, we analysed their effects on cell growth and the mechanism of action using isolated cell nuclei. These ribozymes inhibited the growth of leukaemic cell lines expressing the AML1 -MTG8 and degraded AML1-MTG8 mRNA in isolated nuclei of these cells. However, the reactions gave rise to additional cleavage products. Systematic cleavage analyses using an anti-sense oligonucleotide array revealed that the cleavage was induced by endogenous RNase H at specific sites, in accordance with their calculated melting temperature (Tm) values. With suppression of RNase H by sulfhydryl agents, the DNA/RNA ribozyme had a ribozyme catalytic activity. In addition, the ribozymes and anti-sense oligonucleotides suppressed the AML1-MTG8 protein in the leukaemic cells. CONCLUSIONS The DNA/RNA ribozymes inhibited cell growth primarily via anti-sense effects, the main role of which was the activation of RNase H-digestion by their DNA arms. In addition, the isolated nuclei provided a useful assay system for modelling in vivo conditions for the quantitative evaluation of anti-sense/ribozyme activity.
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Affiliation(s)
- T Kozu
- Saitama Cancer Center Research Institute, Ina, Saitama 362-0806, Japan.
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8
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Giles RV, Spiller DG, Tidd DM. Chimeric oligodeoxynucleotide analogs: chemical synthesis, purification, and molecular and cellular biology protocols. Methods Enzymol 1999; 313:95-135. [PMID: 10595351 DOI: 10.1016/s0076-6879(00)13007-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- R V Giles
- Department of Haematology, University of Liverpool, Royal Liverpool University Hospital, United Kingdom
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Abstract
Traditionally, methods designed to impair translation through direct interactions with target messenger RNA (mRNA) have been designated as "antisense" strategies because of their reliance on the formation of reverse complementary (antisense) Watson-Crick base pairs between the targeting oligodeoxynucleotide (ODN) and the mRNA whose function is to be disrupted. Proof of putative "antisense effects," and other mechanistic studies, would be greatly facilitated by the ability to directly demonstrate hybridization between an antisense (AS) ODN and its mRNA target in vivo. In addition, evidence of AS activity by demonstrating reduced levels of RNA or protein or by showing cleaved target molecules would lend proof of the concept. In this article we discuss how AS ODN may be used to down-regulate target gene expression with an emphasis on those targets chosen for our investigations, and we summarize the methods employed for this type of study.
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Affiliation(s)
- D L Sokol
- Bristol-Myers Squibb (PRI), Pennington, New Jersey, USA
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Fraga D, Yano J, Reed MW, Chuang R, Bell W, Van Houten JL, Hinrichsen R. Introducing antisense oligodeoxynucleotides into Paramecium via electroporation. J Eukaryot Microbiol 1998; 45:582-8. [PMID: 9864848 DOI: 10.1111/j.1550-7408.1998.tb04553.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
A method utilizing electroporation to deliver antisense oligodeoxynucleotides into Paramecium tetraurelia has been developed. For these studies antisense oligonucleotides directed to different regions of the calmodulin mRNA were used. It was found that a pulse delivered at 150-250 V (375-625 V/cm field strength) for 3.9-4.2 ms using a 275 microF capacitor with resistance set at 13 Ohms was sufficient to achieve measurable incorporation of fluorescently-labeled oligodeoxynucleotides in up to 95% of the cells treated. Optimal parameters included using oligodeoxynucleotides of at least 12 bases in length with a 3' blocking group at a dose of around 10 microM. In addition, multiple oligodeoxynucleotides directed to the same target mRNA resulted in at least a 10-fold reduction in the dose of oligodeoxynucleotide required to achieve the desired effects. Taken together, these results indicate that the use of antisense oligodeoxynucleotides can be an easy and useful method for linking genes to specific functions in Paramecium tetraurelia. Finally, this report discusses how different 3' blocking groups and the use of combinations of oligodeoxynucleotides directed to different regions of the same target mRNA can help address concerns about specificity.
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Affiliation(s)
- D Fraga
- Fred Hutchinson Cancer Research Center, Division of Basic Sciences, Seattle, Washington.
