Synthesis and antisense properties of fluoro cyclohexenyl nucleic acid (F-CeNA), a nuclease stable mimic of 2'-fluoro RNA

We report the design and synthesis of 2'-fluoro cyclohexenyl nucleic acid (F-CeNA) pyrimidine phosphoramidites and the synthesis and biophysical, structural, and biological evaluation of modified oligonucleotides. The synthesis of the nucleoside phosphoramidites was accomplished in multigram quantities starting from commercially available methyl-D-mannose pyranoside. Installation of the fluorine atom was accomplished using nonafluorobutanesulfonyl fluoride, and the cyclohexenyl ring system was assembled by means of a palladium-catalyzed Ferrier rearrangement. Installation of the nucleobase was carried out under Mitsunobu conditions followed by standard protecting group manipulations to provide the desired pyrimidine phosphoramidites. Biophysical evaluation indicated that F-CeNA shows behavior similar to that of a 2'-modified nucleotide, and duplexes with RNA showed slightly lower duplex thermostability as compared to that of the more rigid 3'-fluoro hexitol nucleic acid (FHNA). However, F-CeNA modified oligonucleotides were significantly more stable against digestion by snake venom phosphodiesterases (SVPD) as compared to unmodified DNA, 2'-fluoro RNA (FRNA), 2'-methoxyethyl RNA (MOE), and FHNA modified oligonucleotides. Examination of crystal structures of a modified DNA heptamer duplex d(GCG)-T*-d(GCG):d(CGCACGC) by X-ray crystallography indicated that the cyclohexenyl ring system exhibits both the (3)H(2) and (2)H(3) conformations, similar to the C3'-endo/C2'-endo conformation equilibrium seen in natural furanose nucleosides. In the (2)H(3) conformation, the equatorial fluorine engages in a relatively close contact with C8 (2.94 ?) of the 3'-adjacent dG nucleotide that may represent a pseudo hydrogen bond. In contrast, the cyclohexenyl ring of F-CeNA was found to exist exclusively in the (3)H(2) (C3'-endo like) conformation in the crystal structure of the modified A-form DNA decamer duplex [d(GCGTA)-T*-d(ACGC)](2.) In an animal experiment, a 16-mer F-CeNA gapmer ASO showed similar RNA affinity but significantly improved activity compared to that of a sequence matched MOE ASO, thus establishing F-CeNA as a useful modification for antisense applications.     

Synthesis and RNA binding selectivity of oligonucleotides modified with five-atom thioacetamido nucleic acid backbone structures

Convenient chemical synthesis and incorporation of dithymidine and thymidine-cytidine dimer blocks connected with a five-atom amide linker N3'-CO-CH2-S-CH2 into oligonucleotides (ONs) are reported. The UV-Tm experiments for binding affinities of these mixed backbone ONs with complementary DNA and RNA sequences revealed important results such as significantly higher RNA-binding selectivity as compared with complementary DNA. NMR studies of the dimer blocks suggested a marginal increase in the N-type sugar conformations over that of the native DNA.     

LNA (locked nucleic acid) and analogs as triplex-forming oligonucleotides

The triplex-forming abilities of some conformationally restricted nucleotide analogs are disclosed and compared herein. 2'-Amino-LNA monomers proved to be less stabilising to triplexes than LNA monomers when incorporated into a triplex-forming third strand. N2'-functionalisation of 2'-amino-LNA monomers with a glycyl unit induced the formation of exceptionally stable triplexes. Nucleotide analogs containing a C2',C3'-oxymethylene linker (E-type furanose conformation) or a C2',C4'-propylene linker (N-type furanose conformation) had no significant effect on triplex stability proving that conformational restriction per se is insufficient to stabilise triplexes.     

Nonenzymatic synthesis of RNA and DNA oligomers on hexitol nucleic acid templates: the importance of the A structure.

