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According to the model we use, externally bound ions contribute the most to the ion-induced aggregation of DNA duplexes. The simulations reveal that for two adjacent DNA duplexes, the number of externally bound Na+ ions is larger than the number of K+ ions over a wide range of chloride concentrations in the presence of PEG, providing a qualitative explanation for the higher propensity of sodium ions to compact DNA under crowded conditions. The qualitative picture is confirmed by an estimate of the corresponding free energy of DNA aggregation that is at least 0.2kBT per base pair more favorable in solution with NaCl than with KCl at the same ion concentration. The estimated attraction free energy of DNA duplexes in the presence of Na+ depends noticeably on the DNA sequence; we predict that AT-rich DNA duplexes are more readily condensed than GC-rich ones in the presence of Na+. Counter-intuitively, the addition of a small amount of a crowding agent with high affinity for the specific condensing ion may lead to the weakening of the ion-mediated DNA\u2013DNA attraction, shifting the equilibrium away from the DNA condensed phase.<\/jats:p>","DOI":"10.1063\/5.0159341","type":"journal-article","created":{"date-parts":[[2023,10,10]],"date-time":"2023-10-10T06:17:04Z","timestamp":1696918624000},"update-policy":"https:\/\/doi.org\/10.1063\/aip-crossmark-policy-page","source":"Crossref","is-referenced-by-count":4,"title":["Why Na+ has higher propensity than K+ to condense DNA in a crowded environment"],"prefix":"10.1063","volume":"159","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5515-059X","authenticated-orcid":false,"given":"Egor S.","family":"Kolesnikov","sequence":"first","affiliation":[{"name":"Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology 1 , 141700 Dolgoprudny, Russia"},{"name":"Department of Physics, Virginia Tech 2 , Blacksburg, Virginia 24061, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5348-6070","authenticated-orcid":false,"given":"Ivan Yu.","family":"Gushchin","sequence":"additional","affiliation":[{"name":"Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology 1 , 141700 Dolgoprudny, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8392-8661","authenticated-orcid":false,"given":"Petr A.","family":"Zhilyaev","sequence":"additional","affiliation":[{"name":"The Center for Materials Technologies, Skolkovo Institute of Science and Technology 3 , Bolshoy Boulevard 30, bld. 1, Moscow 121205, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4930-6612","authenticated-orcid":false,"given":"Alexey V.","family":"Onufriev","sequence":"additional","affiliation":[{"name":"Department of Physics, Virginia Tech 2 , Blacksburg, Virginia 24061, USA"},{"name":"Department of Computer Science, Virginia Tech 4 , 2160C Torgersen Hall, Blacksburg, Virginia 24061, USA"},{"name":"Center for Soft Matter and Biological Physics, Virginia Tech 5 , Blacksburg, Virginia 24061, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"317","published-online":{"date-parts":[[2023,10,10]]},"reference":[{"key":"2023101010165305400_c1","doi-asserted-by":"publisher","first-page":"251","DOI":"10.1038\/38444","volume":"389","year":"1997","journal-title":"Nature"},{"key":"2023101010165305400_c2","doi-asserted-by":"publisher","first-page":"17174","DOI":"10.1073\/pnas.0608311103","volume":"103","year":"2006","journal-title":"Proc. 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