Quantitative hybridization-arrest of mRNA in Xenopus oocytes using single-stranded complementary DNA or oligonucleotide probes

Invention and Early History of Gapmers

Gapmers are antisense oligonucleotides composed of a central DNA segment flanked by nucleotides of modified chemistry. Hybridizing with transcripts by sequence complementarity, gapmers recruit ribonuclease H and induce target RNA degradation. Since its concept first emerged in the 1980s, much work has gone into developing gapmers for use in basic research and therapy. These include improvements in gapmer chemistry, delivery, and therapeutic safety. Gapmers have also successfully entered clinical trials for various genetic disorders, with two already approved by the U.S. Food and Drug Administration for the treatment of familial hypercholesterolemia and transthyretin amyloidosis-associated polyneuropathy. Here, we review the events surrounding the early development of gapmers, from conception to their maturity, and briefly conclude with perspectives on their use in therapy.

Modulation of RNA function by oligonucleotides recognizing RNA structure

Numerous RNA structures are responsible for regulatory processes either because they constitute a signal, like the hairpins or pseudoknots involved in ribosomal frameshifting, or because they are binding sites for proteins such as the trans-activating responsive RNA element of the human immunodeficiency virus whose binding to the viral protein Tat and cellular proteins allows full-length transcription of the retroviral genome. Selective ligands able to bind with high affinity to such RNA motifs may serve as tools for dissecting the molecular mechanisms in which they are involved. Such ligands might also constitute prototypes of therapeutic agents when RNA structures play a role in the expression of dysfunctional genes or in the multiplication of pathogens. Different classes of ligands (aminoglycosides, interacalating agents, peptides) are of interest to this aim. However, oligonucleotides deserve particular consideration. They have been extensively used in the frame of the antisense strategy. The apparent simplicity of this rational approach is, at first sight, very attractive. Indeed, numerous successful studies have been published describing the efficient inhibition of translation, splicing, or reverse transcription in cell-free systems, in cultured cells, or in vivo by oligomers complementary to an RNA region. However, RNA structures restrict the access of the target site to the antisense sequence: The competition between the intramolecular association of RNA regions weakens or even abolishes the antisense effect. Various possibilities have been developed to circumvent this limitation. This includes both rational and combinatorial strategies. High-affinity oligomers were designed to invade the RNA structure. Alternatively, triplex-forming oligonucleotides (TFO) and aptamers may recognize the folded RNA motif. Whereas the use of TFOs is rather limited owing to the strong sequence constraints for triple-helix formation, in vitro selection offers a way to explore vast oligoribo or oligodeoxyribo libraries to identify strong, selective oligonucleotide binders. The candidates (aptamers) selected against the TAR RNA element of HIV-1, which form stable loop-loop (kissing) complexes with the target, provide interesting examples of oligonucleotides recognizing a functional RNA structure through an important contribution of tertiary interactions.

Modified mRNA rescue of maternal CK1/8 mRNA depletion in Xenopus oocytes

This work addresses two issues, the use of antisense oligodeoxynucleotides to deplete specific mRNAs in Xenopus oocytes to analyze their functions during development and the role of cytokeratin filaments in cells of the early Xenopus embryo. We have shown previously that depletion of cytokeratin CK1/8 mRNA causes defects in the early embryo. In this study, we show that the oligos, modified with phosphoramidate linkages to improve stability, are capable of degrading exogenous mRNA up to 27 hours after injection in the oocyte. For this reason, the phenotype could not be rescued by injection of a synthetic CK1/8 mRNA. However, modification of the synthetic CK1/8 mRNA, which prevents annealing of the antisense oligonucleotide used for depleting the endogenous CK1/8 mRNA, did result in the rescue of the CK1/8 depletion phenotype. These results demonstrate that the phenotype observed after depletion of the CK1/8 mRNA is truly caused by the lack of CK1/8 protein. Injection of the closely related type II cytokeratin (CK55) did not result in the same level of rescue of the CK1/8 depletion phenotype, suggesting that structurally similar members of the cytokeratin family, expressed at different stages of development, cannot substitute for each other in the early embryo.