Hexitol nucleic acid (HNA) is an analogue of DNA containing the standard nucleoside bases, but with a phosphorylated 1,5-anhydrohexitol backbone. HNA oligomers form duplexes having the nucleic acid A structure with complementary DNA or RNA oligomers. The HNA decacytidylate oligomer is an efficient template for the oligomerization of the 5'-phosphoroimidazolides of guanosine or deoxyguanosine. Comparison of the oligomerization efficiencies on HNA, RNA, and DNA decacytidylate templates under various conditions suggests strongly that only nucleic acid double helices with the A structure support efficient template-directed synthesis when 5'-phosphoroimidazolides of nucleosides are used as substrates.     

Design,synthesis and anti-influenza virus activities of terminal modified antisense oligonucleotides

Four novel terminal modified antisense oligonucleotides (ODNs) were designed, synthesized and tested for their anti-influenza virus activity. Initial biological studies indicated that lipophilic and rimantadin emodificated Flutide exhibited more potent anti-H1N1 activity than Flutide. Among them, lipophilic modificated ODN (Flutide-I) showed the most antiviral activity. The EC₅₀ value of Flutide-I for inhibiting H1N1 induced cytopathic effect (CPE) and H1N1 RNA were respectively (0.26 ± 0.16) μM and (0.11 ± 0.03) μM. The cytotoxicity of these compounds has also been assessed. No significant cytotoxicities were found for any of these compounds with the concentrations up to 20 μM.     

Synthesis of a new intercalating nucleic acid analogue with pyrenol insertions and the thermal stability of the resulting oligonucleotides towards DNA over RNA

Abstract  

A new intercalating nucleic acid monomer Y was obtained via alkylation of pyren-1-ol with (S)-(+)-2-(2,2-dimethyl-1,3-dioxolan-4-yl)ethanol under Mitsunobu conditions followed by hydrolysis with 80% aqueous acetic acid to give a diol which was tritylated with 4,4′-dimethoxytrityl chloride followed by treatment with 2-cyanoethyltetraisopropylphosphordiamidite in the presence of N,N′-diisopropylammonium tetrazolide. In this way the monomer Y was obtained as its dimethoxytrityl-protected phosphoramidite building block for standard DNA synthesis. The corresponding oligonucleotides from Y have nearly identical hybridization properties with those of intercalating nucleic acid (INA) where neighboring oxygen and carbon atoms are interchanged in the linker. The synthesis of monomer Y avoids the use of allergic intermediates which are a problem in the synthesis of INA.     

Locked nucleic acid (LNA): fine-tuning the recognition of DNA and RNA

Locked nucleic acid is an RNA derivative in which the ribose ring is constrained by a methylene linkage between the 2'-oxygen and the 4'-carbon. This conformation restriction increases binding affinity for complementarity sequences and provides an exciting new chemical approach for the control of gene expression and optimization of microarrays.     

Synthesis and properties of oligonucleotides that contain a triazole‐linked nucleic acid dimer

New chemically modified oligonucleotides at the site of the backbone are needed to improve the properties of oligonucleotides. A practical synthesis for a triazole‐linked nucleoside dimer based on a PNA‐like structure has been developed. This involves synthesizing two uracil‐based monomers that contain either an azide or an alkyne functionality, followed by copper‐catalyzed 1,3‐dipolar cycloaddition. This dimer was incorporated within an oligonucleotide via phosphoramidite chemistry and UV‐monitored thermal denaturation data illustrates slight destabilization relative to its target complementary sequence. This chemically modified dimer will allow for a future investigation of its properties within DNA and RNA‐based applications. J. Heterocyclic Chem., (2011).     

Synthesis of fluorophore and quencher monomers for use in scorpion primers and nucleic acid structural probes

We report the syntheses of monomers to incorporate fluorescein and methyl red within the sequence and at the termini of modified oligonucleotides. These monomers have been used in the solid-phase synthesis of fluorogenic oligonucleotides for genetic analysis and the study of multi-stranded nucleic acid structures.     

