Effects of Single-Stranded DNA Base Number and Duplex DNA Formation on Intraparticle Diffusion Behavior

We investigated the effects of the base number of single-stranded DNA and duplex DNA formation on the intraparticle diffusion behavior in amino-functionalized silica particles. The sigmoidal distribution behavior of 50 base single-stranded DNA was explained using the DNA aggregation model. Similar results to those previously reported using 20 base DNA were obtained. However, the DNA aggregate was less likely to form and the diffusion coefficient (D) decreased likely because of electrostatic repulsion and pore hindrance, respectively. The intraparticle diffusion of the duplex DNA participated in its dissociation. After duplex DNA distribution in the particle, the single-stranded DNA formed in solution inside the pores was released. The D values ((3.5–8.1) × 10−8 cm2 s−1) obtained from the initial rate were 10-fold those of single-stranded DNA ((0.69–5.0) × 10−9 cm2 s−1). Therefore, the distribution mechanisms of longer single-stranded and duplex DNA were revealed based on the kinetic analysis.