{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,3]],"date-time":"2026-02-03T20:18:59Z","timestamp":1770149939475,"version":"3.49.0"},"reference-count":59,"publisher":"MDPI AG","issue":"7","license":[{"start":{"date-parts":[[2024,7,12]],"date-time":"2024-07-12T00:00:00Z","timestamp":1720742400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Program of Fundamental Research of the Russian Academy of Sciences","award":["FFZE-2022-0009"],"award-info":[{"award-number":["FFZE-2022-0009"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Computation"],"abstract":"<jats:p>Metal-mediated base pairs in DNA double helix molecules open up broad opportunities for biosensors based on DNA clusters with silver due to their low toxicity and applicability in drug design. Despite intensive experimental and computational research, molecular mechanisms of stabilization of a double helix by silver-mediated base pairs are mainly unknown. We conducted all-atom molecular dynamics simulations of a dodecameric DNA double helix (sequence 5\u2032-TAGGTCAATACT-3\u2032-3\u2032ATCCACTTATGA-5\u2032) with either cytosine\u2013cytosine or cytosine\u2013Ag+\u2013cytosine mismatch in the center of the duplex. We extended the previously proposed set of interaction parameters for a silver ion in the silver-mediated pair in order to allow for its dissociation. With this new potential, we studied how the addition of a silver ion could stabilize a DNA double helix containing a single cytosine\u2013cytosine mismatch. In particular, we found out that the helix with cytosine\u2013Ag+\u2013cytosine mismatch has a greater melting temperature than the helix with cytosine\u2013cytosine one. This stabilization effect of the silver ion is in qualitative agreement with experimental data. The central region of the duplex with cytosine\u2013Ag+\u2013cytosine mismatch (unlike with cytosine\u2013cytosine mismatch) is stable enough to prevent bubble formation at moderate temperatures during melting. The results of this simulation can be used to devise novel metal-mediated DNA structures.<\/jats:p>","DOI":"10.3390\/computation12070145","type":"journal-article","created":{"date-parts":[[2024,7,12]],"date-time":"2024-07-12T11:28:03Z","timestamp":1720783683000},"page":"145","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Molecular Dynamics Simulation of Melting of the DNA Duplex with Silver-Mediated Cytosine\u2013Cytosine Base Pair"],"prefix":"10.3390","volume":"12","author":[{"given":"Elena B.","family":"Gusarova","sequence":"first","affiliation":[{"name":"N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 4 Kosygin Street, Moscow 119991, Russia"}]},{"given":"Natalya A.","family":"Kovaleva","sequence":"additional","affiliation":[{"name":"N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 4 Kosygin Street, Moscow 119991, Russia"}]}],"member":"1968","published-online":{"date-parts":[[2024,7,12]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"2403","DOI":"10.1016\/j.ccr.2010.02.026","article-title":"DNA Modified with Metal Complexes: Applications in the Construction of Higher Order metal\u2212DNA Nanostructures","volume":"254","author":"Yang","year":"2010","journal-title":"Coord. Chem. 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