DNA Lever Nanomachine Based on CHA-Driven Conformational Transitions for the Detection of ctDNA

Abstract

Cancer incidence is high worldwide, and early treatment can reduce mortality rates. Circulating tumor DNA (ctDNA) serves as a biomarker for liquid biopsy, enabling early monitoring of tumor burden and treatment response. DNA nanobiosensors have become an important tool for detecting ctDNA due to their high efficiency and low cost. In this study, we developed a DNA lever nanomachine (DLN) based on a catalytic hairpin assembly (CHA)-driven conformational transition for the sensitive detection of ctDNA. The principle is to combine the CHA reaction with DNA lever-based mechanical amplification, enabling the detection of target ctDNA by monitoring changes in signal intensity. During the initial preparation stage, the nanomachine remains in a fluorescence-quenched state. When target ctDNA is present, CHA is activated, triggering downstream signal transduction and initiating a synergistic process of “target capture-conformational transition-signal amplification”, ultimately leading to the restoration and amplification of the fluorescence signal. Additionally, by adjusting the fulcrum position, this machine enhances mechanical efficiency through an effort-saving lever mechanism. It minimizes internal driving force requirements by optimizing the torque load value at the load end, thereby further improving system responsiveness. The established fluorescent biosensing platform achieves satisfactory linear correlation with ctDNA concentrations ranging from 1 pM to 100 nM, with a limit of detection of 0.776 pM. This method offers a new strategy for CHA-based DNA mechanical fluorescence sensing and holds significant application potential in biological sample detection.