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Abstract
Antisense molecules and ribozymes capture the imagination with their promise of rational drug design and exquisite specificity. However, they are far more difficult to produce than was originally anticipated, and their ability to eliminate the function of a single gene has never been proven. Furthermore, a wide variety of unexpected non-antisense effects have come to light. Although some of these side effects will almost certainly have clinical value, they make it hard to produce drugs that act primarily through true antisense mechanisms and complicate the use of antisense compounds as research reagents. To minimize unwanted non-antisense effects, investigators are searching for antisense compounds and ribozymes whose target sites are particularly vulnerable to attack. This is a challenging quest.
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Affiliation(s)
- A D Branch
- Department of Medicine, Mount Sinai School of Medicine, New York, NY 10029, USA
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Abstract
The high affinity of even relatively short sequences of DNA for their target mRNA suggests that antisense agents represent an ideal method of suppressing specific gene products both in vitro and in vivo. In experiments performed thus far, an effect on the target mRNA in cultured vascular cells and in the vessel wall can be documented. The in vitro activity, toxicity, and pharmacokinetic data of antisense oligonucleotides are encouraging, and the in vivo animal experiments demonstrating suppression of neointimal formation are very promising. If animals trials presently under way show continued suppression not only of intimal formation but also of loss of lumen caliber after a single application, then effective delivery of antisense oligonucleotides is a realistic possibility. Nevertheless, some words of caution regarding the use of antisense oligonucleotides are warranted. Potential nonspecific effects of antisense oligonucleotides should be carefully considered in studies in which antisense agents are used to define biological functions of specific genes. In particular, demonstration that the target mRNA has been suppressed does not prove that other sequences within the mRNA pool have not also been suppressed. Critical control measures include adding back the target mRNA or protein and demonstrating similar biological effects with antisense sequences, which also suppress target gene expression directed at different regions of the target mRNA. At the clinical level, the systemic effects of antisense oligonucleotides, the dosage required, the timing of administration compared with mechanical intervention, and the toxicity of breakdown products all need to be established. In addition, the most appropriate targets for antisense use in restenosis remain largely obscure. Indiscriminate suppression of cell-cycle genes or proto-oncogenes may be as acutely toxic as current anticancer chemotherapy if the site delivery is not completely localized. Furthermore, much of the clinical evidence suggests that restenosis is a chronic process, continuing to develop weeks to months after the procedure. If this is the case, then the current approaches that rely on a transient, local application of an antisense agent may fail. If, however, a target gene is identified that is specific to vascular tissue, then repeated administration of an antisense agent may be tolerated via a systemic route. This approach has proved successful in targeting mutated genes with little suppression of closely related genes and with minimal systemic toxicity. An alternative approach is to transfect the target tissue with a gene that makes it susceptible to systemic delivery of a drug that is not normally toxic to mammalian cells.(ABSTRACT TRUNCATED AT 400 WORDS)
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Affiliation(s)
- M R Bennett
- Department of Pathology, University of Washington, Seattle, USA
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Cierniewski CS, Babinska A, Swiatkowska M, Wilczynska M, Okruszek A, Stec WJ. Inhibition by modified oligodeoxynucleotides of the expression of type-1 plasminogen activator inhibitor in human endothelial cells. Eur J Biochem 1995; 227:494-9. [PMID: 7851428 DOI: 10.1111/j.1432-1033.1995.tb20415.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Antisense phosphodiester and phosphorothioate oligodeoxynucleotides (23-residue or 24-residue oligodeoxynucleotides) were constructed for sequences of type-1 plasminogen-activator-inhibitor mRNA to assess their capability to modulate type-1 plasminogen-activator-inhibitor-mediated fibrinolysis. Antisense oligodeoxynucleotides were targeted at the mRNA sequence coding a signal peptide, at a part of the reactive center Ile342-Pro349, and at an internally translated segment Asn265-Leu272. The effect of antisense oligonucleotides on the concentration of type-1 plasminogen activator inhibitor in conditioned media and human endothelial cells was determined by the activity test with fibrin as a substrate, and by immunoprecipitation after metabolic labelling of cells with [35S]methionine. Three phosphorothioate oligodeoxynucleotides were specifically inhibitory while phosphodiester oligodeoxynucleotides with the same sequence did not show any activity. Phosphorothioate oligodeoxynucleotides 2, 4 and 6 inhibited the synthesis of type-1 plasminogen activator inhibitor in endothelial cells in a time-dependent and concentration-dependent manner. These data suggest that antisense oligodeoxynucleotides may be useful in the design of antithrombolytic therapeutics.