Poly (3-(3-pyridyl) acrylic acid) modified glassy carbon electrode for simultaneous determination of dopamine, ascorbic acid and uric acid

Trans-3-(3-pyridyl) acrylic acid (PAA) was deposited on glassy carbon electrode (GCE) by electropolymerization in pH 7.0 phosphate buffer solution (PBS). The poly (3-(3-pyridyl) acrylic acid) (PPAA) film modified glassy carbon electrode shows an excellent electrochemical response for dopamine (DA), ascorbic acid (AA) and uric acid (UA). The cyclic voltammetry oxidation peaks for DA and AA, DA and UA, AA and UA are separated by 150 mV, 130 mV and 280 mV, respectively. This permits the simultaneous determination of AA, DA and UA. The interference of AA with the determination of DA could be eliminated because of the electrostatic interaction between DA cations and the negatively charged PPAA film at pH 7.0. The anodic peak currents of DA, AA and UA increase linearly with concentration in the range of 1-40 micromol L(-1), 10-400 micromol L(-1) and 1.6-80 micromol L(-1), respectively, with a correlation coefficient (r) always higher than 0.998. The detection limit is 0.06 micromol L(-1), 0.8 micromol L(-1) and 1.1 micromol L(-1) for DA, AA and UA, respectively.     

Pyrene-functionalized oligonucleotides and locked nucleic acids (LNAs): tools for fundamental research, diagnostics, and nanotechnology

Pyrene-functionalized oligonucleotides (PFOs) are increasingly explored as tools in fundamental research, diagnostics and nanotechnology. Their popularity is linked to the ability of pyrenes to function as polarity-sensitive and quenchable fluorophores, excimer-generating units, aromatic stacking moieties and nucleic acid duplex intercalators. These characteristics have enabled development of PFOs for detection of complementary DNA/RNA targets, discrimination of single nucleotide polymorphisms (SNPs), and generation of π-arrays on nucleic acid scaffolds. This critical review will highlight the physical properties and applications of PFOs that are likely to provide high degree of positional control of the chromophore in nucleic acid complexes. Particular emphasis will be placed on pyrene-functionalized Locked Nucleic Acids (LNAs) since these materials display interesting properties such as fluorescence quantum yields approaching unity and recognition of mixed-sequence double stranded DNA (144 references).     

Synthesis,structural characterization and in vitro cytotoxic activity of novel polymeric triorganotin(IV) complexes of urocanic acid

Two novel triorganotin carboxylate complexes of the biologically active urocanic acid have been synthesized and characterized. Elemental analysis, melting point, spectroscopic techniques – IR, ¹H, ¹³C and ¹¹⁹Sn NMR – mass spectrometry and X‐ray diffraction studies have been used for structural characterization. Crystal structures of the tin(IV) derivatives show that urocanic acid acts as a bridging bidentate ligand through its imidazole nitrogen atom and its carboxylic group, producing a polymeric one‐dimensional chain. The molecular structures of the complexes, catena‐poly‐tri(n‐butyl)tin(IV) 3‐(3H‐imidazol‐4‐yl)prop‐2‐enoate (1) and catena‐poly‐triphenyltin(IV) 3‐(3H‐imidazol‐4‐yl)prop‐2‐enoate (2), present a distorted trigonal–bipyramidal configuration. This is further confirmed by ¹¹⁹Sn NMR in the solid state. The tin(IV) derivatives form double‐stranded ribbons via N―H^…O―H bonds. Nevertheless, the compounds are essentially monomeric in solution, with a tetrahedral configuration as observed by ¹¹⁹Sn NMR in solution. The cytotoxic activity of the titled compounds has been tested against six human cell lines and the corresponding IC₅₀ values are reported. Both tin(IV) compounds have a high to very high in vitro cytotoxic activity against the tumor cell lines K562, HCT‐15 and MCF‐7. Compound 1 is 86 times more active than cisplatin in the HTC‐15 cell line. Copyright © 2012 John Wiley & Sons, Ltd.     

