Synthesis and Hybridization Properties of Oligodeoxynucleotides Containing 3′-Deoxy-3′-C-methyleneuridine

Abstract

3′-Deoxy-3′-C-methyleneuridine nucleoside 1 ¹ has been incorporated into oligodeoxynucleotides. Relative to the unmodified references, oligomers containing nucleoside 1 displayed reduced binding affinities towards complementary DNA and RNA with a tendency towards RNA-selective hybridization.     

Synthesis and Evaluation of Oligodeoxynucleotides Containing 3′-C-Aminomethyl-and 3′-C-Amethylthymidine

Abstract

3′-C-Aminomethyl- and 3′-C-methylthymidine were synthesized and incorporated into oligodeoxynucleotides. Hybridization and enzyme stability of the modified oligonucleotides containing the 3′-C-branched thymidines are discussed.     

Convenient Synthesis of Oligodeoxynucleotides Containing 2′-Deoxy-6-thioinosine

Abstract

A facile synthesis of oligodeoxynucleotides (ODN) containing 2′-deoxy-6-thioinosine (dI^6S) based on the convertible nucleoside O6-phenyl-2′-deoxyinosine is presented. After standard solid-phase DNA synthesis and removal of the cyanoethyl protecting groups with DBU treatment with aqueous sodium hydrogen sulfide introduces the sulfur functionality, deprotects the other nucleobases and cleaves the ODN from the solid support in a one-pot reaction. In addition, the extinction coefficient of 2′-deoxy-6-thioinosine is determined by enzymatic fragmentation of the resulting ODN in the presence of adenosine deaminase.     

Synthesis and Characterization of Oligodeoxynucleotides Containing 5′,8-Cyclopurine-2′-Deoxyribonucleosides

Abstract

Oligodeoxynucleotides containing the two 5′R and 5′S diastereoisomers of 5′,8-cyclo-2′-deoxyadenosine (CyclodAdo) and 5′,8-cyclo-2′-deoxyguanosine (CyclodGuo) have been synthesized using the phosphoramidite chemistry. The structural assignment and a few biochemical features of these modified DNA fragments are reported.     

Synthesis and Properties of Oligonucleotides Containing 5-Aza-2′-deoxycytidine

Abstract

The preparation of a protected derivative of 5-aza-2′-deoxycytidine carrying the 2-(p-nitrophenyl)ethyl group is described. The new derivative is useful for the preparation of oligonucleotides containing 5-aza-2′-deoxycytidine using a special methodology that avoids the use of ammonia.     

Synthesis and Properties of 2′-O-Methylribonucleotide Methylphosphonate Containing Chimeric Oligonucleotides

Abstract

2′-O-methylribonucleoside methylphosphonamidites are synthesized and incorporated into oligonucleotides to obtain chimeric antisense oligonucleotides. The resulting oligonucleotide binds to their target RNA/DNA sequences efficiently and stable in a medium containing bovine serum.     

Hoogsteen-Duplex DNA: Synthesis and Base Pairing of Oligodeoxynucleotides Containing 1-Deaza-2′-deoxyadenosine

Abstract

Solid-phase synthesis of oligonucleotides containing 1-deazaadenine was carried out employing phosphonate and phosphoramidite chemistry. Hoogsteen base pairing was established for the duplex d(c¹A₂₀)·d(T₂₀).     

Synthesis and Properties of 2′4′- and 3′-5′-Linked Ribodinucleoside Monophosphates Containing 2-Aminoadenosine and Uridine

Abstract

Self complementary diribonucleoside monophosphates containing 2-aminoadenosine (n²A) and uridine (U) residues, (2′-5′) n²ApU (1), (3′-5′) n²ApU (2), (2′-5′) Upn²A (3) and (3′-5′) Upn²A (4), were synthesized by condensation of suitably protected nucleoside and nucleotide units using dicyclohexylcarbodiimide (DCC). The dimers, (3) and (41, were also obtained from uridine 2′,3′-cyclic phosphate and unprotected 2-aminoadenosine using 2,4,6-triisopropylbenzenesulfonyl chloride (TPS-Cl) as the condensing agent. The conformational properties of these dimers were examined by UV, CD and NMR spectroscopy. The results reveal that the 2′-5′ isomers take a stacked conformation, which contains a larger base-base overlap and is more stable against thermal perturbation with respect to the 3′-5′ isomers. The n²ApU isomers have more stacked structure than the Upn²A isomers.     

