{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,9]],"date-time":"2026-05-09T07:01:12Z","timestamp":1778310072888,"version":"3.51.4"},"reference-count":56,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2022,3,23]],"date-time":"2022-03-23T00:00:00Z","timestamp":1647993600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"PIDDAC","award":["UIDB\/00511\/2020"],"award-info":[{"award-number":["UIDB\/00511\/2020"]}]},{"name":"COMPETE2020","award":["POCI-01-0145-FEDER-028659"],"award-info":[{"award-number":["POCI-01-0145-FEDER-028659"]}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["SFRH\/BD\/138883\/2018"],"award-info":[{"award-number":["SFRH\/BD\/138883\/2018"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010661","name":"Horizon 2020 Framework Programme","doi-asserted-by":"publisher","award":["FEDER and FCT\/MCTES"],"award-info":[{"award-number":["FEDER and FCT\/MCTES"]}],"id":[{"id":"10.13039\/100010661","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:p>Aptamers are single-stranded oligonucleotides, formerly evolved by Systematic Evolution of Ligands by EXponential enrichment (SELEX), that fold into functional three-dimensional structures. Such conformation is crucial for aptamers\u2019 ability to bind to a target with high affinity and specificity. Unnatural nucleotides have been used to develop nucleic acid mimic (NAM) aptamers with increased performance, such as biological stability. Prior knowledge of aptamer-target interactions is critical for applying post-SELEX modifications with unnatural nucleotides since it can affect aptamers\u2019 structure and performance. Here, we describe an easy-to-apply <jats:italic>in silico<\/jats:italic> workflow using free available software \/ web servers to predict the tertiary conformation of NAM, DNA and RNA aptamers, as well as the docking with the target molecule. Representative 2\u02b9-O-methyl (2\u02b9OMe), locked nucleic acid (LNA), DNA and RNA aptamers, with experimental data deposited in Protein Data Bank, were selected to validate the workflow. All aptamers\u2019 tertiary structure and docking models were successfully predicted with good structural similarity to the experimental data. Thus, this workflow will boost the development of aptamers, particularly NAM aptamers, by assisting in the rational modification of specific nucleotides and avoiding trial-and-error approaches.<\/jats:p>","DOI":"10.1371\/journal.pone.0264701","type":"journal-article","created":{"date-parts":[[2022,3,23]],"date-time":"2022-03-23T17:30:18Z","timestamp":1648056618000},"page":"e0264701","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":33,"title":["Modelling aptamers with nucleic acid mimics (NAM): From sequence to three-dimensional docking"],"prefix":"10.1371","volume":"17","author":[{"given":"Ricardo","family":"Oliveira","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0321-9089","authenticated-orcid":true,"given":"Eva","family":"Pinho","sequence":"additional","affiliation":[]},{"given":"Ana Lu\u00edsa","family":"Sousa","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1765-7178","authenticated-orcid":true,"given":"\u00d3scar","family":"Dias","sequence":"additional","affiliation":[]},{"given":"Nuno Filipe","family":"Azevedo","sequence":"additional","affiliation":[]},{"given":"Carina","family":"Almeida","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2022,3,23]]},"reference":[{"key":"pone.0264701.ref001","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1016\/j.bioeng.2007.06.001","article-title":"SELEX-A (r)evolutionary method to generate high-affinity nucleic acid ligands","author":"R Stoltenburg","year":"2007","journal-title":"Biomolecular Engineering"},{"key":"pone.0264701.ref002","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1039\/C6MB00538A","article-title":"Biological applications of xeno nucleic acids","author":"K Morihiro","year":"2017","journal-title":"Molecular BioSystems"},{"key":"pone.0264701.ref003","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1016\/j.biotechadv.2018.11.001","article-title":"Three decades of nucleic acid aptamer technologies: Lessons learned, progress and opportunities on aptamer development","author":"T Wang","year":"2019","journal-title":"Biotechnology Advances. 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