Specific inhibition of expression of a human collagen gene (COL1A1) with modified antisense oligonucleotides. The most effective target sites are clustered in double-stranded regions of the predicted secondary structure for the mRNA

HIV RNA dimerisation interference by antisense oligonucleotides targeted to the 5' UTR structural elements

The HIV-1 genome consists of two identical RNA molecules non-covalently linked by their 5' unstranslatable regions (5' UTR). The high level of sequence and structural conservation of this region correlates with its important functional involvement in the viral cycle, making it an attractive target for antiviral treatments based on antisense technology. Ten unmodified DNA antisense oligonucleotides (ODNs) targeted against different conserved structural elements within the 5' UTR were assayed for their capacity to interfere with HIV-1 RNA dimerisation, inhibit gene expression, and prevent virus production in cell cultures. The results show that, in addition to the well-characterised dimerisation initiation site (DIS), targeting of the AUG-containing structural element may reflect its direct role in HIV-1 genomic RNA dimerisation in vitro. Similarly, blocking the 3' end sequences of the stem-loop domain containing the primer biding site interferes with RNA dimerisation. Targeting the apical portion of the TAR element, however, appears to promote dimerisation. ODNs targeted against the conserved polyadenylation signal [Poly(A)], the primer binding site (PBS), the major splicing donor (SD) or the major packaging signal (Psi), and AUG-containing structural elements led to a highly efficient inhibition of HIV-1 gene expression and virus production in cell culture. Together, these results support the idea that ODNs possess great potential as molecular tools for the functional characterisation of viral RNA structural domains. Moreover, the targeting of these domains leads to the potent inhibition of viral replication, underscoring the potential of conserved structural RNA elements as antiviral targets.

siRNAs target sites selection of ezrin and the influence of RNA interference on ezrin expression and biological characters of osteosarcoma cells

Ezrin, one of the ezrin/radixin/moesin (ERM) protein family which act as membrane organizers and linkers between plasma membrane and cytoskeleton, has attracted much attention as a crucial factor for tumor metastasis. Overexpression of ezrin has been correlated with the metastatic potential of several cancers especially for osteosarcoma. Short interfering RNA (siRNA) downregulate gene expression through an enzyme-mediated process named RNA interference (RNAi). RNAi has rapidly come to be recognized as a powerful tool for the study of gene function and a potential target therapy. In the present study, the human osteosarcoma cell line MG63 was cultured. Three siRNAs targeting ezrin mRNA were designed by the multiple computational methods and then were sythesized. These siRNAs were transfected into osteosarcoma cells. Then the expression of ezrin mRNA and protein in osteosarcoma cells was detected. The cellular proliferation and apoptosis was evaluated. C726–U730, C1653–A1661 and G1749–A1771 were selected to be the suitable target sites through the multiple computational methods because of their ideal secondary structures and hybridization thermodynamics. siRNAs against G1749–A1771 downregulated the expression level of ezrin mRNA and protein, inhibit the cellular proliferation and promoted the cellular apoptosis effectively. There is a significant correlation between the multiple computational methods and the efficacy of the corresponding siRNAs. siRNAs targeting ezrin may have therapeutic potential as inhibitors of osteosarcoma metastasis.

Ezrin mRNA target site selection for DNAzymes using secondary structure and hybridization thermodynamics

Ezrin, a membrane organizer and linker between plasma membrane and cytoskeleton, is well documented to play an important role in the metastatic capacity of cancer cells especially for osteosarcoma cells. It has provided an ideal target for cancer gene therapy. RNA-cleaving 10-23 DNAzymes, consisting of a 15-nucleotide catalytical domain flanked by two target-specific complementary arms, can cleave the target mRNA at purine-pyrimidine dinucleotide effectively. In the present study, we designed and screened the target sites for 10-23 DNAzymes against ezrin mRNA by using multiple computational methods with combination of secondary structural and hybridization thermodynamic parameters. Then, we testified the activities of the DNAzymes directed against these selected target sites in vitro. Our results show that AU1751 is the most effective target site of ezrin mRNA for DNAzymes because of its ideal secondary structure and hybridization thermodynamics. So, there is a significant correlation between the multiple computational methods and the efficacy of the corresponding DNAzymes. These provide a rational, efficient way for DNAzymes selection.

Antisense DNA parameters derived from next-nearest-neighbor analysis of experimental data

BACKGROUND

The enumeration of tetrameric and other sequence motifs that are positively or negatively correlated with in vivo antisense DNA effects has been a useful addition to the arsenal of information needed to predict effective targets for antisense DNA control of gene expression. Such retrospective information derived from in vivo cellular experiments characterizes aspects of the sequence dependence of antisense inhibition that are not predicted by nearest-neighbor (NN) thermodynamic parameters derived from in vitro experiments. However, quantitation of the antisense contributions of motifs is problematic, since individual motifs are not isolated from the effects of neighboring nucleotides, and motifs may be overlapping. These problems are circumvented by a next-nearest-neighbor (NNN) analysis of antisense DNA effects in which the overlapping nature of nearest-neighbors is taken into account.

RESULTS

Next-nearest-neighbor triplet combinations of nucleotides are the simplest that include overlapping sequence effects and therefore can encompass interactions beyond those of nearest neighbors. We used singular value decomposition (SVD) to fit experimental data from our laboratory in which phosphorothioate-modified antisense DNAs (S-DNAs) 20 nucleotides long were used to inhibit cellular protein expression in 112 experiments involving four gene targets and two cell lines. Data were fitted using a NNN model, neglecting end effects, to derive NNN inhibition parameters that could be combined to give parameters for a set of 49 sequences that represents the inhibitory effects of all possible overlapping triplet interactions in the cellular targets of these antisense S-DNAs. We also show that parameters to describe subsets of the data, such as the mRNAs being targeted and the cell lines used, can be included in such a derivation. While NNN triplet parameters provided an adequate model to fit our data, NN doublet parameters did not.

CONCLUSIONS

The methodology presented illustrates how NNN antisense inhibitory information can be derived from in vivo cellular experiments. Subsequent calculations of the antisense inhibitory parameters for any mRNA target sequence automatically take into account the effects of all possible overlapping combinations of nearest-neighbors in the sequence. This procedure is more robust than the tallying of tetrameric motifs that have positive or negative antisense effects. The specific parameters derived in this work are limited in their applicability by the relatively small database of experiments that was used in their derivation.

Attenuation of alpha1 collagen production with antisense ribonucleic acid in cultured hypertrophic scar fibroblasts

BACKGROUND

It has been demonstrated that hypertrophic scar fibroblasts (HSFs) overexpress collagen messenger ribonucleic acid (mRNA) and protein, especially alpha1 collagen. Antisense nucleic acids are effective in inhibiting harmful or uncontrolled gene expression, suggesting that antisense ribonucleic acid (RNA) can effectively downregulate the expression of alpha1 collagen gene and attenuate the scars.

