Abstract
Binding of charged nanoparticles to nonmodified DNA and RNA target molecules on microarrays allows detection of these nucleic acids by locating bound nanoparticles on microarray surface. Two computational models have been developed to study the ionic interaction of colloidal particles and biopolymer molecules on a microarray surface. One model represents a basic approach based on mass action law for simulation charge effects versus the chemical composition of the interacting array surface and nanoparticle. The second model is implementation of the advanced Gouy-Chapman-Stern-Graham model for describing effects on liquid-solid interface. We found that both models predict selective binding of colloidal particles to large target molecules on the surface with no binding to smaller capture molecules. This binding regime is considered to be very beneficial for application of charged nanoparticles for detection of nonmodified DNA and RNA target molecules on microarrays. The theoretical considerations are in qualitative agreement with the experimental results for detecting large target DNA and a 50-base long synthetic oligonucleotide on the amino-modified microarray substrate. The experimental and theoretical results of this study allow further development of the label-free microarray technology demonstrated previously for gene expression analysis that is free of reverse transcription and dye labeling.