Short antisense oligonucleotide-mediated inhibition is strongly dependent on oligo length and concentration but almost independent of location of the target sequence

A novel dual lock method for down-regulation of genes, in which a target mRNA is captured at 2 independent positions by linked locked nucleic acid antisense oligonucleotides

Nuclear factor κB (NFκB), which is composed of the RelA and p50 subunits, binds to NFκB response elements (NREs) and stimulates the transcription of inflammation-related genes. Here, locked nucleic acid (LNA) antisense oligonucleotides (ASOs) complementary to the termini of the 3'- and 5'-untranslated regions (UTRs) of the RelA mRNA were generated; these molecules were named 3'-LNA and 5'-LNA, respectively. To evaluate their effects on NFκB activity, HeLa cells were co-transfected with the LNA ASOs and a luciferase reporter gene carrying an NRE. Transfection of the cells with 3'-LNA reduced NFκB activity by 30-40%, without affecting RelA mRNA accumulation. Concomitant transfection of HeLa cells with 5'-LNA and 3'-LNA resulted in a 70% reduction in NFκB activity. Furthermore, partial poly(A) tail shortening occurred in LNA ASO-transfected cells. We also employed triethylene glycol as a spacer to link 5'-LNA and 3'-LNA. Reporter gene assays showed that the spacer-linked LNA ASO reduced NFκB activity similarly to a combination of 5'-LNA and 3'-LNA. In addition, an in vitro translation assay revealed that spacer-linked LNA ASOs inhibited the translation of a target mRNA in a specific manner. In summary, this study describes a novel antisense method capturing the target mRNA at independent positions.

Terminally modified, short phosphorothioate oligonucleotides as inhibitors of gene expression in cells

Phosphorothioates are excellent antisense inhibitors, which are active both in cells and in vivo. Since their affinity to complementary ribonucleic acids is rather low, long strands (⩾20-mers) are typically required to achieve the desired biological activity. However, mismatch discrimination of long inhibitors is reduced. In contrast, shorter phosphorothioates exhibit better sequence specificity, but have in most cases too low affinity for practical applications in cells. We screened a range of terminal modifiers of a 14-mer phosphorothioate sequence, which is complementary to mRNA of a representative gene, whose protein product is fluorescent (DsRed2) and easy to monitor in cells. We found that optimal combinations of 5'- and 3'-modifications include 5'-trimethoxystilbene with 3'-uracil(anthraquinone)-cap, 5'-chloic acid derivative with 3'-uracyl(anthraquinone)-cap and 5'-cholic acid derivative with three 3'-LNA moieties. In contrast to the LNA, stabilizing and activity-enhancing effects of other mentioned modifiers for PTO/RNA duplexes have not been previously reported. We observed that the 14-mer inhibitor carrying 5'-cholic acid derivative with three 3'-LNA moieties inhibits expression of DsRed2 in cells stronger than the unmodified 21-mer. Mismatch discrimination of this inhibitor was found to be comparable to that of the unmodified 14-mer.

Short, terminally modified 2'-OMe RNAs as inhibitors of microRNA

We applied 14-mer 2'-OMe RNAs as inhibitors of selected micro RNAs. To improve their properties, we introduced a trimethoxystilbene residue at the 5'-terminus and three 2'-fluoro-2'-deoxynucleotides at the 3'-terminus to obtain potent inhibitors, whose mismatch discrimination is substantially better than that of typically applied >18-mers.

Polymer nanocarriers for the delivery of small fragments of nucleic acids: oligonucleotides and siRNA

The success of the application of new therapeutic methods based on RNA interfering strategies requires the in vivo delivery of active ODN or siRNA down to the intracellular compartment of the target cells. This article aims to review the studies related to the formulation of RNA interfering agents in polymer nanocarriers. It will present the different types of polymer nanocarriers used as well as the biological activity of the resulting ODN and siRNA loaded nanocarriers. As will be explained, the part of the in vitro studies provided useful data about the intracellular delivery of the formulated RNA interfering agents. Investigations performed in vivo have considered animal models of different relevant diseases. Results from these investigations have clearly demonstrated the interest of several polymer nanocarriers tested so far to deliver active RNA interfering effectors in vivo making possible their administration by the intravenous route.

