Chemical tools for discriminating single nucleotide variants: from design principles to clinical applications

Small variations in nucleic acids, such as single-nucleotide variants (SNVs), can have a profound phenotypic impact and are essential and often confirmatory biomarkers for disease diagnosis. Because of the subtle structural and energetic difference between an SNV and its wild-type (WT) counterpart, accurate discrimination of minute SNVs in complex biological and clinical samples, especially in the presence of high concentrations of WT sequences, presents a formidable analytical challenge. In this review, we provide a comprehensive overview of three mainstream chemical tools for recognizing and discriminating SNVs, with an emphasis on their underlying thermodynamic, kinetic, and enzymatic principles. We also discuss two emerging clinical applications of SNV discrimination tools in the point-of-care diagnosis of infectious diseases and precision management of cancer, which have enabled numerous recent innovations in assay development and device fabrication. By illustrating the design principles and clinical applications, we hope this review will help guide the best use of chemical tools for detecting, quantifying, and enriching SNVs and inspire new ideas, technological advances, and engineering strategies for addressing ongoing clinical challenges.