Chimeric Oligonucleotides Research Articles

Targeted beta-globin gene conversion in human hematopoietic CD34(+ )and Lin(-)CD38(-)cells.

Chimeric oligonucleotides have been used successfully to correct point and frameshift mutations in several cell types, as well as in animal and plant models. However, their application to primitive human blood cells has been limited. In this investigation, chimeric oligonucleotides designed to direct a site-specific nucleotide exchange in the human beta-globin gene (an A to T substitution within codon 6) were introduced into normal human CD34(+) and Lin(-)CD38(-) cells via microinjection. This A to T nucleotide exchange introduces the single site mutation responsible for sickle cell anemia. In 23% of experimental samples, gene conversion was detected in the progeny of microinjected CD34(+) and Lin(-)CD38(-) cells that were cultured for at least 4 weeks. In addition, gene conversion was detected in the erythroid progeny of Lin(-)CD38(-) cells at the mRNA level. Conversion rates as high as 10-15% in 11% (five of 44) of experimental samples were confirmed by allele-specific PCR and sequence analysis of genomic DNA from the progeny of microinjected Lin(-)CD38(-) cells. Given that as few as 10% normal hematopoietic cells are sufficient to keep patients free of sickle cell disease, the level of conversion we have achieved in some samples may well be of therapeutic benefit in patients with sickle cell disease.

Gene correction frequency by chimeric RNA-DNA oligonucleotide using nuclear extracts.

Gene correction frequency by chimeric RNA-DNA oligonucleotide using nuclear extracts.

Gene replacement by homologous recombination in plants.

After the elucidation of the sequence of the yeast genome a major effort was started to elucidate the biological function of all open reading frames of this organisms by targeted gene replacement via homologous recombination. The establishment of the complete sequence of the genome of Arabidopsis thaliana would principally allow a similar approach. However, over the past dozen years all attempts to establish an efficient gene targeting technique in flowering plants were in the end not successful. In contrast, in Physcomitrella patens an efficient gene targeting procedure has been set up, making the moss a valuable model system for plant molecular biologists. But also for flowering plants recently several new approaches--some of them based on the availability of the genomic sequence of Arabidopsis--were initiated that might finally result on the set up of a general applicable technique. Beside the production of hyper-recombinogenic plants either via expression or suppression of specific gene functions or via undirected mutagenesis, the application of chimeric oligonucleotides might result in major progress.

Chimeric oligonucleotides based on 2'-O-modified oligoribonucleotides with the terminal 3'-3' internucleotide linkage as potential inhibitors of MDR 1 gene expression

Chimeric constructs were synthesized based on oligoribonucleotides modified at the 2"-position of the ribose (2"-O-tetrahydropyranyl- or 2"-O-methyl-) and at the 3"-terminus of the oligonucleotide chain (terminal 3"—3" internucleotide linkage), which are complementary to a region of MDR 1 mRNA. A comparative study of the properties of these chimeric constructs was performed. The chimeric oligomers with the modified 3"-terminus are characterized by high stability with respect to 3"-exonucleases, form stable complementary complexes with RNA, and can activate RNase H in a duplex with RNA.

Crystallization of the Zalpha domain of the human editing enzyme ADAR1 complexed with a DNA-RNA chimeric oligonucleotide in the left-handed Z-conformation.

The Zalpha domain of human double-stranded RNA adenosine deaminase (ADAR1) has been crystallized with a hexanucleotide containing alternating deoxyribose and ribose furanose sugars. Solution circular dichroism experiments show that this double-stranded chimera (dCrG)(3) initially adopts the right-handed A-conformation. However, addition of stoichiometric amounts of Zalpha causes a rapid transition to the Z-conformation. Raman spectroscopy of crystals of the Zalpha-(dCrG)(3) complex confirm that the chimeric oligonucleotide is stabilized in the Z-conformation. A complete data set has been obtained at 2.5 A resolution. The Zalpha-(dCrG)(3) crystals belong to the tetragonal I422 space group, with unit-cell parameters a = b = 104.2, c = 117.6 A. Work is under way to solve the structure by molecular replacement.