Role of ubiquitin carboxyl terminal hydrolase in the differentiation of human acute lymphoblastic leukemia cell line, Reh

We have previously demonstrated that the phorbol ester 12-O-tetradecanoylphorbol 13-acetate (TPA), induces differentiation of the acute lymphoblastic leukemia cell line, Reh, to a mature non-dividing state. Associated with this differentiation is the expression of ubiquitin carboxyl terminal hydrolase (UCH-L1). To investigate the role of UCH-L1 in TPA-induced Reh differentiation and apoptosis, molecular and chemical inhibition was used. Molecularly, a sequence-specific antisense oligodeoxynucleotide (AODN) directed against UCH-L1 transcript was used to inhibit the expression of the gene. In addition, its complementary sense oligodeoxynucleotide (SODN) was used to indicate the specificity of AODN action. Chemically, sodium borohydride (NaBH4), an inhibitor of UCH-L, was used to block the transcript product. TPA-induced changes in Reh cell growth and morphology, UCH-L1 protein expression, apoptosis contour, surface phenotype, and enzymatic profile were assessed in the presence or absence of NaBH4, AODN or SODN. As previously reported, TPA induced Reh cells to differentiate into monocytoid B lymphocytes and stimulated the apoptotic pathway. However, adding NaBH4 or AODN inhibited the TPA effect on all parameters measured except apoptosis. The sequence in which NaBH4 or AODN were added in relation to TPA did not affect any of the response variables measured. The use of SODN did not influence any of the parameters measured, indicating the specificity of the action. Thus, we conclude that UCH-L1 is involved in the differentiation process of the lymphoblastic leukemia cell line, Reh. Our data suggest that TPA-induced apoptosis of Reh cells has a separate pathway from that of differentiation or that UCH-L1 expression is independent of the apoptotic pathway.

Specificity of antisense oligonucleotides in vivo

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.

Antisense c-myc oligodeoxyribonucleotide cellular uptake

Antisense oligonucleotides have therapeutic potential as inhibitors of gene expression. However, the mechanism by which an intact oligonucleotide reaches the intracellular site of action is unknown. In this study, we use an oligodeoxyribonucleotide 21-mer complementary to the translation initiation codon of the c-myc protooncogene to study the mechanism of oligonucleotide uptake and internalization into Rauscher Red 5-1.5 cells. We find trypsin-sensitive and trypsin-insensitive surface binding, in addition to internalization. Uptake is partially energy dependent and inhibited by charged molecules, including DNA, ATP, a random sequence oligonucleotide, and dextran sulfate. Uptake does not appear to occur via a traditional receptor-mediated uptake pathway because chloroquine, monensin, and phenylarsine oxide pretreatment does not significantly decrease internalization. An anion channel inhibitor, SITS, and the salts, NaCl, Na2SO4, and NH4Cl, significantly decrease oligonucleotide uptake. Whether uptake occurs via a channel or a novel uptake mechanism is still unknown. A model is proposed which reasonably simulates the experimental data.

Antisense inhibition of beta-glucuronidase expression in preimplantation mouse embryos: a comparison of transgenes and oligodeoxynucleotides

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.

Gene expression in Xenopus oocytes

1. Gene expression in Xenopus oocytes is now an integral part of many molecular cloning strategies. 2. For some genes, such as those encoding the ion channels, this system has emerged as the only available means to authenticate and examine the biological activities of the cloned DNA. 3. This review discusses some of the current applications of Xenopus oocytes in modern molecular biology.

Requirement of ets-2 expression for Xenopus oocyte maturation

A molecular clone of the Xenopus laevis ets-2 gene was isolated from an oocyte complementary DNA library. The amount of messenger RNA (mRNA) in each oocyte or embryo was almost constant during oogenesis and was maintained until the blastula stage of embryonic development, indicating that the observed 3.2-kilobase transcript is a maternal message. The only normal adult tissue in which ets-2 mRNA was detected was the ovary. Injection of antisense oligonucleotides homologous to the ets-2 sequence into oocytes led to degradation of the mRNA and blocked hormone-induced germinal vesicle breakdown. The ets-2 product is thus required for the meiotic maturation of Xenopus oocytes.