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Affiliation(s)
- C S Cierniewski
- Department of Biophysics, Medical University in Lodz, Poland
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Giles RV, Spiller DG, Tidd DM. Detection of ribonuclease H-generated mRNA fragments in human leukemia cells following reversible membrane permeabilization in the presence of antisense oligodeoxynucleotides. Antisense Res Dev 1995; 5:23-31. [PMID: 7542045 DOI: 10.1089/ard.1995.5.23] [Citation(s) in RCA: 84] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The involvement of ribonuclease H (RNase H) in antisense phenomena in intact cells has, to date, only been adequately demonstrated for microinjected Xenopus systems. The significance of RNase H for the antisense effects of oligodeoxynucleotides observed in human and other mammalian cell cultures has remained obscure, in part because of inadequate analytic methods. In this report we show that the "reverse ligation-mediated PCR" (RL-PCR) procedure permits amplification of RNA fragments produced by oligodeoxynucleotide-directed RNase H activity. We have used this procedure to demonstrate RNase H-dependent antisense effects in irreversibly permeabilized (dead) cells and reversibly permeabilized (live) cells.
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Affiliation(s)
- R V Giles
- Department of Biochemistry, University of Liverpool, UK
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Pascolo E, Hudrisier D, Sproat B, Nguyen TT, Toulmé JJ. Relative contribution of photo-addition, helper oligonucleotide and RNase H to the antisense effect of psoralen-oligonucleotide conjugates, on in vitro translation of Leishmania mRNAs. Biochim Biophys Acta 1994; 1219:98-106. [PMID: 8086483 DOI: 10.1016/0167-4781(94)90251-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We investigated the properties of two antisense oligonucleotides, 11 alpha Pso and 14TMP, 11 and 14 nucleotides long, respectively, and conjugated to psoralen derivatives. These oligonucleotides were complementary to the mini-exon sequence of Leishmania amazonensis. Upon ultraviolet (UV) irradiation these oligomers were selectively cross-linked to DNA or RNA target sequences, either 14 or 35 nucleotides long. The yield of photo-addition was much lower on the longer targets than on the shorter ones, due to the presence of a hairpin structure. The co-addition of a helper oligonucleotide, whose binding site, on the 35-mer, was adjacent to that of the psoralen-derivatized antisense oligomer, improved the cross-linking efficiency. We then determined the effect of 14TMP on in vitro translation of Leishmania mRNA in cell-free extracts. Non-irradiated antisense oligonucleotide/mRNA complexes reduced the protein synthesis in wheat germ extract but not in rabbit reticulocyte lysate. Conversely, UV irradiation induced a 14TMP-dependent reduction of translation in reticulocyte lysate whereas the inhibition was not improved in the wheat germ extract. These results are discussed with respect to the involvement of RNase-H in the oligonucleotide-mediated effect on protein synthesis.
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Affiliation(s)
- E Pascolo
- Laboratoire de Biophysique Moléculaire, INSERM U386, Université de Bordeaux II, France
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Fakler B, Herlitze S, Amthor B, Zenner H, Ruppersberg J. Short antisense oligonucleotide-mediated inhibition is strongly dependent on oligo length and concentration but almost independent of location of the target sequence. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)33991-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Morgan R, Edge M, Colman A. A more efficient and specific strategy in the ablation of mRNA in Xenopus laevis using mixtures of antisense oligos. Nucleic Acids Res 1993; 21:4615-20. [PMID: 8233799 PMCID: PMC311199 DOI: 10.1093/nar/21.19.4615] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Previously, antisense oligodeoxyribonucleotides (oligos) have been used to ablate specific mRNAs from the maternal RNA pool of Xenopus laevis oocytes. However, this strategy is limited by the dose of oligo which can be used and the fact that 100% cleavage of the target RNA is rare. Further, non-specific cleavage of other RNAs can also occur. We demonstrate that the use of several oligos against the histone H4 RNA results in a marked improvement in the efficiency of target degradation, due to synergistic action between oligos and the existence of RNA in at least two different secondary structures. We show, by using a set of overlapping oligos complementary to the entire H4 RNA, that the amount of oligo required for efficient target ablation is greatly lowered and non-specific effects are reduced.