Synthesis and Properties of Oligonucleotide Chimeras Containing 5′-Amino-2′-deoxy-2′-fluoroarabinonucleosides

Abstract

Oligonucleotide analogues comprised of 2′-deoxy-2′-fluoro-β-D-arabinose units joined via P3′-N5′ phosphoramidate linkages (2′F-ANA^5′N) were prepared for the first time. Among the compounds prepared were a series of 2′OMe-RNA-[GAP]-2′OMe-RNA ‘chimeras’, whereby the “GAP” consisted of DNA, DNA^5′N, 2′F-ANA or 2′F-ANA^5′N segments. The chimeras with the 2′F-ANA and DNA gaps exhibited the highest affinity towards a complementary RNA target, followed by the 5′-amino derivatives, i.e., 2′F-ANA > DNA > 2′F-ANA^5′N > DNA^5′N. Importantly, hybrids between these chimeras and target RNA were all substrates of both human RNase HII and E.coli RNase HI. In terms of efficiency of the chimera in recruiting the bacterial enzyme, the following order was observed: gap DNA > 2′F-ANA > 2′F-ANA^5′N > DNA^5′N. The corresponding relative rates observed with the human enzyme were: gap DNA > 2′F-ANA^5′N > 2′F-ANA > DNA^5′N.     

Synthesis and Properties of Dinucleoside Monophosphates Containing 2-Aminoadenine 8,2′-S- and Uracil 6,2′-O-Cyclonucleosides

Abstract

Two sequence isomers of dinucleoside monophosphates containing 8,2′-anhydro-2,6-diamino-8-mercapto-9-β-D-arabinofuranosylpurine (2NH₂A^s) and 6,-anhydro-6-hydroxy-1-ß-D-arabinofuranosyluracil (U^o), 2NH₂A^s pU^o (1) and U^o p2NH₂A^s (2) were synthesized by the phosphodiester method. Examination of the UV, CD and NMR spectra of these dimers led us to the conclusion that, whereas compound (1) did not take a stacked conformation, compound (2) took a well stacked conformation in which the bases were stacked along a left-handed screw axis. Both the dimers formed a complex with ethidium bromide.     

Synthesis and Evaluation of Oligodeoxynucleotides Containing 3′-O-Ethyl-4′-C-(hydroxymethyl)thymidine: Introduction of a Novel Class of Phosphodiester Internucleoside Linkages

Abstract

3′-O-Ethyl-4′-C-(hydroxymethyl)thymidine (5) was synthesized and converted into the phosphoramidite building block 8. Novel oligodeoxynucleotide analogues containing 4′-C-hydroxymethyl phosphodiester internucleoside linkages were synthesized on an automated DNA-synthesizer. The hybridization properties and enzymatic stability were studied on oligomers with one to four modifications. The 3′-end modified oligodeoxynucleotides were resistent towards 3′-exonuclease degradation and showed only moderate lowered affinity towards complementary DNA compared with oligodeoxynucleotides bearing modifications in the middle.     

Synthesis and Evaluation of Novel Oligodeoxynucleotides Containing 3′-C-(3-Benzoyloxypropyl)thymidine and Bicyclo Nucleoside Derivatives

Abstract

The stereoselective synthesis of 3′-C-Allyluridine derivative 2 has been accomplished. This nucleoside was used as a key synthon for the synthesis of oligodeoxynucleotides containing 3′-C-(3-benzoyloxypropyl)thymidine (X) or bicyclo nucleoside (Y+Z) monomers. Preliminary thermal experiments are reported.     