AIMS

This study was conducted to observe the effect of recombinant plasmid pREP9-COL1 on alpha1 collagen expression in HSFs and clarify the prospect of antisense RNA on scar treatment.

METHODS

The alpha1 collagen gene fragment including the region of 5' UTR to exon (229 bp) was cloned in the eukaryotic expression plasmid pREP9 in the antisense orientation relative to the RSV-LTR promoter to reconstruct the pREP9- COL1 plasmid. Then it was transferred into HSFs through lipofectamine. The expression of alpha1 collagen was examined by immunostaining, reverse-transcriptase polymerase chain reaction, and Western blots.

RESULTS

The recombinant plasmid pREP9-COL1 with a correct sequence was constructed successfully; pREP9-COL1 consistently inhibited human alpha1 collagen gene expression at both mRNA and protein levels.

CONCLUSIONS

Antisense RNA was effective in downregulating alpha1 collagen expression of HSFs. Therefore, this approach offered a prospect of scar treatment by attenuation of alpha1 collagen production with antisense RNA.

Treatment with antisense oligonucleotide reduces the expression of type I collagen in a human-skin organ-wound model: implications for antifibrotic gene therapy

Increased collagen expression during wound healing causes scar formation, abnormal contracture, low tensile strength, functional impairment, and disfigurement. A novel ex vivo wound-injury model demonstrated that AS60, an antisense oligonucleotide (ASO) to type I collagen, reduced the mRNA and protein expression of type 1 collagen. Following a cutaneous wound injury in a human-skin organ culture, AS60 injection resulted in a 36% (P < 0.001) and 30% decrease (P < 0.001) in type 1 collagen mRNA and protein expression after 7 days. Similarly, transfection of cultured human fibroblasts with ASO resulted in a 36% decrease (P < 0.001) and a 31% decrease (P < 0.001) in type 1 collagen mRNA and protein expression. Immunofluorescence of human skin organ culture treated with ASO showed a specific reduction in collagen expression. Using AS60 to reduce collagen expression in human skin may have implications for its use as a gene therapy agent to reduce the formation of fibrotic scarring.

Bioconjugation of oligonucleotides for treating liver fibrosis

Liver fibrosis results from chronic liver injury due to hepatitis B and C, excessive alcohol ingestion, and metal ion overload. Fibrosis culminates in cirrhosis and results in liver failure. Therefore, a potent antifibrotic therapy is urgently needed to reverse scarring and eliminate progression to cirrhosis. Although activated hepatic stellate cells (HSCs) remain the principle cell type responsible for liver fibrosis, perivascular fibroblasts of portal and central veins as well as periductular fibroblasts are other sources of fibrogenic cells. This review will critically discuss various treatment strategies for liver fibrosis, including prevention of liver injury, reduction of inflammation, inhibition of HSC activation, degradation of scar matrix, and inhibition of aberrant collagen synthesis. Oligonucleotides (ODNs) are short, single-stranded nucleic acids, which disrupt expression of target protein by binding to complementary mRNA or forming triplex with genomic DNA. Triplex forming oligonucleotides (TFOs) provide an attractive strategy for treating liver fibrosis. A series of TFOs have been developed for inhibiting the transcription of alpha1(I) collagen gene, which opens a new area for antifibrotic drugs. There will be in-depth discussion on the use of TFOs and how different bioconjugation strategies can be utilized for their site-specific delivery to HSCs or hepatocytes for enhanced antifibrotic activities. Various insights developed in individual strategy and the need for multipronged approaches will also be discussed.

Receptor-mediated hepatic uptake of M6P-BSA-conjugated triplex-forming oligonucleotides in rats

Excessive production of extracellular matrix, predominantly type I collagen, results in liver fibrosis. Earlier we synthesized mannose 6-phosphate-bovine serum albumin (M6P-BSA) and conjugated to the type I collagen specific triplex-forming oligonucleotide (TFO) for its enhanced delivery to hepatic stellate cells (HSCs), which is the principal liver fibrogenic cell. In this report, we demonstrate a time-dependent cellular uptake of M6P-BSA-33P-TFO by HSC-T6 cells. Both cellular uptake and nuclear deposition of M6P-BSA-33P-TFO were significantly higher than those of 33P-TFO, leading to enhanced inhibition of type I collagen transcription. Following systemic administration into rats, hepatic accumulation of M6P-BSA-33P-TFO increased from 55% to 68% with the number of M6P per BSA from 14 to 27. Unlike 33P-TFO, there was no significant decrease in the hepatic uptake of (M6P)20-BSA-33P-TFO in fibrotic rats. Prior administration of excess M6P-BSA decreased the hepatic uptake of (M6P)20-BSA-33P-TFO from 66% to 40% in normal rats, and from 60% to 15% in fibrotic rats, suggesting M6P/insulin-like growth factor II (M6P/IGF II) receptor-mediated endocytosis of M6P-BSA-33P-TFO by HSCs. Almost 82% of the total liver uptake in fibrotic rats was contributed by HSCs. In conclusion, by conjugation with M6P-BSA, the TFO could be potentially used for the treatment of liver fibrosis.

Selection of antisense oligonucleotides based on multiple predicted target mRNA structures

Background

Local structures of target mRNAs play a significant role in determining the efficacies of antisense oligonucleotides (ODNs), but some structure-based target site selection methods are limited by uncertainties in RNA secondary structure prediction. If all the predicted structures of a given mRNA within a certain energy limit could be used simultaneously, target site selection would obviously be improved in both reliability and efficiency. In this study, some key problems in ODN target selection on the basis of multiple predicted target mRNA structures are systematically discussed.

Results

Two methods were considered for merging topologically different RNA structures into integrated representations. Several parameters were derived to characterize local target site structures. Statistical analysis on a dataset with 448 ODNs against 28 different mRNAs revealed 9 features quantitatively associated with efficacy. Features of structural consistency seemed to be more highly correlated with efficacy than indices of the proportion of bases in single-stranded or double-stranded regions. The local structures of the target site 5' and 3' termini were also shown to be important in target selection. Neural network efficacy predictors using these features, defined on integrated structures as inputs, performed well in "minus-one-gene" cross-validation experiments.

Conclusion

Topologically different target mRNA structures can be merged into integrated representations and then used in computer-aided ODN design. The results of this paper imply that some features characterizing multiple predicted target site structures can be used to predict ODN efficacy.

AOBase: a database for antisense oligonucleotides selection and design

Antisense oligonucleotides (ODNs) technology is one of the important approaches for the sequence-specific knockdown of gene expression. ODNs have been used as research tools in the post-genome era, as well as new types of therapeutic agents. Since finding effective target sites within RNA is a hard work for antisense ODNs design, various experimental methods and computational approaches have been proposed. For better sharing of the experimented and published ODNs, valid and invalid ODNs reported in literatures are screened, collected and stored in AOBase. Till now, ∼700 ODNs against 46 target mRNAs are contained in AOBase. Entries can be explored via TargetSearch and AOSearch web retrieval interfaces. AOBase can not only be useful in ODNs selection for gene function exploration, but also contribute to mining rules and developing algorithms for rational ODNs design. AOBase is freely accessible via .

