{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,31]],"date-time":"2026-01-31T03:08:58Z","timestamp":1769828938500,"version":"3.49.0"},"reference-count":43,"publisher":"MDPI AG","issue":"24","license":[{"start":{"date-parts":[[2019,12,11]],"date-time":"2019-12-11T00:00:00Z","timestamp":1576022400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Molecules"],"abstract":"<jats:p>Aptamer selection can yield many oligonucleotides with different sequences and affinities for the target molecule. Here, we have combined computational and experimental approaches to understand if aptamers with different sequences but the same molecular target share structural and dynamical features. NEO1A, with a known NMR-solved structure, displays a flexible loop that interacts differently with individual aminoglycosides, its ligand affinities and specificities are responsive to ionic strength, and it possesses an adenosine in the loop that is critical for high-affinity ligand binding. NEO2A was obtained from the same selection and, although they are only 43% identical in overall sequence, NEO1A and NEO2A share similar loop sequences. Experimental analysis by 1D NMR and 2-aminopurine reporters combined with molecular dynamics modeling revealed similar structural and dynamical characteristics in both aptamers. These results are consistent with the hypothesis that the target ligand drives aptamer structure and also selects relevant dynamical characteristics for high-affinity aptamer-ligand interaction. Furthermore, they suggest that it might be possible to \u201cmigrate\u201d structural and dynamical features between aptamer group members with different primary sequences but with the same target ligand.<\/jats:p>","DOI":"10.3390\/molecules24244535","type":"journal-article","created":{"date-parts":[[2019,12,12]],"date-time":"2019-12-12T03:20:16Z","timestamp":1576120816000},"page":"4535","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["Common Secondary and Tertiary Structural Features of Aptamer\u2013Ligand Interaction Shared by RNA Aptamers with Different Primary Sequences"],"prefix":"10.3390","volume":"24","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1558-462X","authenticated-orcid":false,"given":"Muslum","family":"Ilgu","sequence":"first","affiliation":[{"name":"Roy J Carver Department of Biochemistry, Biophysics and Molecular Biology, Ames, IA 50011, USA"},{"name":"Aptalogic Inc., Ames, IA 50014, USA"},{"name":"Department of Biological Sciences, Middle East Technical University, Ankara 06800, Turkey"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shuting","family":"Yan","sequence":"additional","affiliation":[{"name":"Department of Chemical and Biological Engineering, Iowa State University, Ames, IA 50011, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ryan M.","family":"Khounlo","sequence":"additional","affiliation":[{"name":"Roy J Carver Department of Biochemistry, Biophysics and Molecular Biology, Ames, IA 50011, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Monica H.","family":"Lamm","sequence":"additional","affiliation":[{"name":"Department of Chemical and Biological Engineering, Iowa State University, Ames, IA 50011, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5496-1814","authenticated-orcid":false,"given":"Marit","family":"Nilsen-Hamilton","sequence":"additional","affiliation":[{"name":"Roy J Carver Department of Biochemistry, Biophysics and Molecular Biology, Ames, IA 50011, USA"},{"name":"Aptalogic Inc., Ames, IA 50014, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2019,12,11]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1021\/ar900093g","article-title":"Molecular dynamics and quantum mechanics of RNA: Conformational and chemical change we can believe in","volume":"43","author":"Ditzler","year":"2010","journal-title":"Acc. 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