DNA reversibly adsorbs to a charged surface when divalent metal ions mediate the DNA-surface interaction. Understanding the nature of these DNA-ion-surface interactions at the atomic level may provide insight that can guide the design of future nanoscale devices. Alkaline earth metal ions have the divalent charge necessary to bind double-strand DNA (dsDNA) to a negatively charged surface, such as a carboxylate-terminated alkanethiol monolayer, and exhibit size-dependent trends that may be exploited in the design of DNA-based nanoscale devices. Because charge-transfer and other quantum effects may play a role in DNA-ion-surface binding, density functional theory (DFT) is used to compute binding energies of explicitly solvated Ca2+, Sr2+, and Ba2+ ions and ligands that represent a carboxylate-terminated surface (acetate), the phosphate backbone of dsDNA (dimethyl phosphate), and the major groove of dsDNA (guanine). Relativistic effective core potentials are used to model the metal ions and a dielectric continuum is used to model bulk water. Due to the size and flexibility of the first solvation shells of these metal ions, which are modeled explicitly using DFT, a larger solvent cavity is necessary to accurately model hydrated Ca2+, Sr2+, and Ba2+ ions with a combined explicit and continuum solvent model. Using a solvent accessible surface cavity, DFT predicts size-dependent trends, but the carboxylate-terminated monolayer and the backbone of dsDNA were found to have similar binding energies. Due to the energetic penalty of removing a first solvation shell water molecule, indirect binding is preferred over direct binding for all metal ion and ligand complexes studied. Comparison to guanine binding energies may revel DNA versus surface preferred binding for each alkaline earth metal ion studied.

Size-dependent alkaline earth metal ion interactions with DNA and a charged surface

Macromolecular Chemistry: The Second Century

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ACS Spring 2020 National Meeting & Expo

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.