Phosphorothioate oligodeoxynucleotides: what is their origin and what is unique about them?

Synthesis of novel deoxynucleoside S-methylphosphonic acids using S-(diisopropylphosphonomethyl)isothiouronium tosylate, a new equivalent of mercaptomethylphosphonate

The synthesis of the novel nucleotide analogues 5'-deoxynucleoside-5'-S-methylphosphonates, starting from 5'-deoxy-5'-haloribonucleosides, 5'-O-tosylribonucleosides, and 2'-O-triflylnucleosides, is described. The phosphonothiolation of these compounds was achieved using S-(diisopropylphosphonomethyl)isothiouronium tosylate, a new, odourless, and efficient equivalent of mercaptomethylphosphonate. The thiolate anion of mercaptomethylphosphonate was generated in situ from the isothiouronium salt in both protic and aprotic solvents using two equivalents of sodium iso-propoxide. The prepared nucleoside 5'-S-methylphosphonates were deprotected, and the free phosphonic acids were transformed into diphosphoryl derivatives (the NTP analogues). Both mononucleotides and NTP analogues were studied as substrates/inhibitors of several enzymes that are involved in the nucleoside/nucleotide metabolism.

Effect of MANT-nucleotides on L-type calcium currents in murine cardiomyocytes

Membranous adenylyl cyclases play a major role in G-protein-coupled receptor signalling and regulate various cellular responses, such as cardiac contraction. Cardiac apoptosis and development of cardiac dysfunction is prevented in mice lacking AC 5, a predominant isoform in the heart. In the search for a potent and selective AC 5 inhibitor, we recently identified 2'(3')-methylanthraniloyl-inosine-5'-triphosphate(MANT-ITP) as the most potent AC 5 inhibitor with a K ( i ) of 13 nM. Therefore, AC inhibition of MANT-ITP was assessed in ventricular cardiomyocytes and compared to three other MANT-nucleotides to evaluate its effect on cardiac signalling. Basal and isoproterenol-induced L-type calcium currents (I (Ca,L)) in murine ventricular cardiomyocytes were recorded by whole-cell patch-clamp technique, using four different MANT-nucleotides. The effects of the MANT-nucleotides on I (Ca,L) were unexpectedly complex. All MANT-nucleotides exhibited an inhibitory effect on basal I (Ca,L). Additionally, several MANT-nucleotides, i.e., MANT-ITPγS, MANT-ATP, and MANT-ITP, caused a strong initial increase in basal I (Ca,L) within the first 2.5 min that appeared to be unrelated to AC 5 inhibition. However, we detected a significant reduction on isoproterenol-induced I (Ca,L) with MANT-ITP, supporting the notion that AC 5 plays an important role in agonist-stimulated activation of I (Ca,L). Collectively, MANT-nucleotides are useful tools for the characterization of recombinant ACs, for fluorescence studies and crystallography, but in intact cardiomyocytes, caution must be exerted since MANT-nucleotides apparently possess additional effects than AC 5 inhibition, limiting their usefulness as tools for intact cell studies.

Dinucleotides containing 3'-S-phosphorothiolate linkages

The 3'-S-phosphorothiolate (3'-SP) linkage has proven to be a very useful analogue of the phosphodiester group in nucleic acid derivatives; it is achiral and also shows good resistance to nucleases. Whilst oligonucleotides containing a 3'-SP linkage are best prepared using phosphoramidite chemistry, the corresponding dinucleotides are most efficiently synthesised using a Michaelis-Arbuzov reaction between a nucleoside 5'-phosphite and a nucleoside 3'-S-disulphide. The method described here is for a thymidine dinucleotide and is based on the use of a silyl phosphite, which is more reactive than simple alkyl phosphites and also simplifies the deprotection strategy. Full experimental details and spectroscopic data for the synthetic intermediates and the target dinucleotide are provided.

An exocyclic methylene group acts as a bioisostere of the 2'-oxygen atom in LNA

We show for the first time that it is possible to obtain LNA-like (Locked Nucleic Acid 1) binding affinity and biological activity with carbocyclic LNA (cLNA) analogs by replacing the 2'-oxygen atom in LNA with an exocyclic methylene group. Synthesis of the methylene-cLNA nucleoside was accomplished by an intramolecular cyclization reaction between a radical at the 2'-position and a propynyl group at the C-4' position. Only methylene-cLNA modified oligonucleotides showed similar thermal stability and mismatch discrimination properties for complementary nucleic acids as LNA. In contrast, the close structurally related methyl-cLNA analogs showed diminished hybridization properties. Analysis of crystal structures of cLNA modified self-complementary DNA decamer duplexes revealed that the methylene group participates in a tight interaction with a 2'-deoxyribose residue of the 5'-terminal G of a neighboring duplex, resulting in the formation of a CH...O type hydrogen bond. This indicates that the methylene group retains a negative polarization at the edge of the minor groove in the absence of a hydrophilic 2'-substituent and provides a rationale for the superior thermal stability of this modification. In animal experiments, methylene-cLNA antisense oligonucleotides (ASOs) showed similar in vivo activity but reduced toxicity as compared to LNA ASOs. Our work highlights the interchangeable role of oxygen and unsaturated moieties in nucleic acid structure and emphasizes greater use of this bioisostere to improve the properties of nucleic acids for therapeutic and diagnostic applications.

Diastereomerically pure nucleoside-5'-O-(2-thio-4,4-pentamethylene-1,3,2-oxathiaphospholane)s--substrates for synthesis of P-chiral derivatives of nucleoside-5'-O-phosphorothioates

A method for stereocontrolled chemical synthesis of P-substituted nucleoside 5'-O-phosphorothioates has been elaborated. Selected 3'-O-acylated deoxyribonucleoside- and 2',3'-O,O-diacylated ribonucleoside-5'-O-(2-thio-4,4-pentamethylene-1,3,2-oxathiaphospholane)s were chromatographically separated into P-diastereomers. Their reaction with anions of phosphorus-containing acids was highly stereoselective (≥90%) and furnished corresponding P-chiral α-thiodiphosphates and their phosphonate analogs with satisfactory yield.

