DNA Hybridization on Silica Surface for Gene Chip Design Studied with Molecular Dynamics Simulations

Nucleic acid hybridization behavior has attracted research attention due to their unique pairing interactions. The short nucleic acid probes such as miRNA or 16s regions of microbial genomes are being applied as biomarker for the detection of various diseases, such as cardiovascular or infectious diseases. To facilitate our experimental design of gene chip for early diagnostic purpose, we performed a fully atomistic Molecular Dynamics simulation to study DNA hybridization behavior on α-cristobalite (101) surfaces, which is partially hydroxylated and also chemically modified with aldehyde chains. Drawn on the atomistic simulations, we investigated the morphology of the grafted DNA strands on the surface and the interactions between DNA complementary strands, as a function of the surface properties and solution environment (such as ion strength) for the purpose of enhancing hybridization efficiency. The current research will also lay the foundation for future research with the coarse-grained modeling.