8S4N | pdb_00008s4n

An i-motif/B-DNA aptamer with high affinity for influenza A virus

• PDB DOI: https://doi.org/10.2210/pdb8S4N/pdb
• BMRB: 34906
• NAKB: 8S4N

• Classification: DNA BINDING PROTEIN
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2024-02-21 Released: 2024-12-18 
• Deposition Author(s): Tsvetkov, V., Mir, B., Alieva, R., Arutyunyan, A., Oleynikov, I., Novikov, R., Boravleva, E., Kamzeeva, P., Zatsepin, T., Aralov, A., Gonzalez, C., Zavyalova, E.
• Funding Organization(s): Spanish Ministry of Science, Innovation, and Universities

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Unveiling the unusual i-motif-derived architecture of a DNA aptamer exhibiting high affinity for influenza A virus.

Tsvetkov, V., Mir, B., Alieva, R., Arutyunyan, A., Oleynikov, I., Novikov, R., Boravleva, E., Kamzeeva, P., Zatsepin, T., Aralov, A., Gonzalez, C., Zavyalova, E.

(2025) Nucleic Acids Res 53

• PubMed: 39777463 
• DOI: https://doi.org/10.1093/nar/gkae1282
• Primary Citation of Related Structures:  
  8S4N


• PubMed Abstract: 
  

  Non-canonical nucleic acid structures play significant roles in cellular processes through selective interactions with proteins. While both natural and artificial G-quadruplexes have been extensively studied, the functions of i-motifs remain less understood. This study investigates the artificial aptamer BV42, which binds strongly to influenza A virus hemagglutinin and unexpectedly retains its i-motif structure even at neutral pH. However, BV42 conformational heterogeneity hinders detailed structural analysis. Molecular dynamics simulations and chemical modifications of BV42 helped us to identify a potential binding site, allowing for aptamer redesign to eliminate the conformational diversity while retaining binding affinity. Nuclear magnetic resonance spectroscopy confirmed the i-motif/duplex junction with the three-cytosine loop nearby. This study highlights the unique structural features of the functional i-motif and its role in molecular recognition of the target.

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Organizational Affiliation: 
• Center for Mathematical Modeling in Drug Development, Sechenov First Moscow State Medical University, Moscow 119991, Russia.
Department of Cell Biology, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow 119435, Russia.
Instituto de Química Física Blas Cabrera, CSIC, Madrid 28006, Spain.
Chemistry Department, Lomonosov Moscow State University, Moscow 119991, Russia.
Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia.
Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia.
Chumakov Federal Scientific Center for Research and Development of Immunobiological Products (Institute of Poliomyelitis), Russian Academy of Sciences, Moscow 108819, Russia.
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia.

Biological Assembly 1  

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

Biological Assembly Evidence: NMR Distance Restraints

Macromolecule Content 

• Total Structure Weight: 12.88 kDa 
• Atom Count: 850 
• Modeled Residue Count: 43 
• Deposited Residue Count: 43 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (43-MER)	A	43	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-18 
Deposition Author(s): Tsvetkov, V., Mir, B., Alieva, R., Arutyunyan, A., Oleynikov, I., Novikov, R., Boravleva, E., Kamzeeva, P., Zatsepin, T., Aralov, A., Gonzalez, C., Zavyalova, E.

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Funding Organization	Location	Grant Number
Spanish Ministry of Science, Innovation, and Universities	Spain	--

Revision History  

• Version 1.0: 2024-12-18
  Type: Initial release
  
• Version 1.1: 2025-01-22
  Changes: Database references