Conjugation of antisense oligonucleotides to PEGylated carbon nanotubes enables efficient knockdown of PTPN22 in T lymphocytes

PEGylated-carbon nanotubes (PNTs) were evaluated as nanocarriers of antisense oligonucleotides into T-cells using protein tyrosine phosphatase N22 (PTPN22) as a model target gene. PTPN22 is an important predisposing gene and drug target in type 1 diabetes and several other human autoimmune diseases. Here, we generated the first anti-PTPN22 20-mer antisense oligonucleotides (ASOs) and tethered them to PNTs through a cleavable disulfide bond. Spectroscopic and atomic force microscopy analyses were used to determine the loading of ASO onto PNTs, whereas the cleavable nature of the disulfide bond connecting the oligonucleotide to the nanocarrier was confirmed by incubation with dithiothreitol followed by agarose gel electrophoresis. PNT-conjugated ASOs achieved efficient (>50%) knockdown of PTPN22 expression in T-lymphocytes in culture at the mRNA and protein level, as measured by quantitative real-time PCR and Western blotting, respectively. Considering the high biocompatibility and low in vivo toxicity of PNTs, we expect that our approach will be easily translated to achieve in vivo knockdown of PTPN22 and other T lymphocyte targets, thus enabling novel ASO-mediated immunotherapies for type 1 diabetes and other autoimmune diseases.

A dual surface plasmon resonance assay for the determination of ribonuclease H activity

There is a demand for efficient tools for the monitoring of RNase H activity. We report on a new assay which allows for simultaneous (1) real-time monitoring of RNase H activity and (2) detection of cleavage reaction products. The dual assay is implemented using a multichannel surface plasmon resonance (SPR) biosensor with two independently functionalized sensing areas in a single fluidic path. In the first sensing area the RNA cleavage by RNase H is monitored, while the products of the cleavage reaction are captured in the second sensing area with specific DNA probes. The assay was optimized with respect to AON concentration and temperature. A significant improvement was obtained with special chimeric probes, which contain RNA substrate for RNase H and a longer deoxyribonucleotide tail, which enhances the SPR signal. It has been shown that RNase H stabilizes the RNA:DNA hybrid duplex before the cleavage. The potential of the assay is demonstrated in the study in which the ability of natural and modified oligonucleotides to activate RNase H is examined.

Zinc-finger nuclease-driven targeted integration into mammalian genomes using donors with limited chromosomal homology

We previously demonstrated high-frequency, targeted DNA addition mediated by the homology-directed DNA repair pathway. This method uses a zinc-finger nuclease (ZFN) to create a site-specific double-strand break (DSB) that facilitates copying of genetic information into the chromosome from an exogenous donor molecule. Such donors typically contain two approximately 750 bp regions of chromosomal sequence required for homology-directed DNA repair. Here, we demonstrate that easily-generated linear donors with extremely short (50 bp) homology regions drive transgene integration into 5-10% of chromosomes. Moreover, we measure the overhangs produced by ZFN cleavage and find that oligonucleotide donors with single-stranded 5' overhangs complementary to those made by ZFNs are efficiently ligated in vivo to the DSB. Greater than 10% of all chromosomes directly incorporate this exogenous DNA via a process that is dependent upon and guided by complementary 5' overhangs on the donor DNA. Finally, we extend this non-homologous end-joining (NHEJ)-based technique by directly inserting donor DNA comprising recombinase sites into large deletions created by the simultaneous action of two separate ZFN pairs. Up to 50% of deletions contained a donor insertion. Targeted DNA addition via NHEJ complements our homology-directed targeted integration approaches, adding versatility to the manipulation of mammalian genomes.

Noninvasive visualization of RNA delivery with 99mTc-radiolabeled small-interference RNA in tumor xenografts

Small-interference RNAs (siRNAs) are short, double-strand RNA molecules that target specific messenger RNAs for degradation via the process termed RNA interference. The efficacy of RNA interference depends greatly on effective delivery of siRNA, which calls for noninvasive methods for tracing siRNA in vivo. The purpose of this work was to develop a novel (99m)Tc-radiolabeled method to visualize siRNA targeting of a tumor biomarker of human telomerase reverse transcriptase (hTERT) in HepG2 tumor xenografts.

METHODS

After conjugation with S-acetyl N-hydroxysuccinimide-mercaptoacetyltriglycine (NHS-MAG3), antisense RNA with 2'-O-methyl modification was annealed with sense strand to form a duplex and then radiolabeled with (99m)Tc. (99m)Tc-siRNAs were tested for stability in serum by measurement of radiochemical purity and for inhibitory activity by reverse-transcriptase polymerase chain reaction and Western blotting. In vitro cellular uptake was evaluated in HepG2 cells. Biodistribution studies and static imaging were performed in HepG2 tumor-bearing mice.

RESULTS

Radiochemical purity remained highly stable in saline and fresh human serum at room temperature and 37 degrees C. Radiolabeled siRNA demonstrated strong inhibitory effects similar to those of unlabeled siRNA on both hTERT messenger RNA and protein in vitro. (99m)Tc-hTERT siRNA showed more uptake than did control siRNA in HepG2 cells after 1 h of incubation. After administration in HepG2 tumor-bearing mice, (99m)Tc-hTERT siRNA had significantly higher accumulation in tumors and a higher tumor-to-blood ratio than did control siRNA (P < 0.05). Scintigraphy of (99m)Tc-hTERT siRNA showed clear tumor images at 0.5, 1, 3, and 6 h after injection. In contrast, (99m)Tc-control siRNA failed to visualize the tumor. Ratios of uptake in tumor to uptake in contralateral region of hTERT-targeted siRNA were significantly higher than those of control siRNA (P < 0.05) at each time point.