α- l-RNA (α- l- ribo Configured RNA): Synthesis and RNA-Selective Hybridization of α- l-RNA/α- l-LNA Chimera

Synthesis of the novel α- l-ribofuranosyl phosphoramidite derivative 7 was accomplished via the α- l-ribofuranosyl thymine nucleoside 4 . Amidite 7 was used in automated syntheses of chimeric oligonucleotides composed of mixtures of the novel α- l-RNA nucleotide monomer ( αL T, α- l- ribo configured RNA), and DNA, LNA ( T L , locked nucleic acid) or α- l-LNA ( αL T L , α- l- ribo configured locked nucleic acid) nucleotide monomers. For α- l-RNA/DNA and α- l-RNA/α- l-LNA chimeras, RNA-selective hybridization was obtained, for α- l-RNA/α- l-LNA chimera we found increased binding affinity compared to the corresponding DNA:RNA reference duplex. In addition, α- l-RNA/α- l-LNA chimera displayed significant stabilization towards 3′-exonucleolytic degradation. These results indicate that α- l-RNA/α- l-LNA chimeras deserve further evaluation as antisense molecules.

Inhibition of HIV-1 Tat-Dependent Trans Activation by Steric Block Chimeric 2‘-O-Methyl/LNA Oligoribonucleotides

The HIV-1 trans-activation responsive element (TAR) RNA 59-residue stem-loop interacts with the HIV trans-activator protein Tat and other cellular factors to stimulate transcriptional elongation from the viral long terminal repeat (LTR). Inhibition of these interactions blocks full-length HIV transcription and hence replication. We have found that three types of 12-residue oligonucleotide analogues, namely, a 2'-O-methyl oligoribonucleotide (OMe), a chimeric oligonucleotide containing 7xOMe and 5x5-methyl C locked nucleic acid (LNA) residues, and a peptide nucleic acid (PNA), inhibit Tat-dependent in vitro transcription in HeLa cell nuclear extract equally efficiently (50% inhibition at 100-200 nM) and sequence specifically. The results are correlated with surprisingly similar binding strengths to a model 39-residue TAR under transcription conditions. A 12-mer containing 11 contiguous LNA residues was less effective in both Tat-dependent transcription inhibition and TAR 39 binding. Anti-TAR 3'-carboxyfluorescein- (FAM-) labeled OMe and OMe/LNA chimeric 12-mers were also efficient Tat-dependent in vitro transcription inhibitors as were 3'-FAM-labeled OMe oligonucleotides containing some phosphorothioate (PS) linkages. By use of a HeLa cell line containing stably integrated plasmids expressing firefly luciferase under HIV-LTR/Tat dependence as well as a Renilla luciferase constitutive control, we showed submicromolar, selective, dose-dependent, and sequence-dependent intracellular inhibition of Tat-TAR trans activation by the anti-TAR 3'-FAM 12-residue 7xOMe/5xLNA oligonucleotide when delivered by cationic lipid. No intracellular activity was observed for the corresponding anti-TAR 3'-FAM OMe 12-mer. An alternating PS-containing 3'-FAM OMe 12-mer oligonucleotide exhibited partial inhibition of trans-activation activity, but this was correlated with a similar effect on control gene expression, suggesting nonspecific inhibition.