Somatostatin modulates voltage-dependent Ca2+ channels in GH3 cells via a specific G(o) splice variant

In rat pituitary GH3 cells Ca2+ current through L-type channels is reduced by somatostatin. This modulation of channel activity by somatostatin receptors is mediated by a guanine nucleotide-binding regulatory protein (G protein). It is sensitive to pertussis toxin, indicating the involvement of a G(o)- or Gi-type G protein in this pathway. The identity of this G protein was determined by suppressing the expression of endogenous G proteins individually via intranuclear injection of antisense oligonucleotides. This method was applied to GH3 cells to screen several G protein alpha, beta and gamma subunits for their roles in the defined signal transduction pathway. The loss of somatostatin's modulating activity on the voltage-dependent Ca2+ channel after oligonucleotide injection revealed the involvement of G(o) alpha 2 beta 1 gamma 3 to the exclusion of other closely related subtypes.

Tryptophan-scanning mutagenesis in the S1 domain of mammalian HCN channel reveals residues critical for voltage-gated activation

Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels are essential regulators in rhythmic activity, membrane excitability and synaptic transmission. There are four subtypes in mammals (HCN1-4); HCN4 has the slowest activation kinetics and HCN1 the fastest. Although voltage gating originates with the voltage-dependent motion of the S4 segment, the different activation kinetics between HCN1 and HCN4 are generated mainly by S1 and the S1-S2 loop. In this study, we investigate the structural basis of the ability of S1 to affect activation kinetics by replacing each individual S1 residue in HCN1 with a tryptophan (Trp) residue, a Trp perturbation scan. Robust currents were generated in 11 out of 19 Trp mutants. Hyperpolarization-activated currents were not detected in four mutants, and two other mutants generated only small currents. Presence or absence of current reflected the predicted alpha-helical structure of the S1 transmembrane segment. Tryptophan replacements of residues responsible for the different kinetics between HCN1 and HCN4 made the activation kinetics slower than the wild-type HCN1. Tryptophan mutations introduced in the middle of S1 (L139W and V143W) prevented normal channel closure. Furthermore, a negatively charged residue at position 139 (L139D) induced a positive voltage shift of activation by 125 mV. Thus, L139 and V143 probably face a mobile part of the S4 voltage sensor and may interact with it. These results suggest that the secondary structure of S1 is alpha-helical and profoundly affects the motion of the voltage sensor.

Effects of perfluorooctane sulfonate on action potentials and currents in cultured rat cerebellar Purkinje cells

Recently, PFOS was reported to be ubiquitously detected in the environment, as well as in human serum, raising concerns regarding its health risks. We investigated the effects of PFOS on action potentials and currents in cultured rat cerebellar Purkinje cells using whole-cell patch-clamp recording. In current-clamp experiments, PFOS significantly decreased the action potential frequency during current injection, the maximum rate of fall and the threshold of action potential, and negatively shifted the resting membrane potential at doses over 30microM. In voltage-clamp experiments, PFOS shifted the half-activation and inactivation voltages of I(Ca), I(Na), and I(K) toward hyperpolarization at 30microM. I(HCN1) expressed in Xenopus oocytes was similarly affected. Incorporation of PFOS into the cell membrane probably increased the surface negative charge density, thereby reducing the transmembrane potential gradient and resulting in hyperpolarizing shifts of both the activation and inactivation of ionic channels. These findings indicate that PFOS may exhibit neurotoxicity.

ROLL: a method of preparation of gene-specific oligonucleotide libraries

The selection of nucleic acid sequences capable of specifically and efficiently hybridizing to target sequences is crucial to the success of many applications, including microarrays, PCR and other amplification procedures, antisense inhibition, ribozyme-mediated cleavage, and RNA interference (RNAi). Methods of selection using nucleotide sequence libraries have several advantages over rational approaches using defined sequences. However, the high complexity of completely random (degenerate) libraries and their high toxicity in cell-based assays make their use in many applications impractical. Gene-specific oligonucleotide libraries, which contain all possible sequences of a certain length occurring within a given gene, have much lower complexity and, thus, can significantly simplify and accelerate sequence screening. Here, we describe a new method for the preparation of gene-specific libraries using the ligation of randomized oligonucleotide probes hybridized adjacently on target polynucleotide templates followed by PCR amplification. We call this method random oligonucleotide ligated libraries (ROLL).

