7LO9

RNA dodecamer containing a GNA A residue

Summary for 7LO9

• Entry DOI: 10.2210/pdb7lo9/pdb
• Descriptor: Chains: A,B,C,D (2 entities in total)
• Functional Keywords: rna crystal structure, glycol nucleic acid, rna
• Biological source: synthetic construct
• Total number of polymer chains: 4
• Total formula weight: 15488.88

Authors

Harp, J.M.,Wawrzak, Z.,Egli, M. (deposition date: 2021-02-09, release date: 2021-12-22, Last modification date: 2024-05-22)

Primary citation

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.
Overcoming GNA/RNA base-pairing limitations using isonucleotides improves the pharmacodynamic activity of ESC+ GalNAc-siRNAs.
Nucleic Acids Res., 49:10851-10867, 2021

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.

PubMed: 34648028
DOI: 10.1093/nar/gkab916

Experimental method

X-RAY DIFFRACTION (1.78 Å)