Fluorescence Analysis of the Properties of Structure-Switching DNA Aptamers Entrapped in Sol–Gel-Derived Silica Materials

The entrapment of structure-switching, fluorescence-signaling DNA aptamers into sol–gel-derived materials has recently been reported as a promising platform for solid-phase aptamer-based biosensors. However, there has not yet been a detailed study of the properties of such functional nucleic acids within different sol–gel-based materials. In this work, we utilized a range of fluorescence-based assays, which were previously used to assess the properties of entrapped proteins, to evaluate the factors that affect the function of structure-switching DNA aptamers upon entrapment within polar and nonpolar sol–gel-derived materials using both bipartite and tripartite constructs of fluorescein-labeled, ATP-binding structure-switching aptamers as model systems. The steady-state and time-resolved aptamer dynamics, thermal and long-term stability, accessibility of entrapped aptamers to quenchers, degree of aptamer leaching, and overall target-binding and signaling capabilities of these entrapped aptamers were assessed relative to solution. These studies demonstrate that the ability of the aptamer complex to remain fully hybridized to its complementary dabcyl-labeled quencher strand ( Q -DNA) upon entrapment is the most important factor in terms of signaling capability. It was also observed that more polar (anionic) materials derived from sodium silicate are optimal for DNA aptamers, since these allow the entrapped aptamer to remain hybridized to its complementary strands and retain the dynamic motion needed to undergo structure switching while providing a minimum degree of leaching. Furthermore, such materials improve both the thermal melting temperature of the Q -DNA strand and the long-term stability of entrapped DNA aptamers.