Mapping 2′-O-Methyl Groups in Ribosomal RNA

Ribosomal RNAs (rRNAs) from all sources contain modified nucleosides, whose numbers range from a few in mitochondrial rRNA to more than 200 in the complete rRNAs of some higher eukaryotes. In eukaryotic rRNA the great majority of modified nucleosides are 2′-O-methylated nucleosides or pseudouridines. The locations of most of the 2′-O-methylated nucleosides in rRNA from some representative eukaryotes are known from studies whose aim was full characterization of rRNA methylation. More recently, and particularly in connection with the discovery of methylation guide RNAs, it is often required to check for the presence or absence of 2′-O-methyl nucleosides at specified locations within rRNA. Three methods that can be applied for such “local” objectives are reviewed. Two of the methods are based on primer extension by reverse transcriptase. They exploit, respectively, a tendency of 2′-O-methyl groups to impede reverse transcriptase at low dNTP concentrations, or the resistance of phosphodiester bonds adjacent to 2′-O-methyl groups to alkaline hydrolysis. Examples of these methods are summarized. Although the two methods are relatively straightforward, they suffer from various experimental limitations, as discussed. The third method is technically more sophisticated but is capable of overcoming the limitations of the first two methods. It is based on the resistance of a target 2′-O-methylated site to cleavage by RNase H when the site is hybridized to an appropriate chimeric oligonucleotide. An overview of the approaches and methods now available for the complete mapping of 2′-O-methyl groups in rRNA is presented.

Prospects of chimeric RNA-DNA oligonucleotides in gene therapy.

A strategy called targeted gene repair was developed to facilitate the process of gene therapy using a chimeric RNA-DNA oligonucleotide. Experiments demonstrated the feasibility of using the chimeric oligonucleotide to introduce point conversion in genes in vitro and in vivo. However, barriers exist in the low and/or inconstant frequency of gene repair. To overcome this difficulty, three main aspects should be considered. One is designing a more effective structure of the oligonucleotide. Trials have included lengthening the homologous region, displacing the mismatch on the chimeric strand and inventing a novel thioate-modified single-stranded DNA, which was demonstrated to be more active than the primary chimera in cell-free extracts. The second aspect is optimizing the delivery system. Producing synthetic carriers for efficient and specific transfection is demanding, especially for treatment in vivo where targeting is difficult. The third and most important aspect lies in the elucidation of the mechanism of the strategy. Investigation of the mechanism of strand exchange between the oligonucleotide molecule and double-stranded DNA in prokaryotes may greatly help to understand the mechanism of gene repair in eukaryotes. The development of this strategy holds great potential for the treatment of genetic defects and other purposes.

In vivo gene repair of point and frameshift mutations directed by chimeric RNA/DNA oligonucleotides and modified single-stranded oligonucleotides.

Synthetic oligonucleotides have been used to direct base exchange and gene repair in a variety of organisms. Among the most promising vectors is chimeric oligonucleotide (CO), a double-stranded, RNA-DNA hybrid molecule folded into a double hairpin conformation: by using the cell's DNA repair machinery, the CO directs nucleotide exchange as episomal and chromosomal DNA. Systematic dissection of the CO revealed that the region of contiguous DNA bases was the active component in the repair process, especially when the single-stranded ends were protected against nuclease attack. Here, the utility of this vector is expanded into Saccharomyces cerevisiae. An episome containing a mutated fusion gene encoding hygromycin resistance and eGFP expression was used as the target for repair. Substitution, deletion and insertion mutations were corrected with different frequencies by the same modified single-stranded vector as judged by growth in the presence of hygromycin and eGFP expression. A substitution mutation was repaired the most efficiently followed by insertion and finally deletion mutants. A strand bias for gene repair was also observed; vectors designed to direct the repair of nucleotide on the non-transcribed (non-template) strand displayed a 5-10-fold higher level of activity. Expanding the length of the oligo-vector from 25 to 100 nucleotides increases targeting frequency up to a maximal level and then it decreases. These results, obtained in a genetically tractable organism, contribute to the elucidation of the mechanism of targeted gene repair.

3'-5' Exonucleolytic activity of DNA polymerases: structural features that allow kinetic discrimination between ribo- and deoxyribonucleotide residues.