Primary structure of Torpedo marmorata chloride channel isolated by expression cloning in Xenopus oocytes

A complementary DNA encoding a voltage-gated chloride channel from Torpedo marmorata electric organ was cloned by expressing hybrid-depleted messenger RNA in Xenopus oocytes. The predicted protein has a sequence of 805 amino acids containing several putative membrane-spanning domains. Expression of the protein in Xenopus oocytes shows that it is sufficient for channel function.

Amylase synthesis as a simple model system for translation and hybrid arrest in Xenopus oocytes

A human alpha-amylase-encoding cDNA has been cloned in a transcription vector. When messenger RNA (mRNA) made in vitro from this construct was injected into Xenopus oocytes, amylase (AMY) activity was detected both in oocyte homogenates and in the incubation medium, indicating that the oocyte machinery correctly translated and processed the protein. Because AMY activity is easy to detect with a blue-starch assay, this expression system was used to determine the parameters of antisense oligodeoxyribonucleotide (oligo) inhibition of translation in the oocytes. Unique oligos complementary to the AMY mRNA sequence were effective in arresting translation, at approximately stoichiometric levels. Mixed oligos also inhibited translation, at levels that suggest that some mismatches may be tolerated in the formation of DNA-RNA hybrids. The AMY system provides a convenient probe of oocyte protein synthesis and processing machinery and can serve as a control substrate in investigations of other mRNAs.

Interleukin 1 induces beta-endorphin secretion via Fos and Jun in AtT-20 pituitary cells

Previous work had shown that interleukin 1 (IL-1), after a long period of treatment, stimulates beta-endorphin release and potentiates the effects of secretagogues in AtT-20 cells, a mouse anterior pituitary cell line. Treatment of AtT-20 cells with IL-1 induced a transient and early stimulation of mRNA expression by both immediate-early protooncogenes Fos and Jun (mouse c-fos and c-jun). The effect appeared within 30 min, and returned to basal levels after 2 hr. Desensitization of protein kinase C by phorbol ester pretreatment had no effect on the ability of IL-1 to induce Fos and Jun mRNA expression. Somatostatin, an inhibitor of cAMP and beta-endorphin secretion, did not reduce the IL-1 effect on Fos and Jun mRNA expression. Addition to AtT-20 cells of antisense oligonucleotides to Fos and Jun abolished the secretion induced by IL-1. These results indicate that immediate-early signals Fos and Jun are involved in IL-1-induced beta-endorphin secretion in AtT-20 cells.

Sequence dependent effects in methylphosphonate deoxyribonucleotide double and triple helical complexes

Deoxyribooligonucleotides containing 19 repeating bases of A, T or U were prepared with normal phosphodiester (dA19, dT19, dU19) or methylphosphonate (dA*19, dT*19, dU*19) linkages. Complexes of these strands have been investigated at 1:1 and 1:2 molar ratios (purine:pyrimidine) by thermal melting and gel electrophoresis. There are dramatic sequence dependent differences in stabilities of complexes containing methylphosphonate strands. Duplexes of dA*19 with dT19 or dU19 have sharp melting curves, increased Tm values, and slopes of Tm versus log (sodium ion activity) plots reduced by about one half relative to their unmodified 'parent' duplexes. Duplexes of dA19 with either dT*19 or dU*19, however, have broader melting curves, reduced Tm values at most salt concentrations and slopes of less than one tenth the values for the unmodified duplexes. Duplex stabilization due to reduced phosphate charge repulsion is offset in the pyrimidine methylphosphonate complexes by steric and other substituent effects. Triple helical complexes with dA19 + 2dT19 and dA19 + 2dU19, which can be detected by biphasic melting curves and gel electrophoresis, are stable at increased Na+ or Mg+2 concentrations. Surprisingly, however, no triple helix forms, even at very high salt concentrations, when any normal strand(s) is replaced by a methylphosphonate strand. Since triple helical complexes with methylphosphonates have been reported for shorter oligomers, inhibition with larger oligomers may vary due to their length and extent of substitution.