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Affiliation(s)
- R Morgan
- School of Biochemistry, University of Birmingham, UK
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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 Res Dev 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Abstract
Antisense oligonucleotides are widely used as inhibitors of gene expression in cultured cells and have been proposed as potential therapeutic agents, but it is not known to what extent they are specific for their intended target RNAs. Statistical considerations indicate that if oligonucleotides can form hybrids with mRNA molecules in vivo by means of short or imperfect regions of complementarity, then the specificity of oligonucleotides as antisense reagents will be greatly compromised. We have used Xenopus oocytes as a model system in which to investigate the potential specificity of antisense oligonucleotides in vivo. We injected perfect and partially matched antisense oligonucleotides into oocytes and measured the resulting degradation of the target RNA in each case. On the basis of the extent to which antisense oligonucleotides can cause cleavage of RNAs at imperfectly matched target sites, we conclude that in this system it is probably not possible to obtain specific cleavage of an intended target RNA without also causing at least the partial destruction of many nontargeted RNAs.
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Affiliation(s)
- T M Woolf
- Department of Biochemistry and Molecular Biology, Harvard University, Cambridge, MA 02138
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Abstract
Calcium-dependent glutamate secretion was reconstituted in Xenopus oocytes by injecting the oocyte with total rat cerebellar messenger RNA (mRNA). Co-injection of total mRNA with antisense oligonucleotides to synaptophysin message decreased the expression of synaptophysin in the oocyte and reduced the calcium-dependent secretion. A similar effect on secretion was observed for oocytes injected with total mRNA together with an antibody to rat synaptophysin. These results indicate that synaptophysin is necessary for transmitter secretion and that the oocyte expression system may be useful for dissecting the molecular events associated with the secretory process.
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Affiliation(s)
- J Alder
- Department of Biological Sciences, Columbia University, New York, NY 10027
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Giles RV, Tidd DM. Increased specificity for antisense oligodeoxynucleotide targeting of RNA cleavage by RNase H using chimeric methylphosphonodiester/phosphodiester structures. Nucleic Acids Res 1992; 20:763-70. [PMID: 1371864 PMCID: PMC312015 DOI: 10.1093/nar/20.4.763] [Citation(s) in RCA: 112] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
One of the inherent problems in the use of antisense oligodeoxynucleotides to ablate gene expression in cell cultures is that the stringency of hybridization in vivo is not subject to control and may be sub-optimal. Consequently, phosphodiester or phosphorothioate antisense effectors and non-targeted cellular RNA may form partial hybrids which are substrates for RNase H. Such processes could promote the sequence dependent inappropriate effects recently reported in the literature. We have attempted to resolve this problem by using chimeric methylphosphonodiester/phosphodiester oligodeoxynucleotides. In contrast to the extensive RNA degradation observed with all-phosphodiester oligodeoxynucleotides, highly modified chimeric antisense effectors displayed negligible, or undetectable, cleavage at non-target sites without significantly impaired activity at the target site. We also note that all of the all-phosphodiester oligodeoxynucleotides tested demonstrated inappropriate effects, and that such undesirable activity could vary widely between different sequences.
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Affiliation(s)
- R V Giles
- Department of Biochemistry, University of Liverpool, Merseyside, UK
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Affiliation(s)
- K E Johnson
- Department of Anatomy, George Washington University Medical Center, Washington, D.C. 20037
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Abstract
Antisense oligodeoxynucleotides [oligo(dN)] have the ability to enter living cells and block the expression of specific genes. However, little is known about the mechanism of cellular uptake of oligo(dN). We have found that oligo(dN) can bind to the cell membranes of eukaryotic cells with much greater efficiency under acidic conditions (pH 4.0-4.5) than at neutral pH. The binding appears to be specific to poly nucleic acids since various sizes of oligo(dN), DNA and RNA, but not mononucleotides, compete for the binding. We have identified a 34 kDa membrane protein from T-cells, which binds to oligo(dT) cellulose at pH 4.5 and can be eluted at pH 7.5. This protein fraction blocked the binding of oligo(dN) to living T-cells in a competitive fashion. Our results suggest that eukaryotic cells have a receptor for oligo(dN) at acidic pH and that the 34 kDa dalton protein on the cell membrane may mediate such binding.
