Selecting small molecule DNA aptamers with significant conformational changes for constructing transcriptional switches and biosensors

Small molecule aptamers discovered by traditional selection methods usually lack conformational changes upon target binding. This limits the use of aptamers as molecular probes for small molecule detection and regulatory elements of genetic circuits. Here, we report a new method called capture and in vitro transcription-systematic evolution of ligands by exponential enrichment (CIVT-SELEX) to select DNA aptamers that can not only bind to small molecule ligands but also undergo significant conformational changes. Through this method, we select a structure-switching aptamer of uridine-5′-diphosphate (UDP). Taking advantage of its conformational changes, we first construct a UDP-responsive transcriptional switch by inserting the aptamer in a genetic circuit and demonstrate that it can respond to the addition of UDP and regulate the transcription of downstream genes. We also build a UDP aptamer-based biosensor that can be used for active glycosyltransferase screening. We believe this method can provide a universal platform for selecting small molecule aptamers with conformational changes and expand the use of aptamers in small molecule detection and genetic regulation.