Conformation matters: siRNAs with antisense strands with 5′-(E)-vinyl-phosphonate-α-l-LNA elicit stronger RNAi-mediated gene silencing than those with 5′-(E)-vinyl-phosphonate-LNA

Abstract

Conformationally constrained nucleotides, LNA or α-l-LNA, at the 5′ terminus of the antisense strand impeded gene silencing of small interfering RNA (siRNA) by hindering phosphorylation, thereby deterring loading into the RNA-induced silencing complex. Installation of a phosphate mimic, (E)-vinyl phosphonate (VP), improved activity considerably. Gene silencing was more efficient when the antisense strand of the siRNA was modified with 5′-VP-α-l-LNA, which adopts a C3′-exo (south) conformation, than when the antisense strand was modified with 5′-VP-LNA, which adopts a C3′-endo (north) pucker. These data underscore the critical role of conformation of nucleotides in RNA interference.