Ten years of antisense inhibition of brain G-protein-coupled receptor function

Antisense oligonucleotides (AOs) are widely used as tools for inhibiting gene expression in the mammalian central nervous system. Successful gene suppression has been reported for different targets such as neurotransmitter receptors, neuropeptides, ion channels, trophic factors, cytokines, transporters, and others. This illustrates their potential for studying the expression and function of a wide range of proteins. AOs may even find therapeutic applications and provide an attractive strategy for intervention in diseases of the central nervous system (CNS). However, a lack of effectiveness and/or specificity could be a major drawback for research or clinical applications. Here we provide a critical overview of the literature from the past decade on AOs for the study of G-protein-coupled receptors (GPCRs). The following aspects will be considered: mechanisms by which AOs exert their effects, types of animal model system used, detection of antisense action, effects of AO design and delivery characteristics, non-antisense effects and toxicological properties, controls used in antisense studies to assess specificity, and our results (failures and successes). Although the start codon of the mRNA is the most popular region (46%) to target by AOs, targeting the coding region of GPCRs is almost as common (41%). Moreover, AOs directed to the coding region of the GPCR mRNA induce the highest reductions in receptor levels. To resist degradation by nucleases, the modified phosphorothioate AO (S-AO) is the most widely used and effective oligonucleotide. However, the end-capped phosphorothioate AOs (ECS-AOs) are increasingly used due to possible toxic and non-specific effects of the S-AO. Other parameters affecting the activity of a GPCR-targeting AO are the length (mostly an 18-, 20- or 21-mer) and the GC-content (mostly varying from 30 to 80%). Interestingly, one-third of the AOs successfully targeting GPCRs possess a GC/AT ratio of 61-70%. AO-induced reductions in GPCR expression levels and function range typically from 21 to 40% and 41 to 50%, respectively. In contrast to many antisense reviews, we therefore conclude that the functional activity of a GPCR after AO treatment correlates mostly with the density of the target receptors (maximum factor 2). However, AOs are no simple tools for experimental use in vivo. Despite successful results in GPCR research, no general guidelines exist for designing a GPCR-targeting AO or, in general, for setting up a GPCR antisense experiment. It seems that the correct choice of a GPCR targeting AO can only be ascertained empirically. This disadvantage of antisense approaches results mostly from incomplete knowledge about the internalisation and mechanism of action of AOs. Together with non-specific effects of AOs and the difficulties of assessing target specificity, this makes the use of AOs a complex approach from which conclusions must be drawn with caution. Further antisense research has to be carried out to ensure the adequate use of AOs for studying GPCR function and to develop antisense as a valuable therapeutic modality.

Beyond Mitomycin: TGF-beta and wound healing

The introduction of the anti-cancer drugs Mitomycin and 5-fluorouracil as anti-scarring agents within the last decade, has greatly improved surgical results of glaucoma filtration surgery. However, a number of problems associated with their use have emerged. At the same time, the transforming growth factor-beta (TGF-beta) has been identified as an important component of wound healing, particularly in the conjunctival scarring response. Recent developments in molecular therapy offer exciting prospects for the modulation of wound healing, specifically those targeting TGF-beta. As TGF-beta is such a potent stimulant of scarring, this review examines its biology and role in ocular wound healing and repair, and discusses promising new approaches to modifying its activity.

Modulating conjunctival wound healing

Advances in molecular and cell biology have led to an expansion in our knowledge and understanding of the processes involved in wound healing. We review existing and potential therapies modulating the conjunctival scarring response, with particular reference to glaucoma filtration surgery. We discuss how the refinement of present antimetabolite regimens can minimise complications and improve surgical results, and advocate their use in carefully selected patient groups. Perhaps the most promising approach is targeting biological molecules. Hence, use of fully human neutralising monoclonal antibodies to the growth factor TGF beta has potential as a useful strategy for modifying conjunctival scarring. Combination therapies may also afford an improved therapeutic index. It is hoped that future therapies can offer safer, more specific, focal and titratable treatment, with far-reaching clinical applications.