CONCLUSION

The (99m)Tc radiolabeling method with NHS-MAG3 chelator can be used successfully in siRNA radiolabeling, allowing for the noninvasive visualization of siRNA delivery in vivo.

Antisense oligonucleotides containing conformationally constrained 2',4'-(N-methoxy)aminomethylene and 2',4'-aminooxymethylene and 2'-O,4'-C-aminomethylene bridged nucleoside analogues show improved potency in animal models

To identify chemistries and strategies to improve the potency of MOE second generation ASOs, we have evaluated gapmer antisense oligonucleotides containing BNAs having N-O bonds. These modifications include N-MeO-amino BNA, N-Me-aminooxy BNA, 2',4'-BNA(NC)[NMe], and 2',4'-BNA(NC) bridged nucleoside analogues. These modifications provided increased thermal stability and improved in vitro activity compared to the corresponding ASO containing the MOE modification. Additionally, ASOs containing N-MeO-amino BNA, N-Me-aminooxy BNA, and 2',4'-BNA(NC)[NMe] modifications showed improved in vivo activity (>5-fold) compared to MOE ASO. Importantly, toxicity parameters, such as AST, ALT, liver, kidney, and body weights, were found to be normal for N-MeO-amino BNA, N-Me-aminooxy BNA, and 2',4'-BNA(NC)[NMe] ASO treated animals. The data generated in these experiments suggest that N-MeO-amino BNA, N-Me-aminooxy BNA, and 2',4'-BNA(NC)[NMe] are useful modifications for applications in both antisense and other oligonucleotide based drug discovery efforts.

RNA targeting therapeutics: molecular mechanisms of antisense oligonucleotides as a therapeutic platform

Dramatic advances in understanding of the roles RNA plays in normal health and disease have greatly expanded over the past 10 years and have made it clear that scientists are only beginning to comprehend the biology of RNAs. It is likely that RNA will become an increasingly important target for therapeutic intervention; therefore, it is important to develop strategies for therapeutically modulating RNA function. Antisense oligonucleotides are perhaps the most direct therapeutic strategy to approach RNA. Antisense oligonucleotides are designed to bind to the target RNA by well-characterized Watson-Crick base pairing, and once bound to the target RNA, modulate its function through a variety of postbinding events. This review focuses on the molecular mechanisms by which antisense oligonucleotides can be designed to modulate RNA function in mammalian cells and how synthetic oligonucleotides behave in the body.

Synthesis and hybridization of oligonucleotides modified at AMP sites with adenine pyrrolidine phosphonate nucleotides

Three structurally diverse types of the protected pyrrolidine nucleoside phosphonates were prepared as the monomers for the introduction of pyrrolidine nucleotide units into modified oligonucleotides on the solid phase. Two different chemistries were used for incorporation of modified and natural units: the phosphotriester method for the former, i.e., monomers containing N-phosphonoalkyl and N-phosphonoacyl moieties attached to the pyrrolidine ring nitrogen atom, and phosphoramidite chemistry for the latter. Since the synthesized pyrrolidine nucleoside phosphonic acids are close mimics of the 3′-deoxynucleoside 5′-phosphates, the incorporation of one modified unit into oligonucleotides gives rise to one 2′,5′ internucleotide linkage. A series of nonamers containing two or three modified units, as well as the fully modified adenine 15-mer, were synthesized in reverse order, i.e., from the 5′ to the 3′ end of the strand. The measurement of thermal characteristics of the complexes of modified nonamers with the complementary strand revealed a destabilizing effect of the introduced modification. The modified adenine homooligonucleotide, was found to form the most stable complex with oligothymidylate of all the tested modified oligonucleotides in terms of ΔTm per modification.

Solid-supported reagents for synthesis of nucleoside monothiophosphates, dithiodiphosphates, and trithiotriphosphates

This unit describes procedures for the selective synthesis of nucleoside monothiophosphates, dithiodiphosphates, and trithiotriphosphates from solid-supported phosphitylating reagents. Rigid and sterically hindered polymer-bound 1,3,2-oxathiaphospholane is reacted selectively with the 5'-hydroxyl group of nucleosides in the presence of 1H-tetrazole. Sulfurization in the presence of Beaucage's reagent (3H-1,2-benzodithiole-3-one 1,1-dioxide) followed by ring-opening with 3-hydroxypropionitrile and basic cleavage in the presence of 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) through the elimination of polymer-bound ethylene episulfide afford nucleoside monothiophosphates. Furthermore, reaction of polymer-bound diphosphitylating and triphosphitylating reagents, prepared from polymer-bound benzyl alcohol, with unprotected nucleosides, sulfurization with Beaucage's reagent, and acidic cleavage using trifluoroacetic acid cocktail produce nucleoside dithiodiphosphates and trithiotriphosphates in moderate yields.

Studies on the hydrolytic stability of 2'-fluoroarabinonucleic acid (2'F-ANA)

The stability of 2'-deoxy-2'-fluoroarabinonucleic acid (2'F-ANA) to hydrolysis under acidic and basic conditions was compared to that of DNA, RNA and 2'F-RNA. In enzyme-free simulated gastric fluid (pH approximately 1.2), 2'F-ANA was found to have dramatically increased stability (virtually no cleavage observed after 2 days) with respect to both DNA (t(1/2) approximately 2 min) and RNA (t(1/2) approximately 3 h (PO) or 3 days (PS)). These results were observed for both phosphodiester and phosphorothioate backbones and with multiple mixed-base sequences. Under basic conditions, 2'F-ANA also showed good stability. In 1 M NaOH at 65 degrees C, 2'F-ANA had a t(1/2) of approximately 20 h, while RNA was entirely degraded in a few minutes. Furthermore, the nuclease cleavage of phosphorothioate 2'F-ANA and DNA by snake venom phosphodiesterase was studied in detail. One diastereomer of the PS-2'F-ANA linkage was found to be much more vulnerable to enzymatic cleavage than the other, which is parallel to the properties observed for PS-DNA. Additional studies of 2'F-ANA-containing oligonucleotides are warranted based on the excellent stability properties described here.