Downregulation of human type III collagen gene expression by antisense oligodeoxynucleotide

The amount of type III collagen is increased during the early healing stage following ligament and tendon injury. Concomitantly, the mechanical properties of the healing tissues are abnormal and the fibril diameters are homogeneously small. It is therefore thought that downregulating type III collagen gene expression after injury may be helpful in improving the quality of healing tissue. In the current study, the efficacy of using antisense oligodeoxynucleotides (ODNs) to downregulate type III collagen gene expression in human patellar tendon fibroblasts (HPTFs) was tested, with Lipofectamine reagent used to deliver the ODN. It was shown that the majority of HPTFs can efficiently uptake antisense ODN from as early as 1 h to as long as 3 days after delivery; also, one selected ODN can consistently inhibit human type III collagen gene expression at both the mRNA and protein levels. Reverse transcriptase-polymerase chain reaction results showed that the inhibitory effects by this ODN were significant at 1 day, as the type III collagen mRNA level was 38.9 +/- 19.6 and 42.8 +/- 28.1% of missense and sense controls, respectively (p < 0.05). At 3 days, these differences could no longer be observed (p >0.05), but the amount of type III collagen protein was significantly less than for missense and sense controls (31.7 +/- 5.5 and 25.3 +/- 5.3%, respectively; p < 0.05). At 5 days after the delivery, these differences in protein were no longer observed (p > 0.05). Immunohistochemical staining of the type III collagen confirmed these results. The findings of this study demonstrate that antisense ODN can downregulate type III collagen gene expression of tendon fibroblasts. Therefore, this approach offers the potential to explore the effect of the reduction of type III collagen in healing ligaments and tendons as a means to improve their mechanical properties.

Prodrug of proline analogue reduces hypoxic pulmonary hypertension in rats

A polymeric prodrug of the proline analogue cis-4-hydroxy-l-proline (CHOP), poly(ethylene glycol)-lysine-CHOP or CHOP-PEG, prevents hypoxic pulmonary hypertension in rats by inhibiting collagen accumulation. A more potent prodrug was synthesized by increasing the loading of CHOP on the carrier from 14 to 100%. Pulmonary antihypertensive efficacy and pharmacokinetics are described in the rat hypoxia model. The antihypertensive effect of CHOP-PEG in rats exposed to 10% O2 for 7d showed approximately 2 x 10(2)-fold greater potency than monomeric CHOP. Routes of administration were compared to determine the lowest dose of CHOP-PEG that reduced right ventricular pressure approximately 50% vs. untreated hypoxic controls at 7d. Total doses required were: continuous s.c. via an osmotic minipump, 0.8 mg; single s.c., 10mg; single i.v., 40 mg; and single intratracheal 90 mg. Efficacy for at least 7d postdosing in pre-established pulmonary hypertension was shown. Using an ELISA-based assay, biphasic i.v. and stable s.c. pharmacokinetic profiles were observed 72 h after single injections and 7d after continuous s.c. infusion. Thus, this CHOP-PEG formulation prevents and reverses chronic hypoxic pulmonary hypertension in rats, is most effective when given by continuous s.c. infusion, and has favorable pharmacokinetic properties. Potent inhibitors of fibrosis appear to be promising agents in treating pulmonary hypertension and possibly other fibrosing diseases.

Emerging therapeutic approaches for osteogenesis imperfecta

Osteogenesis imperfecta (OI) is an incurable genetic brittle-bone disease. Although drug therapy, surgery and physiotherapy represent current treatments for OI, the search is ongoing for effective and innovative new therapies targeting the underlying causes of the disease. In this regard, recent advances in the fields of gene and stem-cell therapies have been considerable. In spite of the many challenges that remain, potential new therapies for OI, which have been tested in cell culture systems, animal models and patients, offer hope for the future development of successful therapies. Recent progress in the field is reviewed here.

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).

Biodistribution and hepatic uptake of triplex-forming oligonucleotides against type alpha1(I) collagen gene promoter in normal and fibrotic rats

Fibrosis is characterized by excessive production of extracellular matrix (ECM) components, predominantly type 1 collagen. Earlier we developed an antigene approach, using a type alpha1(I) promoter specific TFO to inhibit collagen gene expression. In this report, biodistribution and hepatic cellular and subcellular localization of the 25-mer antiparallel phosphorothioate triplex-forming oligonucleotide (APS TFO) were determined after intravenous injection into rats. TFOs distributed to all the major organs, with higher uptake in the liver, kidney, and spleen. The plasma concentration versus time profile of the (33)P-TFO was biphasic, with 4.36 min as t(1/2)(alpha) of distribution and 34.6 min as t(1/2)(beta) of elimination. TFO concentrations in the liver increased nonlinearly with increase in its dose from 0.2 to 50 mg/kg, but decreased when injected into fibrotic rats. Competition studies with polyinosinic acid (polyI) and dextran sulfate suggested the involvement of scavenger receptors in the hepatic uptake of the TFO. Intrahepatic cellular distribution by Kupffer, endothelial, and hepatic stellate cells (HSCs) accounted for almost 70% of the liver uptake of (33)P-TFO, while only 30% was associated with hepatocytes. The level of liver nuclei-associated TFO was much lower relative to that found in the cytoplasm at 2 and 4 h postinjection. TFO, however, inhibited collagen expression as evidenced by Sirius red staining of the liver section of fibrotic rats. In conclusion, systemic delivery of the TFO against type alpha1(I) collagen gene promoter may be used for the treatment of liver fibrosis.

A genomic selection strategy to identify accessible and dimerization blocking targets in the 5'-UTR of HIV-1 RNA

Defining target sites for antisense oligonucleotides in highly structured RNA is a non-trivial exercise that has received much attention. Here we describe a novel and simple method to generate a library composed of all 20mer oligoribonucleotides that are sense- and antisense to any given sequence or genome and apply the method to the highly structured HIV-1 leader RNA. Oligoribonucleotides that interact strongly with folded HIV-1 RNA and potentially inhibit its dimerization were identified through iterative rounds of affinity selection by native gel electrophoresis. We identified five distinct regions in the HIV-1 RNA that were particularly prone to antisense annealing and a structural comparison between these sites suggested that the 3'-end of the antisense RNA preferentially interacts with single-stranded loops in the target RNA, whereas the 5'-end binds within double-stranded regions. The selected RNA species and corresponding DNA oligonucleotides were assayed for HIV-1 RNA binding, ability to block reverse transcription and/or potential to interfere with dimerization. All the selected oligonucleotides bound rapidly and strongly to the HIV-1 leader RNA in vitro and one oligonucleotide was capable of disrupting RNA dimers efficiently. The library selection methodology we describe here is rapid, inexpensive and generally applicable to any other RNA or RNP complex. The length of the oligonucleotide in the library is similar to antisense molecules generally applied in vivo and therefore likely to define targets relevant for HIV-1 therapy.