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Affiliation(s)
- G Goodarzi
- Department of Medical Microbiology/Immunology, Southern Illinois University School of Medicine, Springfield 62708
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Kibler-Herzog L, Zon G, Uznanski B, Whittier G, Wilson WD. Duplex stabilities of phosphorothioate, methylphosphonate, and RNA analogs of two DNA 14-mers. Nucleic Acids Res 1991; 19:2979-86. [PMID: 1711677 PMCID: PMC328260 DOI: 10.1093/nar/19.11.2979] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The duplex stabilities of various phosphorothioate, methylphosphonate, RNA and 2'-OCH3 RNA analogs of two self-complementary DNA 14-mers are compared. Phosphorothioate and/or methylphosphonate analogs of the two sequences d(TAATTAATTAATTA) [D1] and d(TAGCTAATTAGCTA) [D2] differ in the number, position, or chirality (at the 5' terminal linkage) of the modified phosphates. Phosphorothioate derivatives of D1 are found to be less destabilized when the linkage modified is between adenines rather than between thymines. Surprisingly, no base sequence effect on duplex stabilization is observed for any methylphosphonate derivatives of D1 or D2. Highly modified phosphorothioates or methylphosphonates are less stable than their partially modified counterparts which are less stable than the unmodified parent compounds. The 'normal' (2'-OH) RNA analog of duplex D1 is slightly destabilized, whereas the 2'-OCH3 RNA derivative is significantly stabilized relative to the unmodified DNA. For the D1 sequence, at approximately physiological salt concentration, the order of duplex stability is 2'-OCH3 RNA greater than unmodified DNA greater than 'normal' RNA greater than methylphosphonate DNA greater than phosphorothioate DNA. D2 and the various D2 methylphosphonate analogs investigated all formed hairpin conformations at low salt concentrations.
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Abstract
The methods described here of fertilizing stage VI oocytes are lengthy and quite difficult techniques. They would become more attractive if the success rate (i.e., the number of fertilizations compared to the numbers of matured oocytes) could be improved. An important step toward this for the host transfer technique would be to monitor carefully the status of mature Xenopus females ovaries in relation to cyclical HCG stimulation, so that we could predict more accurately whether stage VI oocytes are fertilizable. The in vitro technique would obviously be improved if oocytes could be fertilized without removing their membranes, perhaps by using oviduct extracts. So far, this approach has had only limited success. It seems that the rewards of using these techniques could be great, in terms of understanding the maternal contribution to development. Although our experiments have not yet shown that oocyte injection of DNA has any advantage over egg injection, it is clear that it is possible to make "mRNA-minus mutants" by this approach. In the message depletion experiments mentioned here, we targeted the cleavage of an mRNA which is of low abundance in the full grown oocyte, but preliminary experiments have shown that we can deplete more abundant messages and produce specific phenotypes. Of course such experiments need to be controlled to show that the effect is specific, and the best proof that this is the case is to rescue the effect with injection of the appropriate mRNA. Finally, it seems likely that the method can be used to study the function of both localized molecules, such as the putative primordial germ cell (PGC) or dorsal determinants, and more ubiquitous molecules such as cytoskeletal elements.
