1 research outputs found
Structure-Based Design of Novel Chemical Modification of the 3′-Overhang for Optimization of Short Interfering RNA Performance
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