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Despite the fact that the description of canonical dsRNA is considered the least problematic part of RNA modeling, the imperfect shape and flexibility of dsRNA can lead to imbalances in the simulations of larger RNAs and RNA-containing assemblies. We present a comprehensive set of molecular dynamics (MD) simulations of four canonical A-RNA duplexes. Our focus was directed toward the characterization of the influence of varying ion concentrations and of the size of the solvation box. We compared several water models and four RNA force fields. The simulations showed that the A-RNA shape was most sensitive to the RNA force field, with some force fields leading to a reduced inclination of the A-RNA duplexes. The ions and water models played a minor role. The effect of the box size was negligible, and even boxes with a small fraction of the bulk solvent outside the RNA hydration sphere were sufficient for the simulation of the dsRNA.<\/jats:p>","DOI":"10.1021\/acs.jcim.2c01438","type":"journal-article","created":{"date-parts":[[2023,3,29]],"date-time":"2023-03-29T16:17:35Z","timestamp":1680106655000},"page":"2133-2146","source":"Crossref","is-referenced-by-count":29,"title":["Sensitivity of\nthe RNA Structure to Ion Conditions\nas Probed by Molecular Dynamics Simulations of Common Canonical RNA\nDuplexes"],"prefix":"10.1021","volume":"63","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1593-5282","authenticated-orcid":true,"given":"Petra","family":"Ku\u0308hrova\u0301","sequence":"first","affiliation":[{"name":"Palacky\u0301 University Olomouc , , S\u030clechtitelu\u030a 27 , ,","place":["Olomouc, Czech Republic, 779 00"]},{"name":"Institute of Biophysics of the Czech Academy of Sciences , Kra\u0301lovopolska\u0301 135 , ,","place":["Brno, Czech Republic, 612 00"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2769-1553","authenticated-orcid":true,"given":"Vojte\u030cch","family":"Mly\u0301nsky\u0301","sequence":"additional","affiliation":[{"name":"Institute of Biophysics of the Czech Academy of Sciences , Kra\u0301lovopolska\u0301 135 , ,","place":["Brno, Czech Republic, 612 00"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1066-5677","authenticated-orcid":true,"given":"Michal","family":"Otyepka","sequence":"additional","affiliation":[{"name":"Palacky\u0301 University Olomouc , , S\u030clechtitelu\u030a 27 , ,","place":["Olomouc, Czech Republic, 779 00"]},{"name":"VSB \u2212 Technical University of Ostrava , , 17. listopadu 2172\/15 , , ,","place":["Ostrava, Poruba, Czech Republic, 708 00"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6558-6186","authenticated-orcid":true,"given":"Jir\u030ci\u0301","family":"S\u030cponer","sequence":"additional","affiliation":[{"name":"Palacky\u0301 University Olomouc , , S\u030clechtitelu\u030a 27 , ,","place":["Olomouc, Czech Republic, 779 00"]},{"name":"Institute of Biophysics of the Czech Academy of Sciences , Kra\u0301lovopolska\u0301 135 , ,","place":["Brno, Czech Republic, 612 00"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7137-8225","authenticated-orcid":true,"given":"Pavel","family":"Bana\u0301s\u030c","sequence":"additional","affiliation":[{"name":"Palacky\u0301 University Olomouc , , S\u030clechtitelu\u030a 27 , ,","place":["Olomouc, Czech Republic, 779 00"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2023,3,29]]},"reference":[{"key":"2026081804434946800_cit1","doi-asserted-by":"publisher","first-page":"1105","DOI":"10.1002\/bip.22249","article-title":"Folding\nof RNA Tertiary Structure: Linkages Between Backbone Phosphates, Ions,\nand Water","volume":"99","author":"Draper","year":"2013","journal-title":"Biopolymers"},{"key":"2026081804434946800_cit2","doi-asserted-by":"publisher","first-page":"104","DOI":"10.1016\/j.cbpa.2005.02.004","article-title":"Metal ions\nand RNA folding: a highly charged topic with a dynamic future","volume":"9","author":"Woodson","year":"2005","journal-title":"Curr. 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