Structure-Based Design of Novel Chemical Modification
of the 3′-Overhang for Optimization of Short Interfering RNA
Performance
- Publication date
- Publisher
Abstract
Short interfering RNAs (siRNAs) are
broadly used to manipulate
gene expression in mammalian cells. Although chemical modification
is useful for increasing the potency of siRNAs <i>in vivo</i>, rational optimization of siRNA performance through chemical modification
is still a challenge. In this work, we designed and synthesized a
set of siRNAs containing modified two-nucleotide 3′-overhangs
with the aim of strengthening the interaction between the 3′-end
of the siRNA strand and the PAZ domain of Ago2. Their efficiency of
binding to the PAZ domain was calculated using a computer modeling
program, followed by measurement of RNA–Ago2 interaction in
a surface plasmon resonance biochemical assay. The results suggest
that increasing the level of binding of the 3′-end of the guiding
strand with the PAZ domain, and/or reducing the level of binding of
the sense strand through modifying the two-nucleotide 3′-overhangs,
affects preferential strand selection and improves siRNA activity,
while we cannot exclude the possibility that the modifications at
the 3′-end of the sense strand may also affect the recognition
of the 5′-end of the guiding strand by the MID domain. Taken
together, our work presents a strategy for optimizing siRNA performance
through asymmetric chemical modification of 3′-overhangs and
also helps to develop the computer modeling method for rational siRNA
design