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.