Identification of G protein-coupled receptors by RNase H-mediated hybrid depletion using Xenopus laevis oocytes as expression system

A method has been developed for rapidly identifying putative G protein-coupled receptors isolated initially as small cDNA fragments, following reverse transcription and polymerase chain reaction (PCR) amplification of mRNA. The method is based upon the use of synthetic oligonucleotides deduced from the sequence of the amplified receptor fragments, to direct a RNase H-mediated specific degradation of hybrids formed between the oligonucleotides and the corresponding receptor-encoding mRNA. Loss of an agonist-dependent receptor response in the Xenopus laevis oocyte expression system identifies the amplified receptor fragment. Taking in vitro synthesised serotonin HT2-receptor (SR)-encoding mRNA as a model, it was shown that following incubation with RNase H and SR antisense oligonucleotides, injection of this message no longer caused the acquisition of agonist-dependent membrane currents in voltage-clamped oocytes. In contrast, when corresponding sense oligonucleotides were used, the serotonin-evoked membrane responses in oocytes were acquired as normal. The method should allow the identification of receptors which can functionally be expressed and measured in Xenopus oocytes.

Inhibition of simian virus 40 DNA replication in CV-1 cells by an oligodeoxynucleotide covalently linked to an intercalating agent

An octathymidylate covalently linked via its 3'-end to an acridine derivative inhibited the cytopathic effect of Simian Virus SV40 on CV-1 cells in culture. Control experiments revealed that this effect was virus-specific and did not arise as a result of oligonucleotide degradation by nucleases. A photoactive probe was covalently attached to the 5'-end of the oligonucleotide-acridine conjugate. Upon UV-irradiation, photocrosslinking was shown to occur at the A. T-rich region within the viral origin of replication. A local triple helix can form at moderate salt concentrations with two octathymidylate-acridine conjugates bound to the octaadenylate sequence. Alternatively the octathymidylate-acridine conjugate can bind to the major groove of duplex DNA forming a local triple helix. Different mechanisms are discussed to explain the inhibition of viral DNA replication.

Rat brain expresses a heterogeneous family of calcium channels

We describe the isolation and characterization of several rat brain cDNAs that are homologous to the alpha 1 subunit of heart and skeletal muscle dihydropyridine-sensitive Ca channels. Northern blot analysis of 32 cDNAs shows that they can be grouped into four distinct classes (A, B, C, and D), each corresponding to a distinct hybridization pattern of brain mRNAs. Southern blot and DNA sequencing suggest that each class of cDNA represents a distinct gene or gene family. In the regions sequenced, the rat brain class C and D gene products share approximately 75% amino acid identity with the rabbit skeletal muscle Ca channel. In addition, the class C polypeptide is almost identical to the rabbit cardiac Ca channel (97% identity). In contrast, the rat brain class A and B cDNAs are more distantly related to dihydropyridine-sensitive Ca channels (47-64% amino acid identity) and to the brain class C and D genes (51-55% amino acid identity). To examine the functional significance of the isolated brain cDNAs, hybrid depletion experiments were performed in Xenopus oocytes. Antisense oligonucleotides against class A and B cDNAs each partially inhibited, and a class C oligonucleotide almost fully inhibited, the expression of Ba current in rat brain mRNA injected oocytes; but none of the oligonucleotides affected the expression of voltage-gated Na or K conductances. The clone characterization and sequencing results demonstrate that a number of distinct, yet related, voltage-gated Ca-channel genes are expressed in the brain. The antisense oligonucleotide experiments specifically show that one or several of the Ca-channel classes are related to the Ca channels observed in rat brain mRNA injected oocytes.

