(770d) Atomistic Simulation and Molecular Field Theory Study of DNA Hybridization in Self-Assembling Monolayer Surfaces

Nucleic acids have unique interfacial behavior due to their high charge density and selective hybridization behavior. Nucleic Acid Test (NAT) devices based on nucleotide self-assembling monolayers (SAMs) have been extensively studied and developed for accurate and efficient diagnostic purposes. To provide some much-needed microscopic insight needed for improving such devices, we use fully atomistic molecular dynamics simulations and molecular field theory to investigate DNA SAM surfaces under different solution conditions to understand the impact of grafting probe density, surface hybridization, ion concentration and ion types. The grafting density, namely, the number of DNA chains on SAMs, largely determines the electrostatic repulsion and steric hindrance on the SAMs surface. Different meltdown behaviors between ssDNA and dsDNA are observed on SAMs due to the structural rigidity from the double helical structure. The cations in the solution condense around DNA chains, neutralizing their highly concentrated negative charge and reducing the repulsive forces between the DNA chains. Monovalent Na⁺ and divalent Mg²⁺ cations exhibit different behavior of association with DNA chains.