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Yet the structural basis of DNA\u2013DNA pairing remains unknown. Here, we combine high-resolution atomic force microscopy and atomistic MD simulations to provide the first direct visualization of DNA pairing in the presence of divalent ions. We show that strongly paired DNAs often achieve groove-to-groove alignment, driven by ionic bridges connecting the minor grooves of the two duplexes. These contacts are further stabilized by sequence-specific interactions, whose strength and specificity vary with the ion type. This mechanism of ion-mediated groove alignment provides a molecular framework for the long-hypothesized \u2018helical alignment\u2019 model, in which homologous recognition would be facilitated by preserving structural register between the two helices. Together, our findings reveal a fundamental principle by which divalent ions promote DNA\u2013DNA pairing, with broad implications for chromosomal condensation and genome organization.<\/jats:p>","DOI":"10.1093\/nar\/gkag817","type":"journal-article","created":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T11:32:27Z","timestamp":1787052747000},"source":"Crossref","is-referenced-by-count":1,"title":["Imaging and mechanism of DNA\u2013DNA recognition mediated by divalent ions"],"prefix":"10.1093","volume":"54","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8919-2701","authenticated-orcid":false,"given":"Thomas E","family":"Catley","sequence":"first","affiliation":[{"name":"School of Chemical Materials and Biological Engineering, University of Sheffield , Sheffield S1 3JD 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