The stability, toxicity and effectiveness of unmodified and phosphorothioate antisense oligodeoxynucleotides in Xenopus oocytes and embryos

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.

Ribonucleases H of retroviral and cellular origin

Ribonucleases H (RNases H) are enzymes which catalyse the hydrolysis of the RNA-strand of an RNA-DNA hybrid. Retroviral reverse transcriptases possess RNase H activity in addition to their RNA- as well as DNA-dependent DNA-polymerizing activity. These enzymes transcribe the viral single stranded RNA-genome into double stranded DNA, which then can be handled by the host cell like one of its own genes. Various, sometimes highly repeated, sequences related to retroviruses and like these encompassing two separate domains, one of which potentially codes for a DNA polymerizing, the other for an RNase H activity, are found in genomes of uninfected cells. In addition proteins coded for by cellular genes (e.g. from E. coli and from yeast) are known, which exhibit RNase H activity, the biological function of which is not fully understood. In the light of these facts the question of whether retroviral RNases H could be promising targets for antiviral drugs is discussed.

The c-mos proto-oncogene product is a cytostatic factor responsible for meiotic arrest in vertebrate eggs

The c-mos proto-oncogene product, pp39mos, is present in unfertilized Xenopus eggs, and disappears on fertilization. Microinjection of synthetic mos RNA into two-cell embryos induces cleavage arrest at metaphase. By contrast, egg cytosol extracts, when immunodepleted of endogenous pp39mos, lose their cleavage-arresting activity in injected embryos. These results demonstrate that Mos protein is the cytostatic factor CSF, long known as an endogenous meiotic inhibitor in vertebrate eggs.

Discrimination of heterogenous mRNAs encoding strychnine-sensitive glycine receptors in Xenopus oocytes by antisense oligonucleotides

Three synthetic oligodeoxynucleotides complementary to different parts of an RNA encoding a glycine receptor subunit were used to discriminate heterogenous mRNAs coding for glycine receptors in adult and neonatal rat spinal cord. Injection of the three antisense oligonucleotides into Xenopus oocytes specifically inhibited the expression of glycine receptors by adult spinal cord mRNA. In contrast, the antisense oligonucleotides were much less potent in inhibiting the expression of glycine receptors encoded by neonatal spinal cord mRNA. Northern blot analysis revealed that the oligonucleotides hybridized mostly to an adult cord transcript of approximately 10 kilobases in size. This band was also present in neonatal spinal cord mRNA but its density was about one-fourth of the adult cord message. There was no intense band in the low molecular weight position (approximately 2 kilobases), the existence of which was expected from electrophysiological studies with size-fractionated mRNA of neonatal spinal cord. Our results suggest that in the rat spinal cord there are at least three different types of mRNAs encoding functional strychnine-sensitive glycine receptors.

Antisense oligonucleotide inhibition of encephalomyocarditis virus RNA translation

We report the inhibition of encephalomyocarditis virus (EMCV) RNA translation in cell-free rabbit reticulocyte lysates by antisense oligonucleotides (13-17-base oligomers) complementary to (a) the viral 5' non-translated region, (b) the AUG start codon and (c) the coding sequence. Our results demonstrate that the extent of translation inhibition is dependent on the region where the complementary oligonucleotides bind. Non-complementary and 3'-non-translated-region-specific oligonucleotides had no effect on translation. A significant degree of translation inhibition was obtained with oligonucleotides complementary to the viral 5' non-translated region and AUG initiation codon. Digestion of the oligonucleotide:RNA hybrid by RNase H did not significantly increase translation inhibition in the case of 5'-non-translated-region-specific and initiator-AUG-specific oligonucleotides; in contrast, RNase H digestion was necessary for inhibition by the coding-region-specific oligonucleotide. We propose that (a) 5'-non-translated-region-specific oligonucleotides inhibit translation by affecting the 40S ribosome binding and/or passage to the AUG start codon, (b) AUG-specific oligonucleotides inhibit translation initiation by inhibiting the formation of an active 80S ribosome and (c) the coding-region-specific oligonucleotide does not prevent protein synthesis because the translating 80S ribosome can dislodge the oligonucleotide from the EMCV RNA template.

