8S4N
An i-motif/B-DNA aptamer with high affinity for influenza A virus
Summary for 8S4N
| Entry DOI | 10.2210/pdb8s4n/pdb |
| NMR Information | BMRB: 34906 |
| Descriptor | DNA (43-MER) (1 entity in total) |
| Functional Keywords | aptamer, dna, influenza, hemagglutinin, i-motif, dna binding protein |
| Biological source | synthetic construct |
| Total number of polymer chains | 1 |
| Total formula weight | 12884.24 |
| Authors | Tsvetkov, V.,Mir, B.,Alieva, R.,Arutyunyan, A.,Oleynikov, I.,Novikov, R.,Boravleva, E.,Kamzeeva, P.,Zatsepin, T.,Aralov, A.,Gonzalez, C.,Zavyalova, E. (deposition date: 2024-02-21, release date: 2024-12-18, Last modification date: 2025-01-22) |
| Primary citation | Tsvetkov, V.,Mir, B.,Alieva, R.,Arutyunyan, A.,Oleynikov, I.,Novikov, R.,Boravleva, E.,Kamzeeva, P.,Zatsepin, T.,Aralov, A.,Gonzalez, C.,Zavyalova, E. Unveiling the unusual i-motif-derived architecture of a DNA aptamer exhibiting high affinity for influenza A virus. Nucleic Acids Res., 53:-, 2025 Cited by 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. PubMed: 39777463DOI: 10.1093/nar/gkae1282 PDB entries with the same primary citation |
| Experimental method | SOLUTION NMR |
Structure validation
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