A cyclopentane conformational restraint for a peptide nucleic acid: design,asymmetric synthesis,and improved binding affinity to DNA and RNA

[structure: see text] A strategy to restrict the highly flexible backbone conformation of a peptide nucleic acid (PNA) by incorporation of a cyclopentane ring is proposed. An asymmetric synthesis of cyclopentane-modified PNA is reported, and its binding properties were determined. The cyclopentane ring leads to a significant improvement in the binding properties of the resulting PNA to DNA and RNA.     

Synthesis and biocidal activity of modified poly(vinyl alcohol)

Functionalized polymers and their polymer nature give them more advantages than the corresponding small molecules. In this respect, polymeric ammonium and phosphonium salts were prepared by chemical modifications of poly(vinyl alcohol) (PVA) aiming to explore their antimicrobial activities against pathogenic bacteria and fungi. The modifications were performed by chloroacetylation with chloroacetyl chloride. Incorporation of the ammonium and phosphonium salts was conducted by the reaction of chloroacetylated poly(vinyl alcohol) (CPVA) with triethylamine (TEA), triphenylphosphine (TPP), and tributylphosphine (TBP). The antimicrobial activity of the polymers against variety of test microorganisms was examined by the cut plug and viable cell counting methods of shake cultures of 10 times dilute nutrient broth and Sabouraud^’s media, seeded with the test microorganisms. It was found that the immobilized polymers exhibited antimicrobial activity against the Gram negative bacteria (Escherichia coli, Pseudomonas aeruginosa, Shigella sp. and Salmonella typhi) and Gram positive bacteria (Bacillus subtilis and B. cereus) and the dermatophyte fungus (Trichophyton rubrum). The growth inhibition of the test microorganisms (ratio of surviving cell number, M/C) varied according to the composition of the active group in the polymer and the test organism. It increased by increasing the concentration of the polymer. Triphenyl phosphonium salt of the modified poly(vinyl alcohol) exhibited the most biocidal activity against both Gram-negative and Gram-positive bacteria after 24 h.     

Locked nucleic acid (LNA) recognition of RNA: NMR solution structures of LNA:RNA hybrids

Locked nucleic acids (LNAs) containing one or more 2'-O,4'-C-methylene-linked bicyclic ribonucleoside monomers possess a number of the prerequisites of an effective antisense oligonucleotide, e.g. unprecedented helical thermostability when hybridized with cognate RNA and DNA. To acquire a detailed understanding of the structural features of LNA giving rise to its remarkable properties, we have conducted structural studies by use of NMR spectroscopy and now report high-resolution structures of two LNA:RNA hybrids, the LNA strands being d(5'-CTGAT(L)ATGC-3') and d(5'-CT(L)GAT(L)AT(L)GC-3'), respectively, T(L) denoting a modified LNA monomer with a thymine base, along with the unmodified DNA:RNA hybrid. In the structures, the LNA nucleotides are positioned as to partake in base stacking and Watson-Crick base pairing, and with the inclusion of LNA nucleotides, we observe a progressive change in duplex geometry toward an A-like duplex structure. As such, with the inclusion of three LNA nucleotides, the hybrid adopts an almost canonical A-type duplex geometry, and thus it appears that the number of modifications has reached a saturation level with respect to structural changes, and that further incorporations would furnish only minute changes in the duplex structure. We attempt to rationalize the conformational steering induced by the LNA nucleotides by suggesting that the change in electronic density at the brim of the minor groove, introduced by the LNA modification, is causing an alteration of the pseudorotational profile of the 3'-flanking nucleotide, thus shifting this sugar equilibrium toward N-type conformation.     

Functionalized LNA (locked nucleic acid): high-affinity hybridization of oligonucleotides containing N-acylated and N-alkylated 2''-amino-LNA monomers

A molecular dynamics (MD) simulation, synthesis and very efficient hybridization for a series of N-acylated and N-alkylated derivatives of 2'-amino-LNA are reported.     