Short antisense oligonucleotides with novel 2'-4' conformationaly restricted nucleoside analogues show improved potency without increased toxicity in animals

The potency of second generation antisense oligonucleotides (ASOs) in animals was increased 3- to 5 -fold (ED(50) approximately 2-5 mg/kg) without producing hepatotoxicity, by reducing ASO length (20-mer to 14-mer) and by employing novel nucleoside modifications that combine structural elements of 2'-O-methoxyethyl residues and locked nucleic acid. The ability to achieve this level of potency without any formulation agents is remarkable and likely to have a significant impact on the future design of ASOs as therapeutic agents.

Solid-phase synthesis of stereoregular oligodeoxyribonucleoside phosphorothioates using bicyclic oxazaphospholidine derivatives as monomer units

Nucleoside 3'-O-bicylic oxazaphospholidine derivatives were designed as monomer units for a solid-phase synthesis of stereoregular oligodeoxyribonucleoside phosphorothioates (PS-ODNs). The trans-isomers of appropriately designed nucleoside 3'-O-bicyclic oxazaphospholidine derivatives were generated exclusively by the reaction between the 3'-OH of the corresponding protected nucleosides and 2-chloro-1,3,2-oxazaphospholidine derivatives. The resultant trans-oxazaphospholidine isomers were configurationally stable, and their diastereopurity was not impaired by epimerization in the presence of an acidic activator during the condensation on a solid support. As a result, the formation of both (Rp)- and (Sp)-phosphorothioate internucleotide linkages by using the oxazaphospholidine monomers and the acidic activator proceeded without any loss of diastereopurity (diastereoselectivity > or = 99:1). In addition, ab initio molecular orbital calculations showed that the epimerization of oxazaphospholidine derivatives was most likely to proceed via an edge inversion process that was accelerated by N-protonation. The calculations rationalized not only the relations between the ring structure and the configurational stability of the oxazaphospholidines observed in this study but also the observations reported in the literature that the inversion of tricoordinated organophosphorus compounds were accelerated by acids or nucleophiles.

Spermine moiety attached to the C-5 position of deoxyuridine enhances the duplex stability of the phosphorothioate DNA/complementary DNA and shows the susceptibility of the substrate to RNase H

Novel phosphorothioate-modified oligodeoxynucleotides (S-ODNs) containing a deoxyuridine derivative bearing a spermine moiety at the C-5 position were synthesized. The study of the thermal stability and the thermodynamic stability showed that the modified S-ODNs have been able to form the stable duplexes with the complementary DNA. It was also found that the duplex composed of the modified S-ODN and its complementary RNA strand is the substrate for Escherichia coli RNase H, and the cleavage of the RNA strand by the enzyme was almost similar as in the case of the unmodified one.

Effective delivery of antisense peptide nucleic acid oligomers into cells by anthrax protective antigen

Peptide nucleic acid (PNA) is highly stable and binds to complementary RNA and DNA with high affinity, but it resists cellular uptake, thereby limiting its bioavailability. We investigated whether protectiveantigen (PA, a non-toxic component of anthrax toxin) could transport antisense PNA oligomers into reporter cells that contain luciferase transgenes with mutant beta-globin IVS2 intronic inserts, which permit aberrant pre-mRNA splicing and impair luciferase expression. PNA oligomers antisense to mutant splice sites in these IVS2 inserts induced luciferase expression when effectively delivered into the cells. PNA 18-mers with C-terminal poly-lysine tails [PNA(Lys)(8)] demonstrated modest sequence-specific antisense activity by themselves at micromolar concentrations in luc-IVS2 reporter cell cultures. However, this activity was greatly amplified by PA. Antisense PNA(Lys)(8) with but not without PA also corrected the IVS2-654 beta-globin splice defect in cultured erythroid precursor cells from a patient with beta-thalassemia [genotype, IVS2-654(beta(0)/beta(E))], providing further evidence that anthrax PA can effectively transport antisense PNA oligomers into cells.

Significance of stereochemistry of 3'-terminal phosphorothioate-modified primer in DNA polymerase-mediated chain extension

Influence of stereochemistry of the 3'-terminal phosphorothioate (PS)-modified primers was studied in a single base extension (SBE) assay to evaluate any improvements in specificity. SBE reactions were catalyzed by members of the high fidelity Pfu family of DNA polymerases with (exo+) or without (exo-) 3' --> 5' exonucleolytic activity. The diastereomerically pure PS-labeled primers used in these studies were obtained either by the stereospecific chemical synthesis invented in our laboratory or by the more conventional ion-exchange chromatographic method for separation of a mixture of diastereomers (R(P) and S(P)). When the SBE reaction was performed in the presence of mispaired 2'-deoxyribonucleoside triphosphates (dNTPs), the "racemic" 3'-phosphorothioate primer mixture resulted in a lower level of 3' --> 5' exonuclease-mediated cleavage products in comparison to the SBE reactions carried out with the corresponding unmodified primer. When the diastereomerically pure RP 3'-phosphorothioate primer was examined, the results were largely the same as for the racemic 3'-phosphorothioate primer mixture. In contrast, a 3'-PS primer of S(P) configuration displayed significantly improved performance in the SBE reaction. This included the lack of 3' --> 5' proofreading products, less mispriming, and improved yield of incorporation of the correct nucleotide.

Evidences for complex formation between L-dabPNA and aegPNA

Continuing our research on the development of nucleopeptides as ODN analogs for biomedical and bioengineering applications, here we report the synthesis and the chemical-physical characterization of a homoadenine hexamer based on a l-diaminobutyric acid (l-DABA) backbone (dabPNA), and its binding studies with a complementary aegPNA. We demonstrated by CD and UV experiments that the l-dabPNA binds the aegPNA forming a complex with good thermal stability, that we identified as a left-handed triplex.

