Precise Conformational Tuning Facilitated by Tetrahedral DNA Framework Dimers for Enhanced Biomolecular Detection

Abstract

Cellular systems achieve precise biomolecular recognition through dynamic regulation of molecular conformation and spatial arrangement, a complexity that is difficult to replicate in vitro, limiting advancements in biosensing technologies. The nanoscale programmability of tetrahedral DNA frameworks (TDFs) offers a compelling solution, enabling precise control over the spatial arrangement and conformation of nucleic acid targets, making TDFs highly effective for biosensor interface engineering. In this study, we developed dimeric TDF capture probes with tunable interprobe distances (25–45 nm), allowing for the precise stretching and ultrafast detection of single-stranded DNA (ssDNA) targets. By integrating auxiliary probes to modulate local target conformation, hybridization efficiency was significantly enhanced, yielding a 2.9-fold improvement in signal intensity. This approach was successfully applied to single-nucleotide polymorphism (SNP) detection, demonstrating a 2-fold improvement in discrimination sensitivity. Furthermore, integration with a microarray fluorescence chip enabled rapid and accurate quantification of IDH1 mutant allele frequency (MAF), highlighting its potential for glioma classification, disease monitoring, and therapeutic evaluation. These findings underscore the transformative potential of TDF-based interface engineering as a platform for high-performance biosensing and diagnostic applications.