Thermodynamic parameters of the binding of an oligo-alpha-thymidylate to its complementary oligo-beta-adenylate sequences

The temperature dependence of the formation of a double-stranded complex between an oligo-alpha-thymidylate and its complementary sequence, beta-riboadenylate or beta-deoxyriboadenylate, was studied using circular dichroism and compared to the duplexes formed using an oligo-beta-thymidylate. Analysis of the melting profiles allowed us to determine the thermodynamic parameters (delta H, delta S and delta G) associated with the formation of the various duplexes. The order of the stability was found: alpha-dT:beta-dA approximately alpha-dt:beta-rA greater than beta-dT:beta-dA greater than beta-dT:beta-rA.

Mouse Mos protooncogene product is present and functions during oogenesis

We have identified the mouse Mos-encoded protein product, p39mos, in maturing mouse oocytes and have shown that it is indistinguishable from the product expressed in Mos-transformed NIH 3T3 cells. p39mos is detected in oocytes arrested in the first meiotic prophase, during germinal-vesicle breakdown, metaphase I, anaphase I, and in ovulated eggs. We show that microinjection of three different Mos antisense (but not sense) oligodeoxyribonucleotides into germinal vesicle-stage oocytes prevents first polar-body emission and therefore interrupted the normal progression of meiosis. These results show that in mouse oocytes, as in the amphibian Xenopus [Sagata, N., Oskarsson, M., Copeland, T., Brumbaugh, J. & Vande Woude, G.F. (1988) Nature (London) 335, 519-525], the product of Mos is necessary for normal meiotic maturation.

Inhibition of DNA synthesis by cross-linking the template to platinum-thiol derivatives of complementary oligodeoxynucleotides

Unsubstituted oligodeoxynucleotides, or oligodeoxynucleotides linked to poly-(L)-lysine, when hybridized to a 322 base long template, did not inhibit the production of full length DNA copies by the Klenow fragment of E. coli DNA polymerase I. However, synthesis was inhibited if the cysteamine derivative of the same oligomer was cross-linked to the template via PtII. Truncated products were formed by termination of DNA synthesis a small number of bases upstream from the 5'-end of the cross-linked oligomer. AMV reverse transcriptase behaved similarly but was also slightly inhibited by the hybridized oligomer or its poly-lysine derivative.

Comparative inhibition of rabbit globin mRNA translation by modified antisense oligodeoxynucleotides

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.

Specific block of calcium channel expression by a fragment of dihydropyridine receptor cDNA

Although the structure of rabbit skeletal muscle dihydropyridine (DHP) receptor, deduced from cDNA sequence, indicates that this protein is the channel-forming subunit of voltage-dependent calcium channel (VDCC), no functional proof for this prediction has been presented. Two DNA oligonucleotides complementary to DHP-receptor RNA sequences coding for putative membrane-spanning regions of the DHP receptor specifically suppress the expression of the DHP-sensitive VDCC from rabbit and rat heart in Xenopus oocytes. However, these oligonucleotides do not suppress the expression of the DHP-insensitive VDCC and of voltage-dependent sodium and potassium channels. Thus, the gene for DHP receptor of rabbit skeletal muscle is closely related, or identical to, a gene expressed in heart that encodes a component of the DHP-sensitive VDCC. The DHP-sensitive and DHP-insensitive VDCCs are distinct molecular entities.