Synthesis of phosphorothioate oligonucleotides with stereodefined phosphorothioate linkages

A method for solid-phase synthesis of stereodefined PS-oligos via an oxathiaphospholane approach using pure P-diastereomers of nucleoside oxathiaphospholane monomers is described. The oxathiaphospholane monomers are synthesized by phosphitylation of 5'-O-DMTr-N-protected deoxyribonucleosides with 2-chloro-spiro-4,4-pentamethylene-1,3,2-oxathiaphospholane followed by sulfurization. The procedure is general and may be applied to other analogs, depending on the aldehyde (or mercaptoalcohol) used. Starting from an 18O-labeled mercaptoalcohol, the corresponding 18O-labeled phosphitylating reagent and nucleoside monomers can be obtained and used for synthesis of labeled stereodefined PS-oligos, which are useful for studying mechanisms of enzymatic reactions. Details are provided for chromatographic separation of the 5'-O-DMTr-N-protected-deoxyribonucleoside-3'-O-(2-thio-spiro-4,4-pentamethylene-1,3,2-oxathiaphospholane)s into their P-diastereomers, and for manual solid-phase synthesis of PS-oligos. Oxidation of 5'-O-DMTr-N-protected-deoxyribonucleoside-3'-O-(2-thio-spiro-4,4-pentamethylene-1,3,2-oxathiaphospholane)s with selenium dioxide yields their 2-oxo-analogs, which are suitable either for elongation of stereodefined PS-oligos with segments consisting of unmodified nucleotide units possessing phosphate internucleotide linkages, or for generating isotopomeric 18O-labeled PO-oligos of predetermined P-chirality.

2′F-Arabinonucleic acids (2′F-ANA) — History, properties, and new frontiers

The development of arabinonucleosides and oligoarabinonucleotides is described, focusing especially on 2′-deoxy-2′-fluoroarabinonucleosides (araF-N) and -oligonucleotides (2'F-ANA). In addition to their chemical and enzymatic synthesis, we discuss various properties of 2′F-ANA: hydrolytic stability (to nucleases, acids, and bases), binding affinity to complementary strands, structure and conformation, and optimization of RNase H activity. We also discuss the use of 2′F-ANA in gene-silencing approaches (antisense, siRNA), and in the stabilization of higher-order structures (such as triplexes and quadruplexes) including aptamers. Finally, we examine several other oligonucleotide derivatives based on 2′F-ANA and look ahead to the future of 2′-fluoroarabinonucleosides and -oligonucleotides.Key words: arabinonucleic acids, 2′F-ANA, antisense oligonucleotides, siRNA, modified oligonucleotides.

Nonviral approaches for targeted delivery of plasmid DNA and oligonucleotide

Successful gene therapy depends on the development of efficient delivery systems. Although pDNA and ODN are novel candidates for nonviral gene therapy, their clinical applications are generally limited owing to their rapid degradation by nucleases in serum and rapid clearance. A great deal of effort had been devoted to developing gene delivery systems, including physical methods and carrier-mediated methods. Both methods could improve transfection efficacy and achieve high gene expression in vitro and in vivo. As for carrier-mediated delivery in vivo, since gene expression depends on the particle size, charge ratio, and interaction with blood components, these factors must be optimized. Furthermore, a lack of cell-selectivity limits the wide application to gene therapy; therefore, the use of ligand-modified carriers is a promising strategy to achieve well-controlled gene expression in target cells. In this review, we will focus on the in vivo targeted delivery of pDNA and ODN using nonviral carriers.

Discrimination in metal-ion binding to RNA dinucleotides with a non-bridging oxygen or sulfur in the phosphate diester link

Replacement of a non-bridging oxygen in the phosphate diester bond by a sulfur has become quite popular in nucleic acid research and is often used as a probe, for example, in ribozymes, where the normally essential Mg(2+) is partly replaced by a thiophilic metal ion to reactivate the system. Despite these widely applied rescue experiments no detailed studies exist quantifying the affinity of metal ions to such terminal sulfur atoms. Therefore, we performed potentiometric pH titrations to determine the binding properties of pUp((S))U(3-) towards Mg(2+), Mn(2+), Zn(2+), Cd(2+), and Pb(2+), and compared these data with those previously obtained for the corresponding pUpU(3-) complexes. The primary binding site in both dinucleotides is the terminal phosphate group. Theoretically, also the formation of 10-membered chelates involving the terminal oxygen or sulfur atoms of the (thio)phosphate bridge is possible with both ligands. The results show that Mg(2+) and Mn(2+) exist as open (op) isomers binding to both dinucleotides only at the terminal phosphate group. Whereas Cd(pUpU)(-) only exists as Cd(pUpU)(-)(op), Cd(pUp((S))U)(-) is present to about 64 % as the S-coordinated macrochelate, Cd(pUp((S))U)(-)(cl/PS). Zn(2+) forms with pUp((S))U(3-) three isomeric species, that is, Zn(pUp((S))U)(-)(op), Zn(pUp((S))U)(-)(cl/PO), and Zn(pUp((S))U)(-)(cl/PS), which occur to about 33, 12 (O-bound), and 55 %, respectively. Pb(2+) forms the 10-membered chelate with both nucleotides involving only the terminal oxygen atoms of the (thio)phosphate bridge, that is, no indication of S binding was discovered in this case. Hence, Zn(2+) and Cd(2+) show pronounced thiophilic properties, whereas Mg(2+), Mn(2+), and Pb(2+) coordinate to the oxygen, macrochelate formation being of relevance with Pb(2+) only.