We have determined rates for the excision of nucleotides from the 3' termini of chimeric DNA-RNA oligonucleotides using the Klenow fragment (KF) and two other DNA polymerases, from phages T4 and T7. For these studies, we synthesized DNA-RNA chimeric oligonucleotides with RNA residues in defined positions. When a ribonucleotide residue was placed at the 3' terminus, all three DNA polymerases removed it at the same rate as they did for substrates composed solely of deoxynucleotide residues. There was a decrease in the excision rate, however, when a ribonucleotide residue was located at the second or third position from the 3' terminus. When both the second and third positions were occupied by ribonucleotide residues, the excision rate for the 3' terminal nucleotide was reduced even further and was almost identical to the rate observed when the DNA polymerases encountered single-stranded RNA. The magnitude of the effect of ribonucleotide residues on the excision rate was lower when Mn(2+) replaced Mg(2+) as the essential divalent cation. Two KF mutations, Y423A and N420A, selectively affected the excision rates for the chimeric substrates. Specifically, Y423A totally abolished the rate reduction when there was a single ribonucleotide residue immediately preceding the 3' terminus, whereas N420A diminished, but did not eliminate, the rate reduction relative to that of wild-type KF when the single ribonucleotide residue occupied either the second or third position from the 3' terminus. These results are consistent with the structure of a KF-ss DNA complex from which it can be deduced, by modeling, that a 2' OH group on the second sugar from the 3' terminus would sterically clash with the Tyr 423 side chain, and a 2' OH group on the third sugar would clash with the side chain of Asn 420. The corresponding mutations in T4 DNA polymerase did not affect the rate of hydrolysis of the chimeric oligonucleotides. Thus, there appears to be a major difference in the kinetic behavior of KF and T4 DNA polymerase with respect to the exonuclease reaction. These results are discussed with respect to their possible biological relevance to DNA replication.

Identifying ribozyme-accessible sites using NUH triplet-targeting gapmers.

Accurately identifying accessible sites in RNA is a critical prerequisite for optimising the cleavage efficiency of hammerhead ribozymes and other small nucleozymes. Here we describe a simple RNase H-based procedure to rapidly identify hammerhead ribozyme-accessible sites in gene length RNAS: Twelve semi-randomised RNA-DNA-RNA chimeric oligonucleotide probes, known as 'gapmers', were used to direct RNase H cleavage of transcripts with the specificity expected for hammerhead ribozymes, i.e. after NUH sites (where H is A, C or U). Cleavage sites were identified simply by the mobility of RNase H cleavage products relative to RNA markers in denaturing polyacrylamide gels. Sites were identified in transcripts encoding human interleukin-2 and platelet-derived growth factor. Thirteen minimised hammerhead ribozymes, miniribozymes (Mrz), were synthesised and in vitro cleavage efficiency (37 degrees C, pH 7.6 and 1 mM MgCl2) at each site was analysed. Of the 13 Mrz, five were highly effective, demonstrating good initial rate constants and extents of cleavage. The speed and accuracy of this method commends its use in screening for hammerhead-accessible sites.

Nuclease resistance and RNase H sensitivity of oligonucleotides bridged by oligomethylenediol and oligoethylene glycol linkers.

The properties of new chimeric oligodeoxynucleotides made of short sequences (tetramers, pentamers, octamers, and decamers) bridged by hexamethylenediol and hexaethylene glycol linkers have been investigated. These chimeric oligonucleotides showed an improved resistance toward snake venom 3'-phosphodiesterase, with an increased stability when a terminal 3'-3'-internucleotide phosphodiester bond is present. It also has been demonstrated that the hybrid complexes formed by bridged oligonucleotides and a complementary 20-mer RNA are able to elicit the activity of ribonuclease H (RNase H) from Escherichia coli. The substrate properties of chimeric oligonucleotides depend on the length of the oligonucleotide fragments bridged by linkers. Introduction of a nonnucleotide spacer into the native oligonucleotide only slightly hampers the extent of the RNA hydrolysis in the hybrid complexes, whereas a modification of the site of reaction is observed as a possible consequence of the steric disturbance due to the aliphatic linkers. Hence, these new chimeric oligonucleotides, namely, short oligonucleotide fragments bridged by nonnucleotide linkers, demonstrate a favorable combination of exonuclease resistance and high substrate activity toward RNase H. As a consequence, these chimeric oligonucleotides could be proposed as new, promising analogs to be used in the antisense strategy.

