Distribution Behavior of Single-Stranded DNA Molecules in an Amino-Group-Functionalized Silica Microparticle

In this study, we investigated the distribution behavior of single-stranded DNA molecules with 20 bases in silica particles (particle size: ∼30 μm) using confocal fluorescence microspectroscopy. The distribution kinetics was investigated under various conditions, such as the type of base (adenine, thymine, guanine, and cytosine), pore size of the particle (30 and 50 nm), and salt concentration (100, 200, and 500 mM), which changed the distribution behavior. At high salt concentrations, we observed sigmoidal kinetic behavior, which does not occur in the general distribution of small organic molecules but is often observed in protein aggregation and nuclear growth. An analytical model based on DNA aggregation explained the sigmoidal distribution behavior well, and this model also worked well when the number of DNA molecules involved in DNA aggregation was greater than two. The intraparticle diffusion of DNA molecules was analyzed using the pore and surface diffusion model. As a result, the intraparticle diffusion of DNA aggregates mainly occurs according to surface diffusion, and the surface diffusion coefficient has the same value ((2.4-6.7) × 10^-9 cm² s^-1) independent of the pore size and type of base.