RE-SELEX: restriction enzyme-based evolution of structure-switching aptamer biosensors

Aimee A. Sanford, Alexandra E. Rangel, Trevor A. Feagin, Robert G. Lowery, Hector S. Argueta-Gonzalez, Jennifer M. Heemstra

Research output: Contribution to journalArticlepeer-review

32 Scopus citations

Abstract

Aptamers are widely employed as recognition elements in small molecule biosensors due to their ability to recognize small molecule targets with high affinity and selectivity. Structure-switching aptamers are particularly promising for biosensing applications because target-induced conformational change can be directly linked to a functional output. However, traditional evolution methods do not select for the significant conformational change needed to create structure-switching biosensors. Modified selection methods have been described to select for structure-switching architectures, but these remain limited by the need for immobilization. Herein we describe the first homogenous, structure-switching aptamer selection that directly reports on biosensor capacity for the target. We exploit the activity of restriction enzymes to isolate aptamer candidates that undergo target-induced displacement of a short complementary strand. As an initial demonstration of the utility of this approach, we performed selection against kanamycin A. Four enriched candidate sequences were successfully characterized as structure-switching biosensors for detection of kanamycin A. Optimization of biosensor conditions afforded facile detection of kanamycin A (90 μM to 10 mM) with high selectivity over three other aminoglycosides. This research demonstrates a general method to directly select for structure-switching biosensors and can be applied to a broad range of small-molecule targets.

Original languageEnglish
Pages (from-to)11692-11702
Number of pages11
JournalChemical Science
Volume12
Issue number35
DOIs
StatePublished - Sep 21 2021

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