Synthesis and Properties of Some 2′-O-d-Ribofuranosyl-nucleosides

Abstract

A high yield preparation of 9-(2-O-β-d-ribofuranosyl-β-d-ribofuranosyl)-adenine and its pyrimidine analogues has been achieved and their physico-chemical properties were investigated.     

Synthesis of Oligodeoxynucleotides Containing the C-Nucleoside and 2′- Deoxy-2′-Fluoro-ara-Nucleoside Moieties by the H-Phosphonate Method.1,2

Abstract

A module type, computer-controlled, multipurpose synthesizer displaying a novel device for the transport of liquids, was constructed and used in the synthesis of oligomers containing some C-nucleosides and 2′-deoxy-2′-fluoro-ara-nucleoside moieties. H-Phosphonate method was applied in terms of a further adjustment of construction features of the synthesizer versus chemistry of the process. Results of preliminary studies on the effects of the modified nucleosides on the stability of duplexes showed a clear tendency of destabilization of duplexes in the case of C-nucleosides while fluorinated nucleosides in most cases stabilize the formed duplexes.     

Synthesis of 4′-C-Ethynyl and 4′-C-Cyano Purine Nucleosides from Natural Nucleosides and Their Anti-HIV Activity

Abstract

Purine 2′-deoxynucleosides bearing an ethynyl or a cyano group at C-4′ of the sugar moiety were synthesized from the corresponding 2′-deoxynucleosides. These compounds exhibited very potent anti-HIV activity, and remained active against drug resistant HIV strains.     

Synthesis and Properties of Novel 5′-Linked Oligos

Abstract

We have synthesized normal and phosphorothioate oligos with 5′-linked groups, using either a phosphoramidite with the linked group attached or a mercaptopropanol linker. These linked oligos have been studied for cellular uptake as fluorescent labels, and for inhibition of gene expression in a cell free expression system, and in several other biological systems.     

Fluorescence Properties and Base Pair Stability of Oligonucleotides Containing 8-Aza-7-deaza-2′-deoxyisoinosine or 2′-Deoxyisoinosine

Abstract

The fluorescence and the base pairing properties of 8-aza-7-deaza-2′-deoxyisoinosine (1) are described and compared with those of 2′-deoxyisoinosine (2). The corresponding phosphoramidites (11,12) are synthesized using the diphenyl-carbamoyl (DPC) residue for the 2-oxo group protection. The nucleosides 1 and 2 base pair with 2′-deoxy-5-methylisocytidine in DNA duplexes with antiparallel chain orientation and with 2′-deoxycytidine in a parallel DNA. These base pairs are less stable than the canonical dA-dT pair and that of 2′-deoxyinosine (4) with 2′-deoxycytidine. The fluorescence of the nucleosides 1 and 2 is quenched (～95%) in duplex DNA. The residual fluorescence is used to determine the T_m-values, which are found to be the same as determined UV-spectrophotometrically.     

Synthesis of 2′-Deoxy-2′ -Fluoro-D-Arabinopyranopyranosyl Nucleosides and Their 3′,4′-Seco analogues

Abstract

2′-Deoxy-2′-fluoro-D-arabinopyranosyl nucleosides were synthesized by condensation of 1,3,4-tri-O-benzoyl-2-deoxy-2-fluoro-D-arabinopyranose with the appropriate silylated bases in the presence of trimethylsilyl triflate. Scission of the 3′,4′-bond by periodate oxidation followed by sodium borohydride reduction resulted in the formation of the 3′,4′-seco analogues of the 2′-deoxy-2′-fluoro-D-arabinofuranosyl nucleosides.     

Chemical and Enzymatic Synthesis and Antiviral Properties of 2′-Deoxy-2′-fluoroguanosine

Abstract

Chemical and enzymatic methods were employed for the synthesis of the title compound, 2′F-Guo 7. High antiviral activity of 2′F-Guo was established in chick embryo cells infected with influenza virus FPV/Rostock/34 (H7N1) and herpes simplex virus (HSV) type I (1C strain).