A Multi-Model Approach to Nucleic Acid-Based Drug Development

With the advent of functional genomics and the shift of interest towards sequence-based therapeutics, the past decades have witnessed intense research efforts on nucleic acid-mediated gene regulation technologies. Today, RNA interference is emerging as a groundbreaking discovery, holding promise for development of genetic modulators of unprecedented potency. Twenty-five years after the discovery of antisense RNA and ribozymes, gene control therapeutics are still facing developmental difficulties, with only one US FDA-approved antisense drug currently available in the clinic. Limited predictability of target site selection models is recognized as one major stumbling block that is shared by all of the so-called complementary technologies, slowing the progress towards a commercial product. Currently employed in vitro systems for target site selection include RNAse H-based mapping, antisense oligonucleotide microarrays, and functional screening approaches using libraries of catalysts with randomized target-binding arms to identify optimal ribozyme/DNAzyme cleavage sites. Individually, each strategy has its drawbacks from a drug development perspective. Utilization of message-modulating sequences as therapeutic agents requires that their action on a given target transcript meets criteria of potency and selectivity in the natural physiological environment. In addition to sequence-dependent characteristics, other factors will influence annealing reactions and duplex stability, as well as nucleic acid-mediated catalysis. Parallel consideration of physiological selection systems thus appears essential for screening for nucleic acid compounds proposed for therapeutic applications. Cellular message-targeting studies face issues relating to efficient nucleic acid delivery and appropriate analysis of response. For reliability and simplicity, prokaryotic systems can provide a rapid and cost-effective means of studying message targeting under pseudo-cellular conditions, but such approaches also have limitations. To streamline nucleic acid drug discovery, we propose a multi-model strategy integrating high-throughput-adapted bacterial screening, followed by reporter-based and/or natural cellular models and potentially also in vitro assays for characterization of the most promising candidate sequences, before final in vivo testing.

Stimulatory effect of an indirectly attached RNA helicase-recruiting sequence on the suppression of gene expression by antisense oligonucleotides

Antisense oligonucleotides (ODNs) are powerful tools with which to determine the consequences of the reduced expression of a selected target gene, and they may have important therapeutic applications. Methods for predicting optimum antisense sites are not always effective because various factors, such as RNA-binding proteins, influence the secondary and tertiary structures of RNAs in vivo. To overcome this obstacle, we have attempted to engineer an antisense system that can unravel secondary and tertiary RNA structures. To create such an antisense system, we connected the constitutive transport element (CTE), an RNA motif that has the ability to interact with intracellular RNA helicases, to an antisense sequence so that helicase-binding hybrid antisense ODN would be produced in cells. We postulated that this modification would enhance antisense activity in vivo, with more frequent hybridization of the antisense ODN with its targeting site. Western blotting analysis demonstrated that a hybrid antisense ODN targeted to the bcl-2 gene suppressed the expression of this gene more effectively than did the antisense ODN alone. Our results suggest that the effects of antisense ODNs can be enhanced when their actions are combined with those of RNA helicases.

Prioritized selection of oligodeoxyribonucleotide probes for efficient hybridization to RNA transcripts

Only a small fraction of short oligonucleotide probes bind efficiently to complementary segments in long RNA transcripts. Technologies such as array-based transcript profiling and antisense control of gene expression would benefit greatly from a method for predicting probes that bind well to a given target RNA. To develop an algorithm for prioritizing selection of probes, we have analyzed predicted thermodynamic parameters for the binding of several large sets of probes to complementary RNA transcripts. The binding of five of these sets of probes to their RNA targets has been reported by others. In addition, we have used a method for light-directed synthesis of oligonucleotide arrays that we developed to generate two new arrays of surface-bound probes and measured the binding of these probes to their RNA targets. We considered predicted free energies for intramolecular base pairing of the oligonucleotide and its RNA target as well as the predicted free energy of intermolecular hybridization of probe and target. We find that a reliable predictor of probes that will hybridize significantly with their targeted transcripts is the predicted free energy of hybridization minus the predicted free energy for intramolecular folding of the probe.

Determination of optimal sites of antisense oligonucleotide cleavage within TNFalpha mRNA

Antisense oligonucleotides provide a powerful tool in order to determine the consequences of the reduced expression of a selected target gene and may include target validation and therapeutic applications. Methods of predicting optimum antisense sites are not always effective. We have compared the efficacy of antisense oligonucleotides, which were selected in vitro using random combinatorial oligonucleotide libraries of differing length and complexity, upon putative target sites within TNFalpha mRNA. The relationship of specific target site accessibility and oligonucleotide efficacy with respect to these parameters proved to be complex. Modification of the length of the recognition sequence of the oligonucleotide library illustrated that independent target sites demonstrated a preference for antisense oligonucleotides of a defined and independent optimal length. The efficacy of antisense oligonucleotide sequences selected in vitro paralleled that observed in phorbol 12-myristate 13-acetate (PMA)-activated U937 cells. The application of methylphosphonate:phosphodiester chimaeric oligonucleotides to U937 cells reduced mRNA levels to up to 19.8% that of the untreated cell population. This approach provides a predictive means to profile any mRNA of known sequence with respect to the identification and optimisation of sites accessible to antisense oligonucleotide activity.

Transfer of proalpha2(I) cDNA into cells of a murine model of human Osteogenesis Imperfecta restores synthesis of type I collagen comprised of alpha1(I) and alpha2(I) heterotrimers in vitro and in vivo

The oim mouse is a model of human Osteogenesis Imperfecta (OI) that has deficient synthesis of proalpha2(I) chains. Cells isolated from oim mice synthesize alpha1(I) collagen homotrimers that accumulate in tissues. To explore the feasibility of gene therapy for OI, a murine proalpha2(I) cDNA was inserted into an adenovirus vector and transferred into bone marrow stromal cells isolated from oim mice femurs. The murine cDNA under the control of the cytomegalovirus early promoter was expressed by the transduced cells. Analysis of the collagens synthesized by the transduced cells demonstrated that the cells synthesized stable type I collagen comprised of alpha1(I) and alpha2(I) heterotrimers in the correct ratio of 2:1. The collagen was efficiently secreted and also the cells retained the osteogenic potential as indicated by the expression of alkaline phosphatase activity when the transduced cells were treated with recombinant human bone morphogenetic protein 2. Injection of the virus carrying the murine proalpha2(I) cDNA into oim skin demonstrated synthesis of type I collagen comprised of alpha1 and alpha2 chains at the injection site. These preliminary data demonstrate that collagen genes can be transferred into bone marrow stromal cells as well as fibroblasts in vivo and that the genes are efficiently expressed. These data encourage further studies in gene replacement for some forms of OI and use of bone marrow stromal cells as vehicles to deliver therapeutic genes to bone.

