9O47 | pdb_00009o47

RNA dodecamer containing a serinol nucleic acid.

PDB DOI: https://doi.org/10.2210/pdb9O47/pdb
NAKB: 9O47

Classification: RNA
Organism(s): synthetic construct
Mutation(s): No

Deposited: 2025-04-08 Released: 2026-04-22
Deposition Author(s): Harp, J.M., Egli, M.E.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.223 (Depositor), 0.229 (DCC)
R-Value Work:
0.196 (Depositor), 0.210 (DCC)
R-Value Observed:
0.197 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Acyclic serinol nucleic acid modification of siRNAs overcomes seed region mediated off-target effects while maintaining potency.

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.

(2026) Nucleic Acids Res 54

PubMed: 41994868 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1093/nar/gkag345
Primary Citation Related Structures:
9O47

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.

Organizational Affiliation

Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, United States.

Macromolecule Content

Total Structure Weight: 11.96 kDa
Atom Count: 605
Modeled Residue Count: 12
Deposited Residue Count: 24
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 1
Chains: A,B	A, B	12	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5BU Query on 5BU Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain N [auth B] MOL2 format, chain D [auth A] MOL2 format, chain N [auth B] mmCIF format, chain D [auth A] mmCIF format, chain N [auth B]	D [auth A], N [auth B]	5-BROMO-URIDINE-5'-MONOPHOSPHATE C₉ H₁₂ Br N₂ O₉ P IDPVUMJNEZFMNU-UAKXSSHOSA-N		Interactions Focus chain D [auth A] Focus chain N [auth B] Interactions & Density Focus chain D [auth A] Focus chain N [auth B]
5GP Query on 5GP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain L [auth B] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth B] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth B]	E [auth A], G [auth A], J [auth B], L [auth B]	GUANOSINE-5'-MONOPHOSPHATE C₁₀ H₁₄ N₅ O₈ P RQFCJASXJCIDSX-UUOKFMHZSA-N		Interactions Focus chain E [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain L [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain L [auth B]
A1B9T (Subject of Investigation/LOI) Query on A1B9T Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain M [auth B] MOL2 format, chain C [auth A] MOL2 format, chain M [auth B] mmCIF format, chain C [auth A] mmCIF format, chain M [auth B]	C [auth A], M [auth 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 C₁₀ H₁₆ N₃ O₈ P GBTVWYHTXPOXOI-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain M [auth B] Interactions & Density Focus chain C [auth A] Focus chain M [auth B]
C5P Query on C5P Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth A], K [auth B]	CYTIDINE-5'-MONOPHOSPHATE C₉ H₁₄ N₃ O₈ P IERHLVCPSMICTF-XVFCMESISA-N		Interactions Focus chain F [auth A] Focus chain H [auth A] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain H [auth A] Focus chain K [auth B]
C Query on C Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	CYTIDINE-5'-MONOPHOSPHATE C₉ H₁₄ N₃ O₈ P IERHLVCPSMICTF-XVFCMESISA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]