Toward Amide-Modified RNA:  Synthesis of 3‘-Aminomethyl-5‘-carboxy-3‘,5‘-dideoxy Nucleosides

Abstract

Recent discovery of RNA interference has reinvigorated the interest in chemically modified RNA. Chemical approaches may be used to optimize properties of small interfering RNAs, such as thermal stability, cellular delivery, in vivo half-life, and pharmacokinetics. From this perspective, amides as neutral and hydrophobic internucleoside linkages in RNA are highly interesting modifications that so far have not been tested in RNA interference. Amides are remarkably good mimics of the phosphodiester backbone of RNA and can be prepared using a relatively straightforward peptide coupling chemistry. The synthetic challenge that has hampered the progress in this field has been preparation of monomeric building blocks for such couplings, the nucleoside amino acid equivalents. Herein, we report two synthetic routes to enantiomerically pure 3'-aminomethyl-5'-carboxy-3',5'-dideoxy nucleosides, monomers for preparation of amide-modified RNA. Modification of uridine, a representative of natural nucleosides, using nitroaldol chemistry gives the target amino acid in 16 steps and 9% overall yield. The alternative synthesis starting from glucose is somewhat less efficient (17 steps and 6% yield of 3'-azidomethyl-5'-carboxy-3',5'-dideoxy uridine), but provides easier access to modified nucleosides having other heterocyclic bases. The syntheses developed herein will allow preparation of amide-modified RNA analogues and exploration of their potential as tools and probes for RNA interference, fundamental biochemistry, and bio- and nanotechnology.

Synthesis and Gene Silencing Properties of siRNAs Containing Terminal Amide Linkages

“…In fact, siRNA 15 was not effective, probably, since the modified sense strand is preferentially selected. The “5′-capped” siRNAs 14 and 16 partially restored an interfering effect besides methylamide cap blocks the siRNA versus phosphorylation [56–61]. Also, the specific interaction detected between the methylamide and the hAgo 2 middomain would further substantiate a role of the chemical modification in the selective loading of the AS by the protein.…”

Glycine-Linked Nucleoside-β-Amino Acids: Polyamide Analogues of Nucleic Acids

“…Over the past decade, we and others have been working toward the synthesis of such chimeric four- and five-atom charge-neutral amide linked nucleic acid analogues by partial replacement of four-atom phosphodiester linkages at selected positions, for achieving RNA selective binding. Several such chimeric deoxyribo/ribo ON analogues − are known in the literature. Such chimeric ONs recognized and formed duplexes with complementary RNA (cRNA) with a moderate RNA binding selectivity but with diminished affinity, in antiparallel orientation.…”

Synthesis of Ribonucleosidic Dimers with an Amide Linkage from d-Xylose

“…This is in sharp contrast to the synthesis of amide-linked ribonucleoside dimers D , for which the reaction applied to 2′,5′-di- O -protected ribonucleoside intermediates led to the desired products contaminated by the other diastereoisomer arising from free-radical allylation at C3′ on the β-face. Consequently, in this series, the synthesis of these required carboxylic acid monomers has been largely reported from sugars, mainly d -xylose or d -glucose . As previously mentioned, this sugar route to prepare the required carboxylic acid monomers of amide-linked ribonucleoside dimers D turned out to be more efficient: from a protected α- d - erythro -pentofuranos-3-ulose intermediate, a sequence of the Wittig–Horner reaction followed by diastereoselective hydrogenation provided the desired glycosyl precursor, which was then involved in an N -glycosylation to introduce the desired nucleobase.…”