2′-Fluoro-4′-thioarabino-modified oligonucleotides: conformational switches linked to siRNA activity

The synthesis of oligonucleotides containing 2′-deoxy-2′-fluoro-4′-thioarabinonucleotides is described. 2′-Deoxy-2′-fluoro-5-methyl-4′-thioarabinouridine (4′S-FMAU) was incorporated into 18-mer antisense oligonucleotides (AONs). 4′S-FMAU adopts a predominantly northern sugar conformation. Oligonucleotides containing 4′S-FMAU, unlike those containing FMAU, were unable to elicit E. coli or human RNase H activity, thus corroborating the hypothesis that RNase H prefers duplexes containing oligonucleotides that can adopt eastern conformations in the antisense strand. The duplex structure and stability of these oligonucleotides was also investigated via circular dichroism (CD)- and UV- binding studies. Replacement of the 4′-oxygen by a sulfur atom resulted in a marked decrease in melting temperature of AON:RNA as well as AON:DNA duplexes. 2′-Deoxy-2′-fluoro-4′-thioarabinouridine (4′S-FAU) was incorporated into 21-mer small interfering RNA (siRNA) and the resulting siRNA molecules were able to trigger RNA interference with good efficiency. Positional effects were explored, and synergy with 2′F-ANA, which has been previously established as a functional siRNA modification, was demonstrated

Synthesis of 2-substituted derivatives of the naturally occurring glycosidase inhibitor, salacinol and its nitrogen analogues

This thesis describes the synthesis of 2-amino- and amido- derivatives of the nitrogen analogue of the naturally occurring glycosidase inhibitor, salacinol, the attempted synthesis of 2-amino- and acetamido derivatives of salacinol itself, the synthesis of 2-fluorinated and 1,2-ene derivatives of salacinol, and the synthesis of a suitable precursor for elaboration of 4\u27-thionucleosides and 4\u27-thiooligonucleotides. Glycosidases are involved in many biological processes such as cell-cell or cell-virus recognition, immune responses, cell growth, and viral and parasitic infections. The controlled inhibition of glycosidases has potential for the treatment of many diseases such as diabetes, viral infections, and cancer. The synthesis of potential inhibitors of the enzyme human maltase glucoamylase (MGA) that catalyzes the breakdown of glucose-containing oligosaccharides, and hexosaminidase enzymes that cleave the ß-glycosidic linkage of 2-acetamido-2-deoxy-ß-D-glucopyranosides are described. The compounds were intended to mimic the oxacarbenium ion transition state in the enzyme-catalyzed reactions. Seven 2-amino- or 2-amido- derivatives of the nitrogen analogues of salacinol were synthesized. Interestingly, alkylation reactions of the nitrogen atom were observed during hydrogenation of the 2-azido derivatives. Circumvention of this side reaction yielded the 2-substituted analogues which showed marginal activity (<33% at 250µM) against human O-GlcNAcase and Vibrio cholerae NagZ enzymes. The attempted synthesis of 2-amido and 2-amino derivatives of salacinol itself is also described. These compounds undergo rearrangement reactions during or before their formation due to nucleophilic participation of the neighboring amino or acetamido functions, and result in opening of the heterocycle. 2-Deoxy-2-fluorosalacinol and 1,2-ene derivatives of salacinol were synthesized for structure activity studies with human maltase glucoamylase (MGA). The 2-deoxy-1,2-ene derivative of salacinol and 2-deoxy-2-fluorosalacinol inhibited recombinant human maltase glucoamylase with an IC50 values of 150 µM and a Ki value of 6 ± 1 µM, respectively. Finally, the synthesis of 1-O-acetyl-2-deoxy-2-fluoro-3,5-di-O-benzoyl-4-thio-α/ß-D-arabinofuranose, a suitable precursor for the synthesis of 4\u27-thionucleosides is described. This compound was elaborated into 4\u27-thionucleosides and oligonucleotides by my collaborator, J. K. Watts

Effect of phosphorylation on siRNAs modified at the 5′-terminal of the antisense strand (sequences given in )

<p><b>Copyright information:</b></p><p>Taken from "2′-Fluoro-4′-thioarabino-modified oligonucleotides: conformational switches linked to siRNA activity"</p><p></p><p>Nucleic Acids Research 2007;35(5):1441-1451.</p><p>Published online 6 Feb 2007</p><p>PMCID:PMC1865065.</p><p>© 2007 The Author(s).</p