Reduction of target gene expression by a modified U1 snRNA

Although the primary function of U1 snRNA is to define the 5' donor site of an intron, it can also block the accumulation of a specific RNA transcript when it binds to a donor sequence within its terminal exon. This work was initiated to investigate if this property of U1 snRNA could be exploited as an effective method for inactivating any target gene. The initial 10-bp segment of U1 snRNA, which is complementary to the 5' donor sequence, was modified to recognize various target mRNAs (chloramphenicol acetyltransferase [CAT], beta-galactosidase, or green fluorescent protein [GFP]). Transient cotransfection of reporter genes and appropriate U1 antitarget vectors resulted in >90% reduction of transgene expression. Numerous sites within the CAT transcript were suitable for targeting. The inhibitory effect of the U1 antitarget vector is directly related to the hybrid formed between the U1 vector and target transcripts and is dependent on an intact 70,000-molecular-weight binding domain within the U1 gene. The effect is long lasting when the target (CAT or GFP) and U1 antitarget construct are inserted into fibroblasts by stable transfection. Clonal cell lines derived from stable transfection with a pOB4GFP target construct and subsequently stably transfected with the U1 anti-GFP construct were selected. The degree to which GFP fluorescence was inhibited by U1 anti-GFP in the various clonal cell lines was assessed by fluorescence-activated cell sorter analysis. RNA analysis demonstrated reduction of the GFP mRNA in the nuclear and cytoplasmic compartment and proper 3' cleavage of the GFP residual transcript. An RNase protection strategy demonstrated that the transfected U1 antitarget RNA level varied between 1 to 8% of the endogenous U1 snRNA level. U1 antitarget vectors were demonstrated to have potential as effective inhibitors of gene expression in intact cells.

Inhibitory effects of antisense oligonucleotides on the expression of procollagen type III gene in mouse hepatic stellate cells transformed by simian virus 40

The effects of phosphorothioate antisense oligonucleotides (ASO), complementary to the AUG start region, the junctional region of the intron and exon, and to exon of the procollagen type III gene, were investigated in a mouse hepatic stellate cell (HSC) line transformed by the simian virus 40 gene, SV68c-IS cells. ASO were transfected by lipofection. Immunohistochemistry, western and northern blotting showed inhibitory effects on procollagen type III gene expression by ASO that were complementary to the AUG start region and the junctional region of the intron and exon 2. However, ASO complementary to the exon 2 and 3, junctional region of the intron and exon 3, and sense oligonucleotides complementary to each ASO did not show any inhibitory effects. The effects of ASO complementary to the AUG start region were greater than those of ASO complementary to the junctional region. The effects of ASO were transient and a large amount of ASO was required to induce inhibitory effects without lipofection. ASO were effective in inhibiting the expression of the procollagen type III gene in the HSC which is well known to play a critical role in liver fibrosis.

Selecting optimal antisense reagents

Selection of the appropriate target site is crucial to the success of an antisense experiment. The selection is difficult because RNAs fold to form secondary structures, rendering most of the molecule inaccessible to intermolecular base pairing with complementary nucleic acids. Conventional approaches, such as selection by 'sequence-walking' or computer-assisted design, have not brought significant success. Several empirical selection methods have been reported, a number of which are summarised in this review. Of notable significance are the 'global' methods based on mapping of transcripts with the endoribonuclease H (RNase H) and oligonucleotide scanning arrays.

Osteogenesis imperfecta: prospects for molecular therapeutics

Osteogenesis Imperfecta (OI) is a dominant negative disorder of connective tissue. OI patients present with bone fragility and skeletal deformity within a broad phenotypic range. Defects in the COL1A1 or COL1A2 genes, coding, respectively, for the alpha1 and alpha2 chains of type I collagen, are the causative mutations. Over 150 mutations have been characterized. Both quantitative defects, such as null COL1A1 alleles, and qualitative defects, such as glycine substitutions, exon skipping, deletions, and insertions, have been described in type I collagen. Quantitative and structural mutations are associated with the milder and more severe forms of OI, respectively. A more detailed relationship between genotype and phenotype is still incompletely understood; several models have been proposed and are being tested. Transgenic and knock-out murine models for OI have previously been created. We have recently generated a knock-in murine model (the Brittle mouse) carrying a typical glycine substitution in type I collagen. This mouse will permit a better understanding of OI pathophysiology and phenotypic variability. It will also be used for gene therapeutic approaches to OI, especially mutation suppression by hammerhead ribozymes. The present review will provide an update of OI clinical and molecular data and outline gene therapeutic approaches being tested on OI murine models for this disorder.

Effects of RNA secondary structure on cellular antisense activity

The secondary and tertiary structures of a mRNA are known to effect hybridization efficiency and potency of antisense oligonucleotides in vitro. Additional factors including oligonucleotide stability and cellular uptake are also thought to contribute to antisense potency in vivo. Each of these factors can be affected by the sequence of the oligonucleotide. Although mRNA structure is presumed to be a critical determinant of antisense activity in cells, to date little direct experimental evidence has addressed the significance of structure. In order to determine the importance of mRNA structure on antisense activity, oligonucleotide target sites were cloned into a luciferase reporter gene along with adjoining sequence to form known structures. This allowed us to study the effect of target secondary structure on oligonucleotide binding in the cellular environment without changing the sequence of the oligonucleotide. Our results show that structure does play a significant role in determining oligonucleotide efficacy in vivo. We also show that potency of oligonucleotides can be improved by altering chemistry to increase affinity for the mRNA target even in a region that is highly structured.

Determining the influence of structure on hybridization using oligonucleotide arrays

We have studied the effects of structure on nucleic acid heteroduplex formation by analyzing hybridization of tRNAphe to a complete set of complementary oligonucleotides, ranging from single nucleotides to dodecanucleotides. The analysis points to features in tRNA that determine heteroduplex yield. All heteroduplexes that give high yield include both double-stranded stems as well as single-stranded regions. Bases in the single-stranded regions are stacked onto the stems, and heteroduplexes terminate at potential interfaces for coaxial stacking. Heteroduplex formation is disfavored by sharp turns or a lack of helical order in single-stranded regions, competition from bases displaced from a stem, and stable tertiary interactions. The study is relevant to duplex formation on oligonucleotide microarrays and to antisense technologies.

