3′-Amino-5′-carboxymethyl-3′,5′-dideoxy nucleosides for the synthesis of fully amide-linked RNA mimics

Development of Minimal Diguanosinyl Motif toward RNA G-Quadruplex-Like Structures in Solution

Among the non-canonical structures of B-DNA, the G-quadruplex is of particular interest because of its well-defined conformation, high stability, and versatility. Herein we report our studies on the development of an amide-linked minimal diguanosinyl motif that forms a G-quadruplex-like structure in solution in the presence of potassium cations; various linear guanosine amino acid dimers were synthesized with linkers of different chain lengths to investigate the optimum flexibility required to form such structures.

Molecular Construction of Sulfonamide Antisense Oligonucleotides

An efficient and scalable synthesis of new oligonucleotide monomers was developed for replacement of the phosphodiester backbone of RNA by a sulfonamide-containing backbone to enable construction of sulfonamide antisense oligonucleotides (SaASOs). It was shown that by employing these sulfonamide RNA (SaRNA) monomers, it was possible to synthesize oligomers in solution. The properties of a sulfonamide moiety replacement were evaluated by incorporation of a SaRNA-monomer into a DNA strand and performing thermal stability tests of the resulting DNA and RNA-double-strand hybrids. Although sulfonamide modification caused a decrease in melting temperature (T_m) of both hybrids, it was lower for the sulfonamide-containing DNA-RNA hybrid than that for the sulfonamide-containing DNA-DNA hybrid.

Studies on sugar puckering and glycosidic stabilities of 3'-amino-5'-carboxymethyl-3',5'-dideoxy nucleoside mimics

The synthesis of nucleoside amino acid monomers and dimers has been carried out to evaluate and characterize the impact of the neutral amide backbone on key attributes like puckering of the sugar rings and glycosidic bond strengths of these analogs. The conformational analysis suggests that amide-linked nucleotides have a high predilection towards N-type conformers. The glycosidic bond strength was found to be slightly weaker compared to ribonucleosides under acidic conditions at high temperatures. The results will be helpful to explore in future the development of fully amide-linked oligonucleotides for therapeutic purposes.