Antisense oligonucleotides against ‘cardiac’ and ‘skeletal’ DHP-receptors reveal a dual role for the ‘skeletal’ isoform in EC coupling of skeletal muscle cells in primary culture

Two dihydropyridine receptor mRNA isoforms (cardiac and skeletal) are expressed in rat skeletal muscle cells in primary culture. The progressive changes in excitation-contraction coupling mode from dual mode (‘skeletal’ and ‘cardiac’) to predominant ‘skeletal’ one during in vitro myogenesis are thought to be linked to the developmental changes in the relative expression of the two types of molecular entity previously observed in this preparation. In order to test this hypothesis, myotube cultures (5- to 7-day-old) were treated with antisense phosphorothioated oligodeoxynucleotides against cardiac or skeletal alpha1 subunit of L-type calcium channel. The oligodeoxynucleotide uptake by cells was checked by means of imaging of fluorescent oligodeoxynucleotide derivatives within the cells. Optimum concentration used (10 microM in the extracellular medium) and incubation time (70 hours) were empirically determined. Antisense directed against the cardiac type led to a 54% decrease in the averaged L-type calcium current peak density at −10 mV. The same type of experiment was performed with antisense against the skeletal isoform and led to a same order of inhibition (46%). This result clearly shows that the two isoforms can work as a calcium channel. Conversely, analysis of the shape of T-V (relative contractile amplitude versus membrane potential) curves shows that the treatment with ‘skeletal’ antisense depressed the contractile response in the medium membrane potential range whereas treatment with ‘cardiac’ antisense had no effect. This and other results taken together suggest that the skeletal isoform of dihydropyridine receptor is involved in both ‘cardiac’ and ‘skeletal’ types of EC coupling mechanisms at work in early stages of myotubes in vitro development. The type of coupling probably depends on the proximity of the skeletal dihydropyridine receptor and the ryanodine receptor.

Plasmodium falciparum: effect of chemical structure on efficacy and specificity of antisense oligonucleotides against malaria in vitro

Antisense oligodeoxynucleotides (AS ODNs) have shown promise both as potential anti-malarial chemotherapeutic agents and as a means for identifying genes critical for parasite survival. Because conventional ODNs containing phosphodiester (PO) groups are subject to rapid nuclease degradation, ODNs with phosphorothioate (PS) groups are commonly used. However, at high concentration, these lose target specificity, and in some animal models, they become toxic. We compared a variety of chemical modifications (PO, PS, PO-PS hybrids, 2'-O-methyl-2'-deoxy chimeras) and structural modifications (sequence alterations favoring self-stabilizing loop formation) for their ability to inhibit Plasmodium falciparum malaria cultured in vitro. All modifications were done using an AS ODN sequence targeted against dihydrofolate reductase thymidylate synthase (DHFR). Inhibition by PO-PS hybrids containing as few as three PS groups at the 3'- and 5'-ends did not differ significantly from that obtained using compounds containing all-PS groups. Similarly, inhibition by PS chimeric compounds containing 2'-O-methyl modifications did not differ significantly from that of conventional PS compounds. In contrast, while inhibition by PO-PS hybrid chimeras did not differ significantly from that of all-PS compounds at low concentrations, at 1 microM they inhibited parasite growth 25% less (P < 0.001) than all-compounds or PS 2'-O-methyl-2'-deoxy chimeras. Extension of the nucleotide sequence to increase stem-loop formation yielded two compounds which inhibited parasite growth about 20% more than unmodified compounds, though this difference was not significant. Furthermore, most of this increase appears to correlate with the greater number of PS groups associated with the increased ODN length. We conclude that limiting the number of PS groups and inclusion of PO 2'-O-methyl groups may yield compounds with high antisense activity but low non-sequence-dependent effects. Such compounds are currently being tested in vivo.

