Numerical modeling of the effect of histidine protonation on pH distribution and DNA hybridization in electronically active microarrays

This study investigates, through numerical modeling, the effects of protonation of histidine buffer in promoting DNA hybridization in electronically active microarrays within a limited pH range. The numerical model framework developed in this study consists of a number of physical phenomena (conservation and mass transport of species) and chemical equilibrium reactions (hydrolysis of water, heterogeneous DNA hybridization, and protonation of histidine) that govern the hybridization of single-stranded DNA molecules (ssDNA) in active microarrays within an environment of continuous generation of H+ ions and their subsequent consumption by histidine buffer. The study demonstrates, through a numerical model and comparison with published experimental results, that the increase in acidity near anodes due to the hydrolysis of water can be neutralized by a histidine buffer creating a relatively stable pH environment. To account for the dependency of DNA hybridization on the pH of the buffer used, the study also introduces a new hybridization efficiency parameter into the numerical model that is based on experimental data for DNA hybridization.