Investigation of RNA structure-switching aptamers in tunable sol–gel-derived materials

Abstract

In recent years RNA aptamers have emerged as potential recognition elements for solid phase assays, including assays that utilize sol–gel based biohybrid materials. However, there is still very little knowledge regarding the behavior of RNA aptamers when entrapped in sol–gel-derived materials. In this work, we evaluated the performance of an adenosine triphosphate (ATP)-binding structure-switching RNA aptamer in a series of sol–gel derived materials and compared the results to those previously reported for an ATP-binding DNA aptamer. It was observed that the nature of the entrapping material is the key parameter affecting the functionality of the entrapped ATP-binding RNA aptamer, which mainly impacts its ability to remain fully hybridized to signaling DNA strands upon entrapment. We observed that those materials with a high organic content provided the best performance for entrapped RNA aptamers at early times after entrapment. However, upon aging, materials derived from sodium silicate provided the best performance. Overall, the results suggest that polar materials that do not produce alcohol are optimal for entrapment of both DNA and RNA aptamers that bind ATP.