Antisense inhibition of phosphodiesterase expression

Cyclic nucleotide phosphodiesterases (PDEs) are represented by a superfamily of structurally and functionally related enzymes of which more than 30 different forms have so far been identified and grouped into seven broad gene families, some of which contain multiple genes and many splice variants, within a given gene family. Since all of the forms of PDE have the potential to regulate levels of the second messenger, cAMP or cGMP, and some of the forms appear to be tissue specific in their expression and differentially regulated, it would be useful to be able to selectively inhibit a given form of PDE, to study the physiological consequences of this inhibition, with the intent of possible therapeutic application. While gene family-specific pharmacological inhibitors exist for six of the seven gene families, none of these inhibitors is yet capable of distinguishing PDE members within a given gene family in its inhibition. One approach to selectively inhibit a specific form of PDE, without affecting others, is through use of antisense oligonucleotides to block the expression of a given PDE form. This article describes ways to optimally develop and test antisense oligonucleotides to inhibit expression of PDE.

Antisense approaches for investigating mechanisms of abnormal development

Although the use of antisense oligodeoxynucleotides in cell culture systems has been beneficial for examining functional roles of genes in biological processes, very few studies have adapted this valuable approach to developmental studies. This oversight may be due to the fact that many scientists are not familiar with the numerous in vitro approaches available for use as developmental system models. Increased knowledge concerning the mechanisms by which oligonucleotides are incorporated into the cell and how these molecules disrupt targeted gene expression has resulted in improved oligonucleotide design and better controls for these studies. The combined use of developmental in vitro approaches, with improved antisense oligodeoxynucleotide strategies presents valuable experimental models for examining functions and interactions of genes in embryogenesis. This review focuses on a comprehensive description of the characterized properties of oligodeoxynucleotides, control design, and various developmental in vitro approaches for accomplishing these studies in embryonic systems.

Pharmacological differentiation between neuronal and recombinant glutamate receptor channels expressed in Xenopus oocytes

To determine the molecular components of neuronal glutamate receptors, it is important to identify pharmacological tools that allow differentiation between different glutamate receptor types. Here, we utilized the naphthalene derivative Evans Blue (EB) and a collection of other subtype-specific compounds (polyamine toxins, concanavalin A, cyclothiazide) to compare the pharmacological profile of neuronal and recombinant glutamate receptors GluR1-GluR6 expressed in Xenopus oocytes. Submicromolar concentrations of EB selectively reduced the activity of homomeric glutamate receptors GluR1, GluR2(Q) and GluR4. Applied at concentrations above 100 microM, EB potentiated kainate responses of receptors GluR1, GluR3 and GluR4, while receptors GluR2(Q) and GluR6(Q) were completely blocked. Similar experiments were performed on identified neurones in brain slices and after injection of rat brain RNA in Xenopus oocytes. Neuronal kainate responses were (i) potentiated by 100 microM cyclothiazide, (ii) slightly blocked after preincubation in 10 microM concanavalin A, and (iii) not significantly affected by either low (< 1 microM) or high (> 100 microM) concentrations of EB. Their pharmacological properties were markedly different from those of recombinant glutamate receptor channels GluR1-GluR6 investigated in heterologous expression systems.

Differentiation intensifies the susceptibility of pheochromocytoma cells to antisense oligodeoxynucleotide-dependent suppression of acetylcholinesterase activity

To investigate the effect of neuronal differentiation on the capacity of antisense oligonucleotides (AS-ODNs) to suppress the production of acetylcholinesterase (AChE) in rat pheochromocytoma cells, we tested seven 3'-phosphorothioated AS-ODNs targeted to ACHEmRNA and two control ODNs. Three different administration protocols were used: oligonucleotides were added at 1 microM for 24 hours to nondifferentiated PC12 cells, together with nerve growth factor (NGF) or 24 hours following NGF-induced cholinergic differentiation. The content of free thiol groups in lysed cells was measured to evaluate cell number, therefore, survival, and the rate of acetylthiocholine hydrolysis was the measure of AChE activity. Among nondifferentiated cells, over 95% survived treatment with 8 of 9 of the ODNs. Moreover, two AS-ODN suppressed AChE activity in non-differentiated PC12 cells by 16%-20% as compared with 10% suppression by control ODNs (P < or = 0.01). When added concurrently with NGF, one other AS-ODN suppressed AChE activity significantly better (28%) than the control ODNs (16%). Moreover, when added following NGF treatment, which induced a significant increase in AChE activity, four different AS-ODNs but not the control ODNs suppressed 20%-35% of the enhanced AChE activity (p < or = 0.01). Reduced levels of AChE mRNA but no difference in actin mRNA levels were observed by following the kinetics of RT-PCR amplification in differentiated PC12 cells treated with these four AS-ODNs, as compared with control cells. Our findings demonstrate a differentiation-related increase in the susceptibility of PC12 cells to inhibition by specific AS-ODNs, suggesting the use of this model system to select AS-ODNs for suppression of AChE levels in the treatment of neurodegenerative diseases associated with cholinergic malfunction.