Combinatorial selection of a single stranded DNA thioaptamer targeting TGF-beta1 protein

A phosphorothioate single-stranded DNA aptamer (thioaptamer) targeting transforming growth factor-beta1 (TGF-beta1) was isolated by in-vitro combinatorial selection. The aptamer selection procedure was designed to modify the backbone of single-stranded DNA aptamers, where 5' of both A and C are phosphorothioates, since this provides enhanced nuclease resistance as well as higher affinity than that of a phosphate counterpart. The thioaptamer selected from a combinatorial library (5x10(14) sequences) binds to TGF-beta1 protein with an affinity of 90 nM. In this report, sequence, predicted secondary structure, and binding affinity of the selected thioaptamer (T18_1_3) are presented.

1,3,2-Oxathiaphospholane approach to the synthesis of P-chiral stereodefined analogs of oligonucleotides and biologically relevant nucleoside polyphosphates

Among the various classes of modified nucleotides and oligonucleotides, phosphorothioate analogs, in which the sugar-phosphate backbone is modified by the substitution of a sulfur atom for one of the nonbridging oxygen atoms, have been most extensively studied in both in vitro and in vivo experiments. However, this substitution induces P-chirality of the dinucleoside phosphorothioate moiety. Consequently, even short phosphorothioate oligonucleotides synthesized using standard chemical methods exist as mixtures of many diastereoisomers. In our laboratory, the oxathiaphospholane (OTP) method has been developed for a stereocontrolled synthesis of oligo(deoxyribonucleoside phosphorothioate)s. Recently, this approach has been extended to ribonucleoside derivatives, and stereodefined phosphorothioate diribonucleotides were incorporated into oligomers suitable for mechanistic studies on deoxyribozymes. Next, it was found that the OTP ring can be opened with nucleophiles as weak as the phosphate or pyrophosphate anion, giving rise to nucleoside α-thiopolyphosphates. Surprisingly, the reaction between nucleoside OTP and O,O-dialkyl H-phosphonate or O,O-dialkyl H-phosphonothioate led to nucleoside 5'-O-(α-thio-β-O,O-dialkyl-hypophosphate) or 5'-O-(α,β-dithio-β-O,O-dialkyl-hypophosphate), respectively, i.e., derivatives containing a direct P-P bond.

Gene modulation for treating liver fibrosis

Despite tremendous progress in our understanding of fibrogenesis, injury stimuli process, inflammation, and hepatic stellate cell (HSC) activation, there is still no standard treatment for liver fibrosis. Delivery of small molecular weight drugs, proteins, and nucleic acids to specific liver cell types remains a challenge due to the overexpression of extracellular matrix (ECM) and consequent closure of sinusoidal gaps. In addition, activation of HSCs and subsequent release of inflammatory cytokines and infiltration of immune cells are other major obstacles to the treatment of liver fibrosis. To overcome these barriers, different therapeutic approaches are being investigated. Among them, the modulation of certain aberrant protein production is quite promising for treating liver fibrosis. In this review, we describe the mechanism of antisense, antigene, and RNA interference (RNAi) therapies and discuss how the backbone modification of oligonucleotides affects their in vivo stability, biodistribution, and bioactivity. Strategies for delivering these nucleic acids to specific cell types are discussed. This review critically addresses various insights developed with each individual strategy and for multipronged approaches, which will be helpful in achieving more effective outcomes.

The versatility of oligonucleotides as potential therapeutics

Oligonucleotides can in a variety of ways inhibit gene expression by interfering with translation. Oligonucleotides that are complementary to a target mRNA, antisense oligonucleotides, can prevent translation either by cleaving the target or by physically blocking the process. Additionally, oligonucleotides can correct the undesired splicing of pre-mRNA. RNA interference using double-stranded oligoribonucleotides also results in cleavage of the target mRNA. Catalytically competent ribozymes and DNAzymes can have the same effect. Even with no RNA as target, oligonucleotides can be selected as aptamers to bind to any protein to inhibit its activity. Moreover, oligonucleotides can act as decoys particularly for transcription factors to prevent binding to the promoter. A different mode of action is the activation of Toll-like receptors to induce an immune response. Several pathways for drug development are still in their infancy, for example microRNAs and antagomirs.

Antisense oligonucleotides: from design to therapeutic application

1. An antisense oligonucleotide (ASO) is a short strand of deoxyribonucleotide analogue that hybridizes with the complementary mRNA in a sequence-specific manner via Watson-Crick base pairing. Formation of the ASO-mRNA heteroduplex either triggers RNase H activity, leading to mRNA degradation, induces translational arrest by steric hindrance of ribosomal activity, interferes with mRNA maturation by inhibiting splicing or destabilizes pre-mRNA in the nucleus, resulting in downregulation of target protein expression. 2. The ASO is not only a useful experimental tool in protein target identification and validation, but also a highly selective therapeutic strategy for diseases with dysregulated protein expression. 3. In the present review, we discuss various theoretical approaches to rational design of ASO, chemical modifications of ASO, ASO delivery systems and ASO-related toxicology. Finally, we survey ASO drugs in various current clinical studies.

Combinatorial selection of a RNA thioaptamer that binds to Venezuelan equine encephalitis virus capsid protein

A phosphorothioate RNA aptamer (thioaptamer) targeting the capsid protein of Venezuelan equine encephalitis virus (VEEV) was isolated by in vitro combinatorial selection. The selected thioaptamer had a strong binding affinity (approximately 7nM) and high specificity for the target protein. For the binding to the protein, the overall tertiary structure of the thioaptamer is required. We introduce two theoretical methods to examine the effect of phosphorothioate modification on the enhancement of binding affinity and one experimental method to examine the nature of the multiple bands of thioaptamer in a native gel.