Cryptic splicing involving the splice site mutation in the canine model of Duchenne muscular dystrophy

Golden retriever muscular dystrophy arises from a mutation in the acceptor splice site of intron 6 of the dystrophin gene. Skipping of exon 7 disrupts the mRNA reading frame and results in premature termination of translation. We are using this animal model to evaluate treatments for Duchenne muscular dystrophy, including gene repair induced by chimeric oligonucleotides. After injection of golden retriever muscular dystrophy (GRMD) muscle with a chimeric oligonucleotide to repair the lesion, immunostaining revealed a modest increase in the number of dystrophin-positive fibres at the injection sites. Dystrophin gene transcripts containing exon 7 were detected by reverse transcription-polymerase chain reaction, suggesting that low levels of splice site correction may have occurred. However, DNA sequencing of these apparently normal dystrophin gene transcripts revealed that the first five bases of exon 7 were missing. It will be important to be aware of this phenomenon with respect to further gene correction studies in the canine model.

Targeted gene correction by small single-stranded oligonucleotides in mammalian cells.

We demonstrate that relatively short single-stranded oligodeoxynucleotides, 25-61 bases homologous to the target sequence except for a single mismatch to the targeted base, are capable of correcting a single point mutation (G to A) in the mutant beta-galactosidase gene, in nuclear extracts, episome, and chromosome of mammalian cells, with correction rates of approximately 0.05%, 1% and 0.1%, respectively. Surprisingly, these short single-stranded oligonucleotides (ODN) showed a similar gene correction frequency to chimeric RNA-DNA oligonucleotide, measured using the same system. The in vitro gene correction induced by ODN in nuclear extracts was not dependent on the length or polarity of the oligonucleotide. In contrast, the episomal and chromosomal gene corrections were highly dependent on the ODN length and polarity. ODN with a homology of 45 nucleotides showed the highest frequency and ODN with antisense orientation showed a 1000-fold higher frequency than sense orientation, indicating a possible influence of transcription on gene correction. Deoxyoligonucleotides showed a higher frequency of gene correction than ribo-oligonucleotides of the identical sequence. These results show that a relatively short ODN can make a sequence-specific change in the target sequence in mammalian cells, at a similar frequency as the chimeric RNA-DNA oligonucleotide.

Targeted Correction of the Point Mutations of β-Thalassemia and Targeted Mutagenesis of the Nucleotide Associated with HPFH by RNA/DNA Oligonucleotides: Potential for β-Thalassemia Gene Therapy

ABSTRACTAn RNA/DNA chimeric oligonucleotide was found to be effective in the targeted correction of point mutations in Escherichia coli, plant, and mammalian genomes. This strategy, named chimeraplasty, has the potential for gene therapy of many genetic diseases caused by point mutations. β-Thalassemia is a very common human genetic disease and in most cases it is caused by point mutations. To test whether the chimeraplasty can be used to correct the point mutations responsible for β-thalassemia, we introduced one mutated β-globin gene, βE, into MEL cells and successfully corrected the point mutation of the βE gene with the highest correction efficiency of 1.9%. Furthermore, a targeted —202 C→G mutation of the Gγ-globin gene, which is associated with the elevated Gγ-globin gene expression in the adult stage, was introduced into HeLa and CMK cells by an RNA/DNA oligonucleotide. These results indicated that the chimeraplasty has potential for human β-thalassemia gene therapy.

Progress in gene therapy for Duchenne muscular dystrophy.