Antisense oligonucleotides discriminating between two muscular Na+ channel isoforms

Various 15-mer antisense oligodeoxynucleotides (aODNs) were constructed against RNAs coding for two closely related isoforms of the voltage-dependent Na+ channel, i.e. those of human heart (hH1) and skeletal (hSkM1) muscle. When translated in vitro, either RNA yielded a 220 kDa band on polyacrylamide gels, indicating that the translation product had full length. Of six different aODN constructs developed against hH1 RNA, two each inhibited translation completely, moderately or not at all, depending on the target position. The specificity of the effect (no cross reaction at 10 microM) was confirmed by incubation with 15-mer aODNs against hSkM1 RNA. The most effective aODNs were those hybridizing between bases 3840 and 3880 of hSkM1 RNA and the homologous segment of hH1 RNA. When either of the RNAs was co-injected with its most effective (phospho rothioate-capped) aODN into Xenopus oocytes, the production of Na+ channels was strongly suppressed (relative INa for hSkM1: 0.08 +/- 0.05 times control, n = 14; for hH1: 0.11 +/- 0.08, n = 11). We conclude that aODNs are able to discriminate between closely related RNAs. The efficacy of an aODN depends strongly on its RNA target position.

Disruption of Msx-1 and Msx-2 reveals roles for these genes in craniofacial, eye, and axial development

In mouse embryos, the muscle segment homeobox genes, Msx-1 and Msx-2 are expressed during critical stages of neural tube, neural crest, and craniofacial development, suggesting that these genes play important roles in organogenesis and cell differentiation. Although the patterns of expression are intriguing, little is known about the function of these genes in vertebrate embryonic development. Therefore, the expression of both genes, separately and together, was disrupted using antisense oligodeoxynucleotides and whole embryo culture techniques. Antisense attenuation of Msx-1 during early stages of neurulation produced hypoplasia of the maxillary, mandibular, and frontonasal prominences, eye anomalies, and somite and neural tube abnormalities. Eye defects consisted of enlarged optic vesicles, which may ultimately result in micropthalmia similar to that observed in Small eye mice homozygous for mutations in the Pax-6 gene. Histological sections and SEM analysis revealed a thinning of the neuroepithelium in the diencephalon and optic vesicle and mesenchymal deficiencies in the craniofacial region. Injections of Msx-2 antisense oligodeoxynucleotides produced similar malformations as those targeting Msx-1, with the exception that there was an increase in number and severity of neural tube and somite defects. Embryos injected with the combination of Msx-1 + Msx-2 antisense oligodeoxynucleotides showed no novel abnormalities, suggesting that the genes do not operate in a redundant manner.

Strategy for designing specific antisense oligonucleotide sequences

Antisense compounds, various forms of nucleotides or their analogs, inhibit gene function both in vitro and in vivo. Although antisense compounds have been used extensively not only as a basic research tool but also as therapeutics for various diseases, one of the major problems is the difficulty of obtaining optimal sequences to inhibit specific gene functions. Although the terms "sequence-specificity" or "sequence-nonspecificity" are often used, there is no consensus as to how to define and quantitate such sequence specificity. In this review, we introduced hybridization simulation for designing optimal antisense sequences. Each candidate antisense oligonucleotide is assessed by calculating its hybridization energy against potential hybridization sites within the specified database (including GenBank) using a realistic nearest-neighbor thermodynamic model, taking into account mismatches. The specificity of each oligonucleotide is then quantitated by the number of potential cross-hybridizable genes and their degree of cross-hybridization. Furthermore, if antisense sequences exhibit a high potential for hairpin formation, they are not recommended even if they are highly specific. Therefore, to select antisense sequences, one should calculate all the potential factors for each candidate oligonucleotide such as length, location, specificity, hairpin potential, mRNA secondary structure, and dimer formation.