Photochemical cross-linking of psoralen-derivatized oligonucleoside methylphosphonates to rabbit globin messenger RNA

Antisense oligodeoxyribonucleoside methylphosphonates targeted against various regions of mRNA or precursor mRNA are selective inhibitors of mRNA expression both in cell-free systems and in cells in culture. The efficiency with which methylphosphonate oligomers interact with mRNA, and thus inhibit translation, can be considerably increased by introducing photoactivatable psoralen derivatives capable of cross-linking with the mRNA. Oligonucleoside methylphosphonates complementary to coding regions of rabbit alpha- or beta-globin mRNA were derivatized with 4'-(aminoalkyl)-4,5',8-trimethylpsoralens by attaching the psoralen group to the 5' end of the oligomer via a nuclease-resistant phosphoramidate linkage. The distance between the psoralen group and the 5' end of the oligomer can be adjusted by changing the number of methylene groups in the aminoalkyl linker arm. The psoralen-derivatized oligomers specifically cross-link to their complementary sequences on the targeted mRNA. For example, an oligomer complementary to nucleotides 56-67 of alpha-globin mRNA specifically cross-linked to alpha-globin mRNA upon irradiation of a solution of the oligomer and rabbit globin mRNA at 4 degrees C. Oligomers derivatized with 4'-[[N-(2-amino-ethyl)amino]methyl]-4,5',8-trimethylpsoralen gave the highest extent of cross-linking to mRNA. The extent of cross-linking was also determined by the chain length of the oligomer and the structure of the oligomer binding site. Oligomers complementary to regions of mRNA that are sensitive to hydrolysis by single-strand-specific nucleases cross-linked to an approximately 10-30-fold greater extent than oligomers complementary to regions that are insensitive to nuclease hydrolysis.(ABSTRACT TRUNCATED AT 250 WORDS)

Antisense oligodeoxyribonucleotide-directed cleavage of maternal mRNA in Xenopus oocytes and embryos

We have investigated the effect of specific antisense oligodeoxynucleotides (oligos) on endogenous histone H4 mRNA in Xenopus oocytes, eggs and embryos. In unfertilised eggs and non-matured oocytes, one 20-mer oligo (H4-1) mediated the RNAse H-like cleavage of up to 95% of H4 mRNA (which included polysomal mRNA), and cleavage was still obtained when the size of the oligo was reduced to a 10-mer; no cleavage was observed with 6- and 8-mers. The residual uncleaved mRNA appeared to be completely inaccessible to H4-1 since a second injection caused no further cleavage. A second 20-mer (H4-2) directed against a different region of H4 mRNA was much less effective (less than 5% cleavage). In fertilised embryos, injections of H4-1 and an oligo directed against the localised Vg1 mRNA caused less cleavage than in oocytes and also showed signs of inducing localised, non-specific mRNA cleavage. However we have been able to prepare fertilised embryos devoid of Vg1 mRNA by maturing and fertilising oligo-injected oocytes in vitro.

The inhibition of neurite outgrowth in PC12 cells by tubulin antisense oligodeoxyribonucleotides

A model system was designed to determine the effect of antisense oligodeoxyribonucleotides (oligos) on the expression of endogenous tubulin genes, the major component of microtubules, and to study the involvement of individual tubulin isoforms in specific functions, by employing antisense oligos which can block the expression of specific transcripts, both in vitro and in vivo. In reticulocyte cell-free system, specific inhibition of mRNA translation was observed with oligos complementary to the 5' alpha-tubulin-coding region. In vivo inhibition of neurite outgrowth was observed in nerve growth factor-induced PC12 cells. Specific inhibition was observed in cells treated with antisense oligos corresponding to the 5' alpha-tubulin-coding region as well as with antisense oligos corresponding to the 3' alpha-noncoding regions of two different alpha-tubulin isoforms. The results show that both tubulin isoforms are involved in neurite outgrowth and further demonstrate the ability of oligos to block expression of endogenous genes and thus follow the involvement of those gene products in cellular differentiation.

Antimessenger oligodeoxyribonucleotides: an alternative to antisense RNA for artificial regulation of gene expression--a review

Synthetic oligodeoxyribonucleotides (oligos) are now widely used as artificial regulators for gene expression both in cell-free media and in cultured cells. We describe the biological consequence of the various chemical modifications that have been introduced into the molecules to improve their resistance against nuclease attack, their affinity for the target mRNA and their uptake by cells. We also describe the rising generation of antimessenger oligos. Covalently linked to reactive groups these molecules direct irreversible modifications of the complementary nucleic acids. We anticipate that these oligos will be targeted to double-stranded nucleic acids to interfere with gene expression at the DNA level.