Antisense oligonucleotides containing modified bases inhibit in vitro translation of Leishmania amazonensis mRNAs by invading the mini-exon hairpin

Complementary oligodeoxynucleotides (ODNs) that contain 2-aminoadenine and 2-thiothymine interact weakly with each other but form stable hybrids with unmodified complements. These selectively binding complementary (SBC) agents can invade duplex DNA and hybridize to each strand (Kutyavin, I. V., Rhinehart, R. L., Lukhtanov, E. A., Gorn, V. V., Meyer, R. B., and Gamper, H. B. (1996) Biochemistry 35, 11170-11176). Antisense ODNs with similar properties should be less encumbered by RNA secondary structure. Here we show that SBC ODNs strand invade a hairpin in the mini-exon RNA of Leishmania amazonensis and that the resulting heteroduplexes are substrates for Escherichia coli RNase H. SBC ODNs either with phosphodiester or phosphorothioate backbones form more stable hybrids with RNA than normal base (NB) ODNs. Optimal binding was observed when the entire hairpin sequence was targeted. Translation of L. amazonensis mRNA in a cell-free extract was more efficiently inhibited by SBC ODNs complementary to the mini-exon hairpin than by the corresponding NB ODNs. Nonspecific protein binding in the cell-free extract by phosphorothioate SBC ODNs rendered them ineffective as antisense agents in vitro. SBC phosphorothioate ODNs displayed a modest but significant improvement of leishmanicidal properties compared with NB phosphorothioate ODNs.

Retrovirally transduced bone marrow stromal cells isolated from a mouse model of human osteogenesis imperfecta (oim) persist in bone and retain the ability to form cartilage and bone after extended passaging

Bone marrow stromal cells isolated from a model of osteogenesis imperfecta (oim) mice, were transduced with a retrovirus (BAG) carrying the LacZ and neor genes after passage 21. The transduced cells retained the ability to express alkaline phosphatase activity in vitro when treated with recombinant human bone morphogenetic protein two (rhBMP-2), formed cartilage in vitro in aggregate cultures and formed bone in ceramic cubes after 6 weeks of implantation in nude mice. X-gal staining of ceramic cubes seeded with the transduced cells demonstrated the presence of LacZ-positive cells on the edges of bone and also in the lacunae of the newly formed bone 6 weeks after implantation. After infusion into femurs of oim mice, the transduced cells were detected in the marrow cavity and on the edges of the trabecular bone of the injected and contralateral femurs by X-gal staining and PCR analysis at 4, 10, 20, 30 and 40 days after injection. The LacZ gene was also detected in the lung and liver of the recipient mice at 4 and 10 days after injection but not at later time-periods. The present findings suggest that long-term cultured bone marrow stromal cells from osteogenesis imperfecta (OI) animals have the potential to traffic through the circulatory system, home to bone, form bone and continue to express exogenous genes. These findings open the possibility of using these cells as vehicles to deliver normal genes to bone as an alternative approach for the treatment of some forms of OI and certain other bone acquired and genetic diseases.

Tetranucleotide GGGA motif in primary RNA transcripts. Novel target site for antisense design

Selecting effective antisense target sites on a given mRNA molecule constitutes a major problem in antisense therapeutics. By trial-and-error, only 1 in 18 (6%) of antisense oligonucleotides designed to target the primary RNA transcript of tumor necrosis factor-alpha (TNF-alpha) strongly inhibited TNF-alpha synthesis. Subsequent studies showed that the area in RNA targeted by antisense oligonucleotides could be moved effectively 10-15 bases in either direction from the original area. We observed that only molecules that incorporated a tetranucleotide motif TCCC (complementary to GGGA on RNA) yielded potent antisense oligonucleotides against TNF-alpha. A comprehensive literature survey showed that this motif is unwittingly present in 48% of the most potent antisense oligonucleotides reported in the literature. This finding was prospectively used to predict the sequences of additional antisense oligonucleotides for the rat TNF-alpha primary RNA transcript. Over 50% of antisense constructs (13 of 22) containing the TCCC motif were found to effectively inhibit TNF-alpha synthesis. Marked reductions in mRNA were also observed. This motif was found to be most effective when targeting introns in the primary RNA transcript, suggesting a nuclear localization for the antisense action. Predicting target sites based on the presence of this motif in primary RNA transcripts should be of value in the development on new antisense pharmacotherapy.

Autocrine transforming growth factor beta stimulation of extracellular matrix production by fibroblasts from fibrotic human gingiva

Hereditary gingival fibromatosis (HGF) is a fibrotic enlargement of the gingiva. HGF gingiva contains large amounts of collagen and other extracellular matrix (ECM) molecules. In vitro, HGF fibroblasts produce greater amounts of the ECM components fibronectin (FN) and type 1 collagen than normal human gingival (GN) fibroblasts. Transforming growth factor beta (TGF beta) is a cytokine important in regulating tissue repair and regeneration after injury, and stimulating fibroblast proliferation and the production of FN and collagens. The objective of this study was to determine whether HGF fibroblasts produce TGF beta and, with the use of neutralizing antibodies to TGF beta isoforms, if their increased expression of FN and type 1 collagen is under autocrine TGF beta control. The HGF strains produced greater amounts of TGF beta1 and TGF beta2 (P < or = 0.003) as well as FN (P < or = 0.04) and type 1 collagen (P < or = 0.03) (measured by specific ELISA) than the GN strains. Treatment of HGF fibroblasts with anti-TGF beta1, beta2, or beta3, as well as a combination of all 3 antibodies, decreased their FN production by up to 60% (P < or = 0.04), and was able to decrease FN production by HGF fibroblasts to the levels of the GN fibroblasts. When used alone, the neutralizing antibodies decreased type 1 collagen production by the HGF fibroblasts by up to 40% (P = 0.014), and treatment with all 3 antibodies caused decreases of up to 55% (P = 0.0005). The results suggest that autocrine stimulation by the increased amounts of TGF beta isoforms made by HGF fibroblasts contributes to their increased production of FN and type 1 collagen.

Halofuginone: a novel antifibrotic therapy

1. Fibrosis is characterized by extracellular matrix deposition, of which collagen type I is the major constituent. The progressive accumulation of connective tissue resulted in destruction of normal tissue architecture and function. 2. Fibrosis is a common response to various insults or injuries and can be the outcome of any perturbation in the cellular function of any tissue. 3. Halofuginone was found to inhibit collagen alpha 1(I) gene expression and collagen synthesis in a variety of cell cultures including human fibroblasts derived from patients with excessive skin collagen type I synthesis. 4. Halofuginone was found to inhibit collagen alpha 1(I) gene expression and collagen synthesis in animal models characterized by excessive deposition of collagen. In these models, fibrosis was induced in various tissues such as skin, liver, lung, etc. Halofuginone was injected intraperitoneally, added to the foodstuff or applied locally. 5. Halofuginone decreased skin collagen in a chronic graft-versus-host disease patient. 6. The ability of extremely low concentrations of halofuginone to inhibit collagen alpha 1(I) synthesis specifically and transiently at the transcriptional level suggests that this material fulfills the criteria for a successful and effective anti-fibrotic therapy.

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.