Chemical synthesis of oligonucleotides. 3: Synthesis and characterization of N,O-protected ribophosphoesters for applications in RNA synthesis

The chemical synthesis of RNA, in contrast to that of DNA, poses problems due to fi) additional requirement of 2′-hydroxyl protection of the ribose moieties, and (ii) high lability of inter-ribophosphate bonds. Herein we report the synthesis and characterisation of N, O-protected ribophosphoesters 1 which are key monomeric derivatives in phosphotriester methodology for RNA synthesis. Both the isomeric 2′ and 3′-O-phosphates have been obtained and characterised. The utility of the t-butyl dimethylsilyl group for 2′-hydroxyl protection in the phosphotriester method is demonstrated by the synthesis of r(AUAU),r (UAUA) andr (CACA). Part 2, Rajendrakumaret al (1987) NCL communication number 4682     

Titanium(IV) carboxylate complexes: Synthesis,structural characterization and cytotoxic activity

Four titanium(IV) carboxylate complexes [Ti(η⁵-C₅H₅)₂(O₂CCH₂SMes)₂] (1), [Ti(η⁵-C₅H₄Me)₂(O₂CCH₂SMes)₂] (2), [Ti(η⁵-C₅H₅)(η⁵-C₅H₄SiMe₃)(O₂CCH₂SMes)₂] (3) and [Ti(η⁵-C₅Me₅)(O₂CCH₂SMes)₃] (4; Mes = 2,4,6-Me₃C₆H₂) have been synthesised by the reaction of the corresponding titanium derivatives [Ti(η⁵-C₅H₅)₂Cl₂], [Ti(η⁵-C₅H₄Me)₂Cl₂], [Ti(η⁵-C₅H₅)(η⁵-C₅H₄SiMe₃)Cl₂] and [Ti(η⁵-C₅Me₅)Cl₃] and two (for 1–3) or three (for 4) equivalents of mesitylthioacetic acid. Complexes 1–4 have been characterized by spectroscopic methods and the molecular structure of the complexes 1, 2 and 4 have been determined by X-ray diffraction studies. The cytotoxic activity of 1–4 was tested against tumor cell lines human adenocarcinoma HeLa, human myelogenous leukemia K562, human malignant melanoma Fem-x, and normal immunocompetent cells, that is peripheral blood mononuclear cells PBMC and compared with those of the reference complexes [Ti(η⁵-C₅H₅)₂Cl₂] (R1), [Ti(η⁵-C₅H₄Me)₂Cl₂] (R2), [Ti(η⁵-C₅H₅)(η⁵-C₅H₄SiMe₃)Cl₂] (R3) and cisplatin. In all cases, the cytotoxic activity of the carboxylate derivatives was higher than that of their corresponding dichloride analogues, indicating a positive effect of the carboxylato ligand on the final anticancer activity. Complexes 1–4 are more active against K562 (IC₅₀ values from 72.2 to 87.9 μM) than against HeLa (IC₅₀ values from 107.2 to 142.2 μM) and Fem-x cells (IC₅₀ values from 90.2 to 191.4 μM).     

Alpha-LNA (locked nucleic acid with alpha-D-configuration): synthesis and selective parallel recognition of RNA

Alpha-LNA is presented as a stereoisomer of LNA (locked nucleic acid) with alpha-D-configuration. Three different approaches towards the thymine alpha-LNA monomer as well as the 5-methylcytosine alpha-LNA monomer are presented. Different alpha-LNA sequences have been synthesised and their hybridisation with complementary DNA and RNA has been evaluated by means of thermal stability experiments and circular dichroism spectroscopy. In a mixed pyrimidine sequence, alpha-LNA displays unprecedented parallel-stranded and selective RNA binding. Furthermore, a remarkable selectivity for hybridisation with RNA over DNA is indicated.