Download MendeleyOvercoming GNA/RNA base-pairing limitations using isonucleotides improves the pharmacodynamic activity of ESC+ GalNAc-siRNAs.
Schlegel, M.K., Matsuda, S., Brown, C.R., Harp, J.M., Barry, J.D., Berman, D., Castoreno, A., Schofield, S., Szeto, J., Manoharan, M., Charisse, K., Egli, M., Maier, M.A.(2021) Nucleic Acids Res 49: 10851-10867
- PubMed: 34648028
- DOI: https://doi.org/10.1093/nar/gkab916
- Primary Citation of Related Structures:
7LO9 - PubMed Abstract:
We recently reported that RNAi-mediated off-target effects are important drivers of the hepatotoxicity observed for a subset of GalNAc-siRNA conjugates in rodents, and that these findings could be mitigated by seed-pairing destabilization using a single GNA nucleotide placed within the seed region of the guide strand. Here, we report further investigation of the unique and poorly understood GNA/RNA cross-pairing behavior to better inform GNA-containing siRNA design. A reexamination of published GNA homoduplex crystal structures, along with a novel structure containing a single (S)-GNA-A residue in duplex RNA, indicated that GNA nucleotides universally adopt a rotated nucleobase orientation within all duplex contexts. Such an orientation strongly affects GNA-C and GNA-G but not GNA-A or GNA-T pairing in GNA/RNA heteroduplexes. Transposition of the hydrogen-bond donor/acceptor pairs using the novel (S)-GNA-isocytidine and -isoguanosine nucleotides could rescue productive base-pairing with the complementary G or C ribonucleotides, respectively. GalNAc-siRNAs containing these GNA isonucleotides showed an improved in vitro activity, a similar improvement in off-target profile, and maintained in vivo activity and guide strand liver levels more consistent with the parent siRNAs than those modified with isomeric GNA-C or -G, thereby expanding our toolbox for the design of siRNAs with minimized off-target activity.
Organizational Affiliation:
Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA.
