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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.<\/jats:p>","DOI":"10.1093\/nar\/gkae1282","type":"journal-article","created":{"date-parts":[[2024,12,13]],"date-time":"2024-12-13T15:34:52Z","timestamp":1734104092000},"source":"Crossref","is-referenced-by-count":18,"title":["Unveiling the unusual i-motif-derived architecture of a DNA aptamer exhibiting high affinity for influenza A virus"],"prefix":"10.1093","volume":"53","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0494-3332","authenticated-orcid":false,"given":"Vladimir","family":"Tsvetkov","sequence":"first","affiliation":[{"name":"Center for Mathematical Modeling in Drug Development, Sechenov First Moscow State Medical University ,\u00a0 Moscow 119991 ,","place":["Russia"]},{"name":"Department of Cell Biology,\u00a0Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine , Moscow 119435 ,","place":["Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bartomeu","family":"Mir","sequence":"additional","affiliation":[{"name":"Instituto de Qu\u00edmica F\u00edsica Blas Cabrera,\u00a0CSIC , Madrid\u00a028006 ,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rugiya","family":"Alieva","sequence":"additional","affiliation":[{"name":"Chemistry Department, Lomonosov Moscow State University , Moscow 119991 ,","place":["Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander","family":"Arutyunyan","sequence":"additional","affiliation":[{"name":"Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University , Moscow 119991 ,","place":["Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ilya","family":"Oleynikov","sequence":"additional","affiliation":[{"name":"Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University , Moscow 119991 ,","place":["Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roman","family":"Novikov","sequence":"additional","affiliation":[{"name":"Engelhardt Institute of Molecular Biology, Russian Academy of Sciences , Moscow 119991 ,","place":["Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elizaveta","family":"Boravleva","sequence":"additional","affiliation":[{"name":"Chumakov Federal Scientific Center for Research and Development of Immunobiological Products (Institute of Poliomyelitis), Russian Academy of Sciences , Moscow 108819 ,","place":["Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Polina","family":"Kamzeeva","sequence":"additional","affiliation":[{"name":"Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences , Moscow 117997 ,","place":["Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Timofei","family":"Zatsepin","sequence":"additional","affiliation":[{"name":"Chemistry Department, Lomonosov Moscow State University , Moscow 119991 ,","place":["Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3268-2352","authenticated-orcid":false,"given":"Andrey","family":"Aralov","sequence":"additional","affiliation":[{"name":"Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences , Moscow 117997 ,","place":["Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8796-1282","authenticated-orcid":false,"given":"Carlos","family":"Gonz\u00e1lez","sequence":"additional","affiliation":[{"name":"Instituto de Qu\u00edmica F\u00edsica Blas Cabrera,\u00a0CSIC , Madrid\u00a028006 ,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5260-1973","authenticated-orcid":false,"given":"Elena","family":"Zavyalova","sequence":"additional","affiliation":[{"name":"Chemistry Department, Lomonosov Moscow State University , Moscow 119991 ,","place":["Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,1,7]]},"reference":[{"key":"2025010908274129700_B1","doi-asserted-by":"crossref","first-page":"2672","DOI":"10.1002\/anie.200804643","article-title":"The chemical biology of aptamers","volume":"48","author":"Mayer","year":"2009","journal-title":"Angew. 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