8YNP | pdb_00008ynp

RNA duplex containing Methylformamide

• PDB DOI: https://doi.org/10.2210/pdb8YNP/pdb
• NAKB: 8YNP

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


• Deposited: 2024-03-11 Released: 2025-01-22 
• Deposition Author(s): Kondo, J., Abe, H.
• Funding Organization(s): Japan Science and Technology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.172 (Depositor), 0.172 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.152 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Literature

Synthesis of 2'-formamidonucleoside phosphoramidites for suppressing the seed-based off-target effects of siRNAs.

Nomura, K., An, S., Kobayashi, Y., Kondo, J., Shi, T., Murase, H., Nakamoto, K., Kimura, Y., Abe, N., Ui-Tei, K., Abe, H.

(2024) Nucleic Acids Res 52: 10754-10774

• PubMed: 39231537 
• DOI: https://doi.org/10.1093/nar/gkae741
• Primary Citation of Related Structures:  
  8YNO, 8YNP


• PubMed Abstract: 
  

  In this study, we report the synthesis of 2'-formamidonucleoside phosphoramidite derivatives and their incorporation into siRNA strands to reduce seed-based off-target effects of small interfering RNAs (siRNAs). Formamido derivatives of all four nucleosides (A, G, C and U) were synthesized in 5-11 steps from commercial compounds. Introducing these derivatives into double-stranded RNA slightly reduced its thermodynamic stability, but X-ray crystallography and CD spectrum analysis confirmed that the RNA maintained its natural A-form structure. Although the introduction of the 2'-formamidonucleoside derivative at the 2nd position in the guide strand of the siRNA led to a slight decrease in the on-target RNAi activity, the siRNAs with different sequences incorporating 2'-formamidonucleoside with four kinds of nucleobases into any position other than 2nd position in the seed region revealed a significant suppression of off-target activity while maintaining on-target RNAi activity. This indicates that 2'-formamidonucleosides represent a promising approach for mitigating off-target effects in siRNA therapeutics.

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Organizational Affiliation: 
• Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan.
Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8561, Japan.
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.
Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku 102-8554 Tokyo, Japan.
Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan.
CREST, Japan Science and Technology Agency, 7 Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan.
Institute for Glyco-core Research (iGCORE), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi464-8601, Japan.

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 7.89 kDa 
• Atom Count: 684 
• Modeled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*GP*AP*CP*(5BU)P*CP*GP*AP*GP*(HHX)P*CP*C)-3')	A, B	12	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.172 (Depositor), 0.172 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.152 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.604	α = 110.03
b = 27.932	β = 114.81
c = 28.668	γ = 95.76

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-22 
Deposition Author(s): Kondo, J., Abe, H.

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Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	JPMJCR18S1

Revision History  

• Version 1.0: 2025-01-22
  Type: Initial release