Quantifying Mg 2+ binding to ssDNA oligomers: A self-consistent field theory study at varying ionic strengths and grafting densities

Abstract

The performance of aptamer-based biosensors is crucially impacted by their interactions with physiological metal ions, which can alter their structures and chemical properties. Therefore, elucidating the nature of these interactions carries the utmost importance in the robust design of highly efficient biosensors. We investigated Mg 2+ binding to varying sequences of polymers to capture the effects of ionic strength and grafting density on ion binding and molecular reorganization of the polymer layer. The polymers are modeled as ssDNA aptamers using a self-consistent field theory, which accounts for non-covalent ion binding by integrating experimentally-derived binding constants. Our model captures the typical polyelectrolyte behavior of chain collapse with increased ionic strength for the ssDNA chains at low grafting density and exhibits the well-known re-entrant phenomena of stretched chains with increased ionic strength at high grafting density. The binding results suggest that electrostatic attraction between the monomers and Mg 2+ plays the dominant role in defining the ion cloud around the ssDNA chains and generates a nearly-uniform ion distribution along the chains containing varying monomer sequences. These findings are in qualitative agreement with recent experimental results for Mg 2+ binding to surface-bound ssDNA.