Antisense oligodeoxynucleotides as specific tools for studying neuroendocrine and behavioral functions: some prospects and problems

Synthetic antisense oligodeoxynucleotides can inhibit the expression of a gene in a sequence-specific manner at the translational level. Their potential use to understand the role of neuropeptides or neurotransmitters in neuroendocrine and behavioral functions, and perhaps for therapeutic gene suppression, has become of great interest in neuroscience, especially in the cases of absence of available specific antagonists. Whether their action can be fully specific to the target gene and not only sequence-specific is, however, the main question about their application to brain studies. A number of factors such as the mode of action, specificity and chemistry of antisense molecules as well as the carrier vehicle and the time course of antisense treatment, must be carefully considered for the design and successful application of antisense oligonucleotides. Assay systems and controls must be chosen so as to ensure that the observed biological effects of antisense oligodeoxynucleotides do in fact reflect the result of a specific target gene inhibition. This article discusses these biochemical factors with the emphasis on the use of phosphodiester or phosphorothioate oligodeoxynucleotides in neuroendocrine or behavioral studies.

Amplification of antibody production by phosphorothioate oligodeoxynucleotides

A phosphorothioate oligodeoxynucleotide that is complementary (antisense) to the initiation region of the rev gene of HIV-1 causes hypergammaglobulinemia and splenomegaly in mice, and it induces B cell proliferation and differentiation in mouse spleen mononuclear cells (SMNCs) and human peripheral blood mononuclear cells in vitro. The current studies were performed to investigate the specificity of these immunomodulatory effects. Both the sense and antisense rev oligomers stimulated tritiated thymidine incorporation and secretion of immunoglobulin M (IgM) and immunoglobulin G (IgG) by mouse SMNCs in a concentration-dependent fashion, but the antisense oligomer produced greater immune effects. Studies comparing phosphorothioate oligomers (anti-rev, c-myc, and c-myb) either methylated or unmethylated at CpG dinucleotides showed that methylation effectively abrogated the proliferative effect and tended to reduce the immunoglobulin secretory activity, but the latter was not statistically significant except in the case of IgG in anti-rev oligomer-treated cultures. Mice were injected with the sense or antisense rev oligomers singly or in combination. The animals then were immunized with tetanus toxoid and received a booster 21 days later. Oligodeoxynucleotide-treated mice had significantly higher levels of IgM antibodies on days 28 and 35 and of IgG antibodies on days 14 and 35 as compared with mice that were immunized but received vehicle alone. There was no evidence for additive, synergistic, or antagonistic interactions of the sense and antisense rev oligomers. These results indicate that the unmethylated anti-rev oligomer is the most potent of the phosphorothioate oligomers tested at activating lymphocyte proliferation and differentiation and that a single intravenous injection of this oligodeoxynucleotide augments antibody production to a specific antigen as long as 35 days later.

Inhibition of Xhox1A gene expression in Xenopus embryos by antisense RNA produced from an expression vector read by RNA polymerase III

Antisense inhibition of gene expression during Xenopus development was obtained by injecting, into the zygote, an expression vector carrying the adenovirus VAI gene read by RNA polymerase III. This vector yields high levels of antisense RNA in most embryonic cells between mid-blastula transition and tailbud stage. As a target we chose the Xenopus homeobox gene Xhox1A. A 26 bp long oligonucleotide, including the initiation codon of this gene, was inserted in opposite polarity into the vector. Antisense treatment reduces Xhox1A mRNA in embryos up to stage 22 and Xhox1A protein expression up to stage 30. Half of the antisense-treated embryos develop a characteristic phenotype with disorganized somites in the anterior trunk and delayed development of the intestinal tract.