Characterization of antisense oligonucleotides comprising 2'-deoxy-2'-fluoro-beta-D-arabinonucleic acid (FANA): specificity, potency, and duration of activity

Antisense oligonucleotides (AON) are being developed for a wide array of therapeutic applications. Significant improvements in their serum stability, target affinity, and safety profile have been achieved with the development of chemically modified oligonucleotides. Here, we compared 2'-deoxy-2'-fluoro-beta-D-arabinonucleic acid (FANA)-containing AONs with phosphorothioate oligodeoxynucleotides (PS-DNA), 2'-O-methyl-RNA/DNA chimeras and short interfering RNAs (siRNA) with respect to their target knockdown efficacy, duration of action and resistance to nuclease degradation. Results show that two different configurations of FANA/DNA chimeras (altimers and gapmers) were found to have potent antisense activity. Specific target inhibition was observed with both FANA configurations with an estimated EC50 value comparable to that of an siRNA but 20-to 100-fold lower than the other commonly used AONs. Moreover, the FANA/DNA chimeras showed increased serum stability that was correlated with sustained antisense activity for up to 4 days. Taken together, these results indicate that chimeric FANA/DNA AONs are promising new tools for therapeutic gene silencing when increased potency and duration of action are required.

Thioaptamer interactions with prion proteins: sequence-specific and non-specific binding sites

Binding of nucleic acids to the prion protein (PrP) created a conundrum that required distinguishing between non-specific interactions and biologically important polynucleotides. In the process of developing selective ligands for PrP, we found using a single-stranded DNA thioaptamer library that the binding of thioaptamers to PrP occurs on at least two different sites on the protein. Selection against recombinant (rec) PrP of Syrian hamster (SHa) sequence 90-231 folded into an alpha-helical-rich conformation identified a 12-base consensus sequence within a series of 20 thioaptamers, all of which consist of 40 bases. Each thioaptamer was comprised of both normal and thio-dA modified bases. One thioaptamer designated 97 bound to recSHaPrP with affinity of 0.58(+/-0.1) nM; lower affinities for bovine (Bo), and human (Hu) were found, establishing that binding is dependent on the primary structure of PrP. High affinity binding of thioaptamer 97 to PrP was found to be mediated through the dodecyl sequence GACACAAGCCGA within the consensus region with five critical backbone modifications 5' to each dA residue. A control oligonucleotide with an equivalent number of phosphorothioates to thioaptamer 97 and a scrambled consensus sequence could not distinguish among the three PrP sequences. Control oligonucleotides bearing non-selected sequences bound to PrP at a sequence-independent DNA-binding site. In contrast, the high-affinity binding of thioaptamer 97 to PrP depends on (1) backbone modifications, (2) oligonucleotide sequence, and (3) PrP sequence.

Antisense oligonucleotides containing locked nucleic acid improve potency but cause significant hepatotoxicity in animals

A series of antisense oligonucleotides (ASOs) containing either 2′-O-methoxyethylribose (MOE) or locked nucleic acid (LNA) modifications were designed to investigate whether LNA antisense oligonucleotides (ASOs) have the potential to improve upon MOE based ASO therapeutics. Some, but not all, LNA containing oligonucleotides increased potency for reducing target mRNA in mouse liver up to 5-fold relative to the corresponding MOE containing ASOs. However, they also showed profound hepatotoxicity as measured by serum transaminases, organ weights and body weights. This toxicity was evident for multiple sequences targeting three different biological targets, as well as in mismatch control sequences having no known mRNA targets. Histopathological evaluation of tissues from LNA treated animals confirmed the hepatocellular involvement. Toxicity was observed as early as 4 days after a single administration. In contrast, the corresponding MOE ASOs showed no evidence for toxicity while maintaining the ability to reduce target mRNA. These studies suggest that while LNA ASOs have the potential to improve potency, they impose a significant risk of hepatotoxicity.

Synthesis and duplex-forming property of oligonucleotides bearing a novel polyamine-modified intercalator at the terminal or the internal position

Novel oligonucleotides bearing a polyamine-intercalator conjugate modified at the terminal or the internal position were reported. These modified oligonucleotides showed duplex-stabilization effect, and the thermodynamic analysis and the salt concentration dependency of the duplex stability revealed that the polyamine moiety also acted as the duplex stabilizer by neutralization of the phosphate negative charge.

The potential of oligonucleotides for therapeutic applications

Viral-derived particles have been widely used and described in gene therapy clinical trials. Although substantial results have been achieved, major safety issues have also arisen. For more than a decade, oligonucleotides have been seen as an alternative to gene complementation by viral vectors or DNA plasmids, either to correct the genetic defect or to silence gene expression. The development of RNA interference has strengthened the potential of this approach. Recent clinical trials have also tested the ability of aptamer molecules and decoy oligonucleotides to sequestrate pathogenic proteins. Here, we review the potential of oligonucleotides in gene therapy, outline what has already been accomplished, and consider what remains to be done.

Solid-Phase Synthesis of Dinucleoside and Nucleoside-Carbohydrate Phosphodiesters and Thiophosphodiesters

Unprotected nucleosides (ROH) were reacted with two polymers bound to N,N-diisopropylamino-1,3,2-oxathiaphospholane in the presence of 1H-terazole. Oxidation with tert-butyl hydroperoxide or sulfurization with Beaucage's reagent, followed by the 1,3,2-oxathiaphospholane ring opening with unprotected nucleosides or carbohydrates (R'OH) in the presence of DBU, afforded nucleoside-(5'-5')-nucleoside or nucleoside-carbohydrate phosphodiester and thiophosphodiester derivatives through the elimination of polymer-bound ethylene episulfide. This strategy offers the advantages of facile isolation of final products and monosubstitution of unprotected nucleosides and carbohydrates.

Oligonucleotide-Based Therapeutic Options against Hepatitis C Virus Infection

The hepatitis C virus (HCV) is the cause of a silent pandemic that, due to the chronic nature of the disease and the absence of curative therapy, continues to claim an ever-increasing number of lives. Current antiviral regimens have proven largely unsatisfactory for patients with HCV drug-resistant genotypes. It is therefore important to explore alternative therapeutic stratagems whose mode of action allows them to bypass viral resistance. Antisense oligonucleotides, ribozymes, small interfering RNAs, aptamers and deoxyribozymes constitute classes of oligonucleotide-based compounds designed to target highly conserved or functionally crucial regions contained within the HCV genome. The therapeutic expectation for such compounds is the elimination of HCV from infected individuals. Progress in oligonucleotide-based HCV antivirals towards clinical application depends on development of nucleotide designs that bolster efficacy while minimizing toxicity, improvement in liver-targeting delivery systems, and refinement of small-animal models for preclinical testing.

