8YNO | pdb_00008yno

RNA duplex containing Formamide

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

  • Deposited: 2024-03-11 Released: 2024-11-20 
  • Deposition Author(s): Kondo, J., Abe, H.
  • Funding Organization(s): Japan Science and Technology

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 
    0.173 (Depositor), 0.173 (DCC) 
  • R-Value Work: 
    0.151 (Depositor), 0.151 (DCC) 
  • R-Value Observed: 
    0.153 (Depositor) 

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Ligand Structure Quality Assessment 


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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

  • 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.

    • Organizational Affiliation: 
    • Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan.

Macromolecules

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Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (5'-R(*GP*GP*AP*CP*(5BU)P*CP*GP*AP*GP*(HHU)P*CP*C)-3')
A, B
12synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SPM
Query on SPM
Download Ideal Coordinates CCD File 
C [auth A]SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free:  0.173 (Depositor), 0.173 (DCC) 
  • R-Value Work:  0.151 (Depositor), 0.151 (DCC) 
  • R-Value Observed: 0.153 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 27.633α = 90
b = 43.063β = 109.51
c = 28.043γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Science and TechnologyJapanJPMJCR18S1

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-20
    Type: Initial release