A rapid in vitro method for obtaining RNA accessibility patterns for complementary DNA probes: correlation with an intracellular pattern and known RNA structures

A technique is described to identify the rare sequences within an RNA molecule that are available for efficient interaction with complementary DNA probes: the target RNA is digested by RNase H in the presence of a random pool of complementary DNA fragments generated from the same DNA preparation that was used for target RNA synthesis. The DNA region was amplified by PCR, partially digested with DNase and denatured prior to RNA binding. In the presence of single-stranded DNA fragments the RNA was digested with RNase H such that, on average, each molecule was cut once. Cleavage sites were detected by gel electrophoresis either directly with end-labeled RNA or by primer extension. The pattern of accessible sites on c- raf mRNA was determined and compared with the known profile of activity of oligonucleotides found in cells, showing the merit of the method for predicting oligonucleotides which are efficient for in vivo antisense targeting. New susceptible sites in the 3'-untranslated region of c- raf mRNA were identified. Also, four RNAs were probed to ascertain to what extent structure predicts accessibility: the P4-P6 domain of the Tetrahymena group I intron, yeast tRNAAsp, Escherichia coli tmRNA and a part of rat 18S rRNA.

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.

Antisense strategies in neurobiology

The use of antisense oligodeoxynucleotides, targeted to the transcripts encoding biologically active proteins in the nervous system, provides a novel and highly selective means to further our understanding of the function of these proteins. Recent studies of these agents also suggest the possibility of their being used therapeutically for a variety of diseases involving neuronal tissue. In this paper we review studies showing the in vitro and in vivo effects of antisense oligodeoxynucleotides as they relate to neurobiological functions. Particular attention is paid to the behavioral and biochemical effects of antisense oligodeoxynucleotides directed to the various subtypes of receptors for the neurotransmitter dopamine. An example is also provided showing the effects of a plasmid vector expressing an antisense RNA targeted to the calmodulin mRNAs in the PC12 pheochromocytoma cell line. The advantages of antisense oligodeoxynucleotides over traditional pharmacological treatments are assessed, and the advantages of using vectors encoding antisense RNA over the use of antisense oligodeoxynucleotides are also considered. We also describe the criteria that should be used in designing antisense oligodeoxynucleotides and several controls that should be employed to assure their specificity of action.

Inhibition of human TNF alpha and LT in cell-free extracts and in cell culture by antisense oligonucleotides

Antisense oligonucleotides (ODN), complementary to mRNA of human tumor necrosis factor alpha (TNF alpha) and lymphotoxin (LT) were tested for their ability to inhibit TNFs. TNFs production was studied in cell-free systems including wheat germ extract (WGE) and rabbit reticulocyte lysate (RRL). All ODN were effective in WGE at low concentration (0.2 microM), except those targeted to the 3' region of TNF alpha mRNA. A short ODN complementary to a common region between TNF alpha and LT inhibited both TNFs. In contrast, high ODN concentration (50 microM) was needed to inhibit LT mRNA translation in RRL, whereas no clear inhibition of TNF alpha was observed unless RNase H was added to the translation mixture. ODN effects on TNFs production by stimulated cell line in culture were also investigated. Three ODN-one located in the 5'-untranslated region, one spanning the AUG initiation codon and one downstream of this AUG-were the most effective sequences to decrease TNF alpha production. Two ODN targeted to the AUG initiation codon of LT were also able to inhibit its production. In conclusion we confirm the role of RNase H in cell free systems, and we found that there is no correlation between ODN efficiency in a cell-free system nor in cell culture. Efficient ODN could be used for in vitro investigation of the role of TNF alpha and LT in mechanism in which they are involved.

Transcription factor Egr-1 regulates glomerular mesangial cell proliferation

Increase of glomerular mesangial cells (MCs) is a prominent histopathological finding in many types of glomerulonephritis. We have shown previously that expression of the zinc-finger transcription factor, early growth response gene-1 (egr-1), is closely correlated with the proliferation of cultured MCs. To elucidate whether Egr-1 is required for MC proliferation, we inhibited serum-induced Egr-1 expression by phosphothioate-modified antisense oligonucleotides (ODNs). Uptake of antisense ODNs into MCs was demonstrated, and five different egr-1 antisense ODNs were tested for their impact on serum-induced egr-1 mRNA and protein levels and on MC growth. The most potent egr-1 antisense ODN inhibited serum-induced egr-1 mRNA by 68%, protein induction by 58%, and MC replication as measured by [3H]thymidine uptake and cell counts by 78 and 46%, respectively. The effects of antisense ODNs on MC growth correlated closely with their ability to inhibit Egr-1 protein. ODNs acted in a dose-dependent manner, the minimal effective concentration being 1 microM. Control ODNs had no significant effects. In addition, antisense ODNs against egr-1 potently inhibited endothelin-1-induced Egr-1 expression and MC growth. Heparin, a known inhibitor of MC growth, suppressed serum-induced [3H]thymidine uptake by 39% and egr-1 mRNA expression by 44%. We conclude that Egr-1 is an essential part of the mitogenic signal transduction cascade in cultured MCs.

Role of extracellular matrix in experimental vasospasm. Inhibitory effect of antisense oligonucleotide on collagen induction

BACKGROUND AND PURPOSE

Although it has been suggested that collagen plays a role in the pathogenesis of cerebral vasospasm after subarachnoid hemorrhage, there has been no constructive research to prove it directly. In this study we stopped the transcription of the procollagen type I gene by introducing antisense oligonucleotides for its mRNA in a rat femoral artery model of vasospasm induced by blood and assayed the changes in the vasoconstrictive activity of the vessel and expression of the procollagen mRNA.

METHODS

We applied antisense, sense, or missense oligonucleotides, located at the carboxyl propeptide region for alpha 1(I) procollagen mRNA, onto the femoral artery in a rat femoral artery model of vasospasm. The diameter of the artery was measured by angiography. The transcription level of the procollagen gene in the arterial tissue was assayed by use of reverse transcription-polymerase chain reaction. Morphological change in the artery was observed with aldehyde-fuchsin-Masson-Goldner staining.

RESULTS

In the model, when the artery was exposed to antisense oligonucleotides in pluronic gel for 5 days to prevent arterial contraction, the contraction was inhibited at a significant level (76.0% +/- 5.6) when compared with that in control experiments using sense oligonucleotides (64.0% +/- 2.4), missense oligonucleotides (63.5% +/- 3.5), or gel alone (62.1% +/- 5.8). The application of antisense oligonucleotide resulted in a marked decrease in alpha 1(I) procollagen mRNA expression as determined by polymerase chain reaction, indicating that the collagen reduction by antisense oligonucleotides occurred at the transcription level. Histological staining suggested that collagen accumulation at the site in the artery where antisense oligonucleotide had been administered was indeed less than that in the control artery.

CONCLUSIONS

The results indicate that the induction of procollagen type 1 could cause pathogenesis of the arterial contraction induced by blood in a rat femoral vasospasm model.