Polymer-bound oxathiaphospholane: a solid-phase reagent for regioselective monothiophosphorylation and monophosphorylation of unprotected nucleosides and carbohydrates

Two polymers bound to N,N-diisopropylamino-1,3,2-oxathiaphospholane were reacted with unprotected carbohydrates and nucleosides in the presence of 1H-tetrazole, followed by oxidation with tert-butyl hydroperoxide or sulfurization with Beaucage's reagent. The 1,3,2-oxathiaphospholane ring-opening with 3-hydroxypropionitrile, followed by treatment with DBU, afforded the corresponding monophosphate and monothiophosphate derivatives, respectively, through the elimination of polymer-bound ethylene episulfide. Reactions using this strategy offer the advantages of high regioselectivity, monosubstitution, and facile isolation and recovery of products.

2'-deoxy-2'-fluoro-beta-D-arabinonucleic acid (2'F-ANA) modified oligonucleotides (ON) effect highly efficient, and persistent, gene silencing

To be effective in vivo, antisense oligonucleotides (AS ON) should be nuclease resistant, form stable ON/RNA duplexes and support ribonuclease H mediated heteroduplex cleavage, all with negligible non-specific effects on cell function. We report herein that AS ONs containing a 2′-deoxy-2′-fluoro-β-d-arabinonucleic acid (2′F-ANA) sugar modification not only meet these criteria, but have the added advantage of maintaining high intracellular concentrations for prolonged periods of time which appears to promote longer term gene silencing. To demonstrate this, we targeted the c-MYB protooncogene's mRNA in human leukemia cells with fully phosphorothioated 2′F-ANA–DNA chimeras (PS-2′FANA–DNA) and compared their gene silencing efficiency with AS ON containing unmodified nucleosides (PS-DNA). When delivered by nucleofection, chemically modified ON of both types effected a >90% knockdown of c-MYB mRNA and protein expression, but the PS-2′F-ANA–DNA were able to accomplish this at 20% of the dose of the PS-DNA, and in contrast to the PS-AS DNA, their silencing effect was still present after 4 days after a single administration. Therefore, our data demonstrate that PS-2′F-ANA–DNA chimeras are efficient gene silencing molecules, and suggest that they could have significant therapeutic potential.

Oligonucleotide-based antiviral strategies

In the age of extensive global traffic systems, the close neighborhood of man and livestock in some regions of the world, as well as inadequate prevention measures and medical care in poorer countries, greatly facilitates the emergence and dissemination of new virus strains. The appearance of avian influenza viruses that can infect humans, the spread of the severe acute respiratory syndrome (SARS) virus, and the unprecedented raging of human immunodeficiency virus (HIV) illustrate the threat of a global virus pandemic. In addition, viruses like hepatitis B and C claim more than one million lives every year for want of efficient therapy. Thus, new approaches to prevent virus propagation are urgently needed. Antisense strategies are considered a very attractive means of inhibiting viral replication, as oligonucleotides can be designed to interact with any viral RNA, provided its sequence is known. The ensuing targeted destruction of viral RNA should interfere with viral replication without entailing negative effects on ongoing cellular processes. In this review, we will give some examples of the employment of antisense oligonucleotides, ribozymes, and RNA interference strategies for antiviral purposes. Currently, in spite of encouraging results in preclinical studies, only a few antisense oligonucleotides and ribozymes have turned out to be efficient antiviral compounds in clinical trials. The advent of RNA interference now seems to be refueling hopes for decisive progress in the field of therapeutic employment of antisense strategies.

Small interfering RNAs containing full 2'-O-methylribonucleotide-modified sense strands display Argonaute2/eIF2C2-dependent activity

RNA interference (RNAi) is a process by which short interfering RNAs (siRNAs) direct the degradation of complementary single-strand RNAs. In this study, we investigated the effects of full-strand phosphorothioate (PS) backbone and 2'-O-methyl (2'-OMe) sugar modifications on RNAi-mediated silencing. In contrast to previous reports, we have identified active siRNA duplexes containing full 2'-OMe-modified sense strands that display comparable activity to the unmodified analog of similar sequence. The structure of these modified siRNAs is the predominant determinant of their activity, with sequence and backbone composition being secondary. We further show, by using biotin-tagged siRNAs and affinity-tagged hAgo2/eIF2C2, that activity of siRNA duplexes containing full 2'-OMe substitutions in the sense strand is mediated by the RNA-induced silencing complex (RISC) and that strand-specific loading (or binding) to hAgo2 may be modulated through selective incorporation of these modifications.

Nucleoside 5'-triphosphates: self-association, acid-base, and metal ion-binding properties in solution

Adenosine 5'-triphosphate (ATP(4-)) and related nucleoside 5'-triphosphates (NTP(4-)) serve as substrates in the form of metal ion complexes in enzymic reactions taking part thus in central metabolic processes. With this in mind, the coordination chemistry of NTPs is critically reviewed and the conditions are defined for studies aiming to describe the properties of monomeric complexes because at higher concentrations (>1 mM) self-stacking may take place. The metal ion (M(2+)) complexes of purine-NTPs are more stable than those of pyrimidine-NTPs; this stability enhancement is attributed, in accord with NMR studies, to macrochelate formation of the phosphate-coordinated M(2+) with N7 of the purine residue and the formation degrees of the resulting isomeric complexes are listed. Furthermore, the formation of mixed-ligand complexes (including also those with buffer molecules), the effect of a reduced solvent polarity on complex stability and structure (giving rise to selectivity), the use of nucleotide analogues as antiviral agents, and the effect of metal ions on group transfer reactions are summarized.