High-performance bioimaging and biosensing via nucleobase-editing enzymes

Abstract

Nucleobases, the fundamental units of DNA and RNA, undergo diverse chemical modifications and lesions that regulate genomic stability, epigenetic states, and cellular functions. Nucleobase-editing enzymes, including deaminases, methyltransferases/demethylases, and DNA glycosylases, catalyze precise base conversions, modification/demodification, or excision reactions at high resolution without inducing double-stranded breaks. Originally studied in transcriptomic diversification, epigenetic regulation, and DNA repair, these enzymes are now increasingly repurposed as programmable actuators in biosensing and bioimaging applications. In this review, we first outline the catalytic principles of representative nucleobase-editing enzymes, emphasizing substrate recognition, reaction mechanisms, and physiological functions. We then highlight how these enzymes are integrated into biosensing and bioimaging modules across three major modes: nucleobase conversion, where site-directed deamination enables facile fluorescent protein reporter translation or specific DNA probe hybridization signals; nucleobase modification/demodification, where methylation and demethylation events regulate downstream selective enzymatic biocatalysis or programmble functional nucleic acid activation; and nucleobase erasure, where glycosylase-mediated base excisions facilitate specific probe accommodation or effient enzyme-catalyzed amplification. Such nucleobase-editing enzyme-driven systems offer high specificity, efficient amplification, and high compatibility with physiological conditions, enabling sensitive and spatiotemporally resolved monitoring of nucleic acids, proteins, and cellular processes. Finally, we discuss the advantages, challenges, and future directions of this emerging field. Advances in enzyme engineering, delivery strategies, and multiple circuitry integration are expected to yield next-generation bioanalytical platforms with improved precision, scalability, and clinical applicability. Collectively, these developments establish nucleobase-editing enzymes as a versatile molecular toolbox that bridges fundamental enzymology with applied biotechnology for diagnostics, therapeutic monitoring, and synthetic biology.