Imaging and mechanism of DNA-DNA recognition mediated by divalent ions

In the cell, DNA must be tightly packed to facilitate its organisation into the nucleus, where recognition of homologous sequences underpins key processes such as recombination. Yet the structural basis of DNA–DNA pairing remains unknown. Here we combine high-resolution AFM and atomistic MD simulations to provide the first direct visualisation 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 “helical alignment” model, in which homologous recognition is facilitated by preserving structural register between the two helices. Together, our findings reveal a fundamental principle by which divalent ions promote DNA–DNA pairing, with broad implications for chromosomal condensation and genome organization.