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Affiliation(s)
- J Heasman
- Department of Zoology, Cambridge University, England
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Ao A, Erickson RP, Bevilacqua A, Karolyi J. Antisense inhibition of beta-glucuronidase expression in preimplantation mouse embryos: a comparison of transgenes and oligodeoxynucleotides. Antisense Res Dev 1991; 1:1-10. [PMID: 1822245 DOI: 10.1089/ard.1991.1.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Using as a model the inhibition of beta-glucuronidase expression in preimplantation embryos, we have compared injections of transgenes directing the synthesis of antisense RNA and antisense oligodeoxynucleotides to our previous results with cytoplasmic injections of antisense RNAs. Pronuclear injection of an antisense DNA construct containing 1.4 kb of coding region of beta-glucuronidase fused to the mouse metallothionein I promoter results in transient inhibition of gene expression in preimplantation mouse embryos. Pronuclear injection of a smaller antisense DNA construct, overlapping the start codon, failed to inhibit gene expression. Injection of two 20-mer antisense oligodeoxynucleotides, one complementary to sequences including the initiation codon and the second complementary to exon 7 sequences of the beta-glucuronidase gene, failed to inhibit gene expression. In addition, cultures of embryos in the presence of antisense oligodeoxynucleotides had no effect on gene activity. Using radiolabeled oligomers added to the culture medium, we found poor uptake of oligodeoxynucleotides by embryos.
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Affiliation(s)
- A Ao
- Department of Human Genetics, University of Michigan School of Medicine, Ann Arbor 48109
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Christian JL, Kelly GM, Moon RT. Chapter 7 Dominant Mutations of Cytoskeletal Proteins in Xenopus Embryos. Ordering the Membrane-Cytoskeleton Trilayer 1991. [DOI: 10.1016/s0070-2161(08)60784-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Affiliation(s)
- C Prives
- Department of Biological Sciences, Columbia University, New York, New York 10027
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Baker C, Holland D, Edge M, Colman A. Effects of oligo sequence and chemistry on the efficiency of oligodeoxyribonucleotide-mediated mRNA cleavage. Nucleic Acids Res 1990; 18:3537-43. [PMID: 2362806 PMCID: PMC331008 DOI: 10.1093/nar/18.12.3537] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Using the endogenous histone H4 mRNA of Xenopus oocytes as a target, we have previously shown that 20mer oligos complementary to different parts of this sequence vary in their effectiveness at causing mRNA cleavage in vivo, and that some of the RNA can never be cleaved. In this paper we show that the resistant RNA is not localised within one part of the oocyte, and that the relative resistance in vivo of endogenous or synthetic H4 mRNA to the different oligos is preserved in an in vitro assay system using deproteinised RNA. If an prior annealing step is included in vitro, all resistance is abolished. Chemical modification of one oligo by end substitution with methylphosphonate or phosphorothioate residues did not improve cleavage efficiency. Oligos with complete phosphorothioate substitution cause slower cleavage in vivo but persist for longer. Consequently phosphorothioate oligos are effective at lower doses than phosphodiester ones, provided that the incubation time is long enough (24 hours). Increasing oligo length from 20nt to 30nt increases phosphorothioate oligo efficiency over long reaction times in vivo, but decreases efficiency during short in vitro assays. Similar increases in length did not affect phosphodiester oligo performance in vivo, but caused a decrease in efficiency in vitro which was overcome by an annealing step.
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Affiliation(s)
- C Baker
- School of Biochemistry, University of Birmingham, UK
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Affiliation(s)
- C Hélène
- Muséum National d'Histoire Naturelle, INSERM U201-CNRS UA.481, Paris, France
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Woolf TM, Jennings CG, Rebagliati M, Melton DA. The stability, toxicity and effectiveness of unmodified and phosphorothioate antisense oligodeoxynucleotides in Xenopus oocytes and embryos. Nucleic Acids Res 1990; 18:1763-9. [PMID: 1692405 PMCID: PMC330594 DOI: 10.1093/nar/18.7.1763] [Citation(s) in RCA: 134] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The properties of antisense phosphorothioate and unmodified oligodeoxynucleotides have been studied in Xenopus oocytes and embryos. We find that phosphorothioates, like unmodified oligodeoxynucleotides, can degrade Vg1 mRNA in oocytes via an endogenous RNase H-like activity. In oocytes, phosphorothioate oligodeoxynucleotides are more stable than unmodified oligodeoxynucleotides and are more effective in degrading Vg1 mRNA. In embryos, neither unmodified nor phosphorothioate deoxyoligonucleotides were effective in degrading Vg1 message at sub-toxic doses.
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Affiliation(s)
- T M Woolf
- Department of Biochemistry and Molecular Biology, Harvard University, Cambridge
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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