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

Abstract

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 assess...