phosphoramidite and phosphoramidic-acid

A series of siRNA duplexes containing cationic non-bridging 3',5'-linked phosphoramidate (PN) linkages was designed and synthesized using a combination of phosphoramidite and H-phosphonate chemistries. Modified oligonucleotides were assayed for their thermal stability, helical structure, and ability to modulate the expression of firefly luciferase. We demonstrate that PN modifications of siRNAs are, in general, minimally destabilizing with respect to duplex thermal stability; destabilization can be mitigated through the incorporation of 2'-modified RNA-like residues or PN conjugates containing ionizable pendant moieties. We also demonstrate that single cationic dimethylethylenediamine PN linkages have little effect on siRNA potency, whether located in the passenger or guide strand of the duplex. Highly modified siRNA passenger strands were further modified with up to four cationic PN linkages, with little effect on duplex potency or helical structure. We envision that PN modifications could be useful in the production of therapeutic siRNAs with optimal biological properties.

Topics: Amides; Base Sequence; Cations; Cell Survival; Ethylenediamines; Gene Silencing; Genes, Reporter; HeLa Cells; Humans; Luciferases; Nucleic Acid Conformation; Organophosphonates; Organophosphorus Compounds; Phosphoric Acids; RNA Stability; RNA, Small Interfering

This unit describes the synthesis and purification of oligonucleotide N3'-->P5' phosphoramidates, wherein each 3'-oxygen is replaced by a 3'-amine in the 2'-deoxyribose ring. The synthesis of required monomers and application of the method to preparation of phosphodiester- and phosphorothioate-containing chimera of phosphoramidate is also reported.

Topics: Amides; Base Sequence; Chromatography, High Pressure Liquid; Chromatography, Ion Exchange; Deoxyribonucleosides; Dideoxynucleosides; Esters; Molecular Sequence Data; Organophosphorus Compounds; Phosphoric Acids; Phosphorothioate Oligonucleotides; Thymidine; Trityl Compounds; Zalcitabine