Spatial repositioning enables an electrochemical platform for SNP sensing based on a conformationally-switchable hairpin probe

Abstract

Accurate identification of single nucleotide polymorphisms (SNPs) holds significant importance for crop genetic improvement and precision breeding. However, traditional detection methods suffer from high costs, operational complexity, and heavy reliance on specialized equipment, limiting their large-scale application in breeding practices. Here, we present an electrochemical biosensing platform based on conformational change design, specifically tailored for sensitive and selective SNP analysis, achieved through the spatial reconfiguration of conformation-switchable hairpin probes. Upon hybridization with target sequences, the hairpin structure undergoes spatial remodeling to modulate its distance from the electrode surface, enabling signal transduction. This design leverages precise spatial control and structural dynamics to achieve high signal specificity, allowing single-base mismatch discrimination with exceptional reproducibility and sensitivity. The operationally simple biosensing platform demonstrates high specificity in distinguishing single-nucleotide variations. By applying this system to identify SNPs associated with key phenotypic traits related to leaf morphology in soybean genotypes, we validate its potential for genotype screening and molecular breeding applications.