Abstract
We developed a unified model to investigate the impact of physiologically relevant divalent ions Mg2+ and Ca2+ on conformations of double stranded DNA (dsDNA) and single-stranded DNA (ssDNA) in a background of monovalent ions Na+ and Cl-. We introduced explicit ions within the framework of coarse-grained three-interaction-site model (TIS-DNA) to take into account the direct interaction between the counterions and DNA. Simulations using the TIS-DNA model, we could quantitatively reproduce a number of experimental observables for both the dsDNA and ssDNA, without any adjustable parameters. We showed that divalent cations populate distinct conformations in different proportions, depending on the nucleotide sequence. With increase in salt concentration, an increased population of dA30 conformations with crooked helical motifs form while dT30 primarily populates collapsed-coil conformations.
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