Gene transfer research for Duchenne muscular dystrophy (DMD) has brought the goal of successful treatment of this devastating, inherited disease closer to being a reality. Although gene therapeutic approaches for DMD patients are not yet in clinical use, recent advances using DMD animal models are encouraging. Progress in vector design, such as high-capacity adenoviral vectors, targeted adenoviral vectors, and heterodimerization of DNA delivered by adeno-associated virus (AAV) vectors have advanced the field considerably. The recent studies into the pharmacologic-induced read-through of stop codons, the increased study of utrophin and its upregulation, and the introduction of point mutation correction using chimeric oligonucleotides have expanded the field, providing new avenues of inquiry.

27. Future perspectives for Tay-Sachs disease

Publisher Summary This chapter discusses that researchers are currently investigating a variety of intriguing experimental approaches to treat neurodegenerative lysosomal storage disorders like Tay-Sachs disease (TSD). These include substrate deprivation, chemical chaperones, neural stem cell transplantation, and in vivo treatment with chimeric oligonucleotides. Substrate deprivation therapy is designed to decrease the rate of substrate accumulation by inhibition of an early enzyme in the synthesis of the glycolipid precursors of G M2 ganglioside. Potential therapeutic approach for the chronic and adult-onset patients with G M2 gangliosidosis involves the use of small inhibitors that act as chemical chaperones for unstable enzymes with residual activity. Experimental transplantation of neural stem cells in the central nervous system of animal models with various lysosomal diseases is currently underway in several laboratories. Understanding and supporting their needs, medical and emotional, is the cornerstone of medical management for many families who have an affected child, particularly if they have no normal children. The extension of prenatal carrier screening to premarital carrier screening has also proven effective and has met the special cultural needs of the religious community.

Evidence for a four-strand exchange catalyzed by the RecA protein.

Strand exchange between two duplexes is usually initiated as a three-strand event that requires the presence of a single-stranded overhang or gap in one of the two molecules. Here we show that the RecA protein can catalyze a four-strand exchange. Specifically, it can recombine short hairpin substrates with homologous stems provided that one of the hairpins possesses a chimeric DNA/RNA backbone. This four-strand exchange reaction goes to completion in the presence of ATPgammaS and releases a stable heteroduplex upon removal of the RecA protein. Under identical conditions, strand exchange between two DNA hairpins is incomplete and generates a nascent heteroduplex that rapidly dissociates when the RecA protein is denatured. Since presynaptic filament formation does not appear to melt either type of hairpin, we propose that exchange occurs between homologously aligned duplexes that are extended and unwound within a RecA filament. The first reaction provides a mechanism for gene targeting by chimeric double-hairpin oligonucleotides while the second reaction explains the ability of the RecA protein to transiently align double-stranded DNA molecules.

The DNA strand of chimeric RNA/DNA oligonucleotides can direct gene repair/conversion activity in mammalian and plant cell-free extracts.

Chimeric oligonucleotides (chimeras), consisting of RNA and DNA bases folded by complementarity into a double hairpin conformation, have been shown to alter or repair single bases in plant and animal genomes. An uninterrupted stretch of DNA bases within the chimera is known to be active in the sequence alteration while RNA residues aid in complex stability. In this study, the two strands were separated in the hope of defining the role each plays in conversion. Using a series of single-stranded oligonucleotides, comprised of all RNA or DNA residues and various mixtures, several new structures have emerged as viable molecules in nucleotide conversion. When extracts from mammalian and plant cells and a genetic readout assay in bacteria are used, single-stranded oligonucleotides, containing a defined number of thioate backbone modifications, were found to be more active than the original chimera structure in the process of gene repair. Single-stranded oligonucleotides containing fully modified backbones were found to have low repair activity and in fact induce mutation. Molecules containing various lengths of modified RNA bases (2'-O-methyl) were also found to possess low activity. Taken together, these results confirm the directionality of nucleotide conversion by the DNA strand of the chimera and further present a novel, modified single-stranded DNA molecule that directs conversion in plant and animal cell-free extracts.