Specific inhibition of lymphokine biosynthesis and autocrine growth using antisense oligonucleotides in Th1 and Th2 helper T cell clones

T helper cells have recently been divided into two subsets. The Th1 subset secretes and responds to IL-2 in an autocrine manner. The Th2 subset upon mitogen or antigen stimulation releases IL-4. Here we describe a novel technology that allowed us to confirm this distinction. We have used synthetic oligonucleotides complementary to the 5' end of mouse IL-2 and IL-4 to specifically block the biosynthesis of IL-2 or IL-4 in two murine helper T cell clones from the Th1 or Th2 subset. We show that the antisense IL-2 oligonucleotide inhibited the proliferation of the Th1 clone and had no effect on the Th2 clone. In parallel experiments, the antisense IL-4 oligonucleotide blocked the proliferation of the Th2 clone and not the proliferation of the Th1 clone. The inhibition was significantly reversed in both cases by the addition of the relevant lymphokine (IL-2 in the case of the Th1 clone, IL-4 in the case of the Th2 clone). Northern analysis, using cDNA probes specific for the two lymphokines, showed a decrease in the steady-state level of the relevant lymphokine mRNA, suggesting the specific degradation of the mRNA by an RNase H-like enzymatic activity. This strategy, which allows the specific blockade of the biosynthesis of a lymphokine, could be useful for future studies on the role of each T helper subset in physiological immune responses.

Function of c-mos proto-oncogene product in meiotic maturation in Xenopus oocytes

The c-mos proto-oncogene is expressed as a maternal mRNA in oocytes and early embryos of Xenopus laevis, but its translation product pp39mos is detectable only during progesterone-induced oocyte maturation. Microinjection of mos-specific antisense oligonucleotides into oocytes not only prevents expression of pp39mos, but also blocks germinal vesicle breakdown, indicating that it functions during reinitiation of meiotic division.

Destruction of a translationally controlled mRNA in Xenopus oocytes delays progesterone-induced maturation

The maternal mRNA D7 is a moderately abundant transcript in Xenopus laevis whose expression is highest in, and perhaps restricted to, oogenesis and early embryogenesis. The nucleotide sequence of cloned D7 cDNA was determined and shown to have the capacity to code for a 31-kD protein. This amino acid sequence was searched against a protein data base, and no homologous proteins were found. Antibodies directed against D7 recognize in Xenopus embryos a soluble, cytoplasmic protein with an apparent molecular weight on SDS gels of 36,000. The D7 protein is absent from oocytes and first begins to accumulate during oocyte maturation. Its levels are highest during the first day of embryonic development and then decrease; D7 protein was not detected in adult tissues. D7 mRNA was selectively destroyed by injection into oocytes of antisense oligodeoxynucleotides. Analysis of injected oocytes by Northern and Western blotting showed site-specific cleavage and subsequent degradation of the D7 mRNA and the failure of the D7 protein to accumulate during progesterone-induced maturation. The loss of D7 protein affects the maturation process itself, significantly delaying the time course of germinal vesicle breakdown. Thus, D7 is a newly described protein involved in oocyte maturation.

Translation arrest of potato virus X RNA in Krebs-2 cell-free system: RNase H cleavage promoted by complementary oligodeoxynucleotides

Translation arrest of genomic potato virus X (PVX) RNA promoted by complementary oligodeoxynucleotides in Krebs-2 cell-free system is described. 14-15 mer oligodeoxynucleotides complementary to the 5'-proximal cistron of PVX RNA were shown to induce specific truncation of the major non-structural polypeptide coded by PVX RNA. Evidence is presented that effective translational arrest of PVX RNA in the presence of complementary oligonucleotides results from the site-specific cleavage of RNA by endogenous RNase H intrinsic to the Krebs-2 extract. No similar translational arrest was found in the rabbit reticulocyte lysate cell-free system.