9O47

RNA dodecamer containing a serinol nucleic acid.

This is a non-PDB format compatible entry.

Summary for 9O47

• Entry DOI: 10.2210/pdb9o47/pdb
• Descriptor: Chains: A,B, [2-[2-(2-$l^{3}-oxidanylidene-5-methyl-4-oxidanylidene-4,5-dihydro-2~{H}-pyrimidin-1-yl)ethanoylamino]-3-oxidanyl-propyl] dihydrogen phosphate, 5-BROMO-URIDINE-5'-MONOPHOSPHATE, ... (7 entities in total)
• Functional Keywords: rna, serinol nucleic acid
• Biological source: synthetic construct
• Total number of polymer chains: 2
• Total formula weight: 11963.11

Authors

Harp, J.M.,Egli, M.E. (deposition date: 2025-04-08, release date: 2026-04-22, Last modification date: 2026-04-29)

Primary citation

Chickering, T.,Harp, J.M.,Jiang, Y.,Qin, J.,He, G.,Hyde, S.,Ihlefeld, A.,Janas, M.,O'Flaherty, D.K.,Schofield, S.,Szeto, J.,Theile, C.S.,Charisse, K.,Jadhav, V.,Maier, M.A.,Manoharan, M.,Egli, M.,Schlegel, M.K.
Acyclic serinol nucleic acid modification of siRNAs overcomes seed region mediated off-target effects while maintaining potency.
Nucleic Acids Res., 54:-, 2026

PubMed Abstract: Similar in structure to both glycol nucleic acid (GNA) and peptide nucleic acid (PNA), serinol nucleic acid (SNA) combines the acyclic flexibility of GNA with the amide bond found in PNA and can form stable heteroduplexes with DNA and RNA. While the thermal and metabolic stability of SNA and SNA-modified heteroduplexes has been previously reported, we here describe the application of SNA in RNA interference (RNAi) using GalNAc-conjugated small interfering RNAs (siRNAs). Single incorporations were evaluated at each position across both the guide and passenger strands and subsequently evaluated at key positions in mice. Additionally, the off-target potential of siRNAs containing SNA was assessed. We demonstrate the position-dependent tolerance of SNA inside both the guide and passenger strands, and more specifically, high tolerance of SNA incorporation in the seed region of the guide strand, preserving on-target activity while mitigating microRNA-like off-target effects. Furthermore, the crystal structure of an RNA dodecamer containing a single SNA nucleotide was obtained and the resulting SNA structure was used to explain the activity of SNA containing siRNAs. Thus, SNA constitutes another viable modification in the siRNA toolbox for the development of potent and specific RNAi therapeutics.

PubMed: 41994868
DOI: 10.1093/nar/gkag345

Experimental method

X-RAY DIFFRACTION (1.6 Å)