Supercharged DNA origami enhanced signal amplification for ultrasensitive detection of nucleic acid

Abstract

DNA origami has been able to controllably construct highly precise and complex two- or three-dimensional nanostructures of various morphologies. However, their application in the biosensing field is still relatively limited. In this paper, we proposed a portable electrochemical sensor for the detection of nucleic acid targets, using circulating tumor DNA (ctDNA) as an example. This biosensor combined DNA origami with high-curvature gold nanostructures. First, the target was captured by DNA origami in a homogeneous solution and formed the DNA origami-ctDNA (DOC) complex. Subsequently, the DOC complex was further brought to the electrode surface through hybridization with peptide nucleic acids (PNAs) modified on the surface of the gold nanostructures. The high-curvature nanostructured surface reduces entanglement and aggregation between the PNA probes, enhancing their accessibility to DOC. Furthermore, the substantial intrinsic charge of DNA origami can adsorb numerous electroactive [Ru(NH₃)₆]³⁺, whereas PNAs are electrically neutral, significantly enhancing the detection sensitivity and reducing background signals, enabling ultrasensitive detection sensitivity. Additionally, we demonstrated that the DNA origami-based sensor enhanced signal amplification efficiency compared to single-stranded DNA and tetrahedral DNA nanostructures. Through this signal amplification strategy, the sensor achieves highly sensitive (0.26 fM), specific, and selective (in serum) detection of ctDNA, providing a new avenue for nonenzymatic signal amplification and expanding the application of DNA origami in the sensing field.

Keywords: DNA origami; Electrochemical sensor; Gold nanostructures; Nucleic acid; Peptide nucleic acids; Signal amplification.