Potent and selective inhibition of gene expression by an antisense heptanucleotide

Factors that govern the specificity of an antisense oligonucleotide (ON) for its target RNA include accessibility of the targeted RNA to ON binding, stability of ON/RNA complexes in cells, and susceptibility of the ON/RNA complex to RNase H cleavage. ON specificity is generally proposed to be dependent on its length. To date, virtually all previous antisense experiments have used 12-25 nt-long ONs. We explored the antisense activity and specificity of short (7 and 8 nt) ONs modified with C-5 propyne pyrimidines and phosphorothioate internucleotide linkages. Gene-selective, mismatch sensitive, and RNase H-dependent inhibition was observed for a heptanucleotide ON. We demonstrated that the flanking sequences of the target RNA are a major determinant of specificity. The use of shorter ONs as antisense agents has the distinct advantage of simplified synthesis. These results may lead to a general, cost-effective solution to the development of antisense ONs as therapeutic agents.

Efficient and specific ribozyme-mediated reduction of bovine alpha-lactalbumin expression in double transgenic mice

Transgenic mice carrying a bovine alpha-lactalbumin (alpha-lac) specific ribozyme gene under the transcriptional control of the mouse mammary tumor virus long terminal repeat were generated and cross-bred with animals that highly express a bovine alpha-lac transgene (0.4 mg of alpha-lac/ml(-1) of milk). The ribozyme contains the hammerhead catalytic domain, flanked by 12-nt sequences complementary to the 3' untranslated region of bovine alpha-lac transcript. High-level expression of the ribozyme gene was detected by Northern blot analysis in the mammary gland of 7-8 day lactating transgenic mice, from 3 of 12 lines analyzed. Heterozygous expression of the ribozyme resulted in a reduction in the levels of the target mRNA to 78, 58, and 50% of that observed in the nonribozyme transgenic littermate controls for three independent lines. The ribozyme-mediated reduction in the levels of the bovine protein paralleled that observed for the mRNA, and was positively correlated with the level of expression of the ribozyme. In nonribozyme expressing transgenic mice, the level of bovine alpha-lac mRNA and protein was not affected. The specificity of this activity is demonstrated by the absence of a reduction in the levels of the endogenous murine alpha-lac mRNA or protein. These results demonstrate the feasibility of ribozyme-mediated down-regulation of highly-expressed transcripts in transgenic animals.

Potent antisense oligonucleotides to the human multidrug resistance-1 mRNA are rationally selected by mapping RNA-accessible sites with oligonucleotide libraries

Antisense oligonucleotides can vary significantly and unpredictably in their ability to inhibit protein synthesis. Libraries of chimeric oligonucleotides and RNase H were used to cleave and thereby locate sites on human multidrug resistance-1 RNA transcripts that are relatively accessible to oligonucleotide hybridization. In cell culture, antisense sequences designed to target these sites were significantly more active than oligonucleotides selected at random. This methodology should be generally useful for identification of potent antisense sequences. Correlation between oligonucleotide activity in the cell culture assay and in an in vitro RNase H assay supports the proposed role of the enzyme in the mechanism of antisense suppression in the cell.

Triple helix-forming oligonucleotide corresponding to the polypyrimidine sequence in the rat alpha 1(I) collagen promoter specifically inhibits factor binding and transcription

Type I and III fibrillar collagens are the major structural proteins of the extracellular matrix found in various organs including the myocardium. Abnormal and progressive accumulation of fibrillar type I collagen in the interstitial spaces compromises organ function and therefore, the study of transcriptional regulation of this gene and specific targeting of its expression is of major interest. Transient transfection of adult cardiac fibroblasts indicate that the polypurine-polypyrimidine sequence of alpha 1(I) collagen promoter between nucleotides - 200 and -140 represents an overall positive regulatory element. DNase I footprinting and electrophoretic mobility shift assays suggest that multiple factors bind to different elements of this promoter region. We further demonstrate that the unique polypyrimidine sequence between -172 and -138 of the promoter represents a suitable target for a single-stranded polypurine oligonucleotide (TFO) to form a triple helix DNA structure. Modified electrophoretic mobility shift assays show that this TFO specifically inhibits the protein-DNA interaction within the target region. In vitro transcription assays and transient transfection experiments demonstrate that the transcriptional activity of the promoter is inhibited by this oligonucleotide. We propose that TFOs represent a therapeutic potential to specifically influence the expression of alpha 1(I) collagen gene in various disease states where abnormal type I collagen accumulation is known to occur.

Antisense oligodeoxynucleotides selectively suppress expression of the mutant alpha 2(I) collagen allele in type IV osteogenesis imperfecta fibroblasts. A molecular approach to therapeutics of dominant negative disorders

We are investigating the use of antisense oligodeoxynucleotides to selectively suppress expression of the mutant type I collagen allele in osteogenesis imperfecta (OI). In this report, we target a human collagen mutation in its natural cellular context. We used cultured fibroblasts from a case of type IV OI, in which the mutant alpha 2(I) allele produces mRNA with exon 16 deleted due to a point mutation in the splice donor site. Lipid-mediated transfection was used to deliver antisense, sense and missense phosphorothioates targeted to both the abnormal mRNA exon 15/17 junction and the nuclear level point mutation. Significant suppression of the mutant protein chain and mRNA was achieved with antisense oligonucleotide to both mRNA and nuclear levels. Mutant protein was suppressed to 44-47% and mutant alpha 2(I) mRNA to 37-43% of their levels in control cells, indicating decreased mRNA as the basis for suppression. Selectivity of mutant allele suppression was better with an mRNA target: suppression was sequence specific and normal mRNA was expressed at 79% of its level in untreated cells. With a nuclear target, significant suppression of mutant mRNA occurred not only with antisense and sense, but also with missense oligonucleotide, which suppressed mutant mRNA to 60% of its level in untreated cells. We also investigated the time course of suppression of protein and mRNA in response to a 4 h transfection of antisense oligonucleotide. From 24-72 h after transfection, mutant protein was suppressed to approximately 50% of its untreated level and suppression of mutant message was significantly greater than that of normal message. The suppression achieved in these studies is insufficient for clinical intervention, but our results provide support for further development of antisense therapy as an approach to the treatment of dominant negative disorders.

An in vitro messenger RNA binding assay as a tool for identifying hybridization-competent antisense oligonucleotides

The apparent dissociation constants for 32 phosphodiester and 5 phosphorothioate antisense oligodeoxyribonucleotides (ODN) targeted to murine tumor necrosis factor-alpha (mTNF-alpha) mRNA were determined using a gel-shift binding assay. In this assay, radiolabeled ODN were hybridized in solution to a structured mRNA transcript generated in vitro. Free ODN was resolved from bound ODN on a two-phase discontinuous polyacrylamide gel. Excision of gel slices containing free ODN or bound ODN, followed by Cerenkov counting of the slices, was used to prepare apparent binding isotherms for each ODN. Apparent dissociation constants for the anti-mTNF-alpha ODN varied from > 100 microM to 0.4 nM. Slight differences in RNA target site position resulted in significant differences in apparent affinity, particularly for shorter (12-mer) ODN. This binding assay provides an empirical means for selecting ODN sequences possessing high affinity for a target RNA and lends itself to a high throughput assay in which all possible antisense sequences of a given length can be evaluated to obtain the better binders for use in cell culture or in vivo.