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

Area of Science:

• Biomolecular engineering
• Nanotechnology
• Biosensing

Background:

• Cellular systems excel at biomolecular recognition via dynamic conformational and spatial regulation, a feat difficult to replicate in vitro, hindering biosensor development.
• Tetrahedral DNA frameworks (TDFs) offer nanoscale programmability for precise control over nucleic acid target arrangement and conformation, ideal for biosensor interface engineering.

Purpose of the Study:

• To develop dimeric TDF capture probes for tunable interprobe distances (25-45 nm) to enable precise stretching and ultrafast detection of single-stranded DNA (ssDNA) targets.
• To enhance hybridization efficiency and signal intensity through auxiliary probes that modulate local target conformation.
• To demonstrate the application of this TDF-based approach for sensitive single-nucleotide polymorphism (SNP) detection and IDH1 mutant allele frequency (MAF) quantification.

Main Methods:

• Development of dimeric tetrahedral DNA frameworks (TDFs) with adjustable interprobe spacing.
• Integration of auxiliary probes to optimize target DNA conformation and hybridization.
• Application of TDF probes in conjunction with microarray fluorescence for ssDNA detection and SNP analysis.

Main Results:

• Achieved precise stretching and ultrafast detection of single-stranded DNA (ssDNA) targets using dimeric TDF probes with tunable distances.
• Enhanced hybridization efficiency by 2.9-fold through auxiliary probe-mediated modulation of target conformation, significantly improving signal intensity.
• Demonstrated a 2-fold improvement in discrimination sensitivity for single-nucleotide polymorphism (SNP) detection.
• Enabled rapid and accurate quantification of IDH1 mutant allele frequency (MAF) using TDFs integrated with a microarray fluorescence chip.

Conclusions:

• TDF-based interface engineering provides a versatile platform for high-performance biosensing, enabling precise control over molecular interactions.
• The developed TDF system offers significant improvements in detection speed, signal intensity, and sensitivity for nucleic acid targets.
• This approach holds substantial potential for advancing diagnostic applications, including glioma classification, disease monitoring, and therapeutic evaluation.