High-Efficiency 3D DNA Walker Immobilized by a DNA Tetrahedral Nanostructure for Fast and Ultrasensitive Electrochemical Detection of MiRNA

Abstract

Herein, by directly limiting the reaction space, an ingenious three-dimensional (3D) DNA walker (IDW) with high walking efficiency is developed for rapid and sensitive detection of miRNA. Compared with the traditional DNA walker, the IDW immobilized by the DNA tetrahedral nanostructure (DTN) brings stronger kinetic and thermodynamic favorability resulting from its improved local concentration and space confinement effect, accompanied by a quite faster reaction speed and much better walking efficiency. Once traces of target miRNA-21 react with the prelocked IDW, the IDW could be largely activated and walk on the interface of the electrode to trigger the cleavage of H2 with the assistance of Mg2+, resulting in the release of amounts of methylene blue (MB) labeled on H2 from the electrode surface and the obvious decrease of the electrode signal. Impressively, the IDW reveals a conversion efficiency as high as 9.33 × 108 in 30 min with a much fast reaction speed, which is at least five times beyond that of typical DNA walkers. Therefore, the IDW could address the inherent challenges of the traditional DNA walker easily: slow walking speed and low efficiency. Notably, the IDW as a DNA nanomachine was utilized to construct a sensitive sensing platform for rapid miRNA-21 detection with a limit of detection (LOD) of 19.8 aM and realize the highly sensitive assay of biomarker miRNA-21 in the total RNA lysates of cancer cell. The strategy thus helps in the design of a versatile nucleic acid conversion and signal amplification approach for practical applications in the areas of biosensing assay, DNA nanotechnology, and clinical diagnosis.

Novel Porphyrinic Covalent Organic Polymer with Polarity-Switchable Dual Wavelength for Accurate and Sensitive Photoelectrochemical Sensing

“…In Figure 2C,D, the positive and negative slopes for PTCA and TPAPP separately suggested the intrinsic n-type and p-type semiconductor features, which correspond to the obtained anodic and cathodic photocurrents. 34,35 However, TPAPP-PTCA PCOP exhibited combination characteristics of n-type and p-type semiconductors (Figure 2E). As a result, PCOP could respond to the dual-polarity photocurrent under light excitation with different wavelengths.…”

Ultrahigh-Speed 3D DNA Walker with Dual Self-Protected DNAzymes for Ultrasensitive Fluorescence Detection and Intracellular Imaging of microRNA

“…As one of the most promising artificial DNA molecular nanomachines, the DNA walkers have shown significant advantages in terms of programmability in functionality and structure due to the ability to walk automatically along a predetermined trajectory with the help of the driving force. − Among them, 3D DNA walkers have superior performance in rate and efficiency of movement as a result of the larger localized concentration of substrate DNA and freer oscillating modes of swing arms compared with 1D DNA walkers. − and 2D DNA walkers, − so they are widely used for the rapid detection of low-abundance biomarkers. − In addition, owing to the vulnerability of protein enzymes to complex microenvironments in vivo , the DNAzyme-mediated amplification reaction, as a classical nonprotein signal amplification method that can bind and cleave specific substrates with the aid of cofactors, holds an extensive application in intracellular analyte detection. − Given the advantages of 3D DNA walkers and DNAzymes, DNAzyme-based 3D DNA walkers are often applied to the detection of miRNAs in vivo , − a kind of biomarker with extremely low abundance in living cells. − However, researchers barely considered the possibility of intracellular degradation of DNAzymes and tend to employ the inefficient initiation method of one target miRNA initiating one swing arm to walk, correspondingly leading to poor stability and insufficient walking rates of the designed DNA walker. − In addition, conventional DNAzyme-based 3D DNA walkers are almost confronted with a limited movement area owing to the length constraint of swing arms and probable derailment caused by random collisions of the walking arms and the substrates, resulting in limited signal amplification . Therefore, a DNAzyme-based 3D DNA walker capable of efficient initiation, high stability, high-speed walking, and large signal accumulation urgently needs to be developed.…”

A universal orthogonal imaging platform for living-cell RNA detection using fluorogenic RNA aptamers

“…6,9,10 Owing to their compact size (19–24 nucleotides) and comparatively more straightforward biological processes than proteins and DNA, 11,12 miRNAs are considered valuable biomarkers for disease diagnosis and therapy targets. 13–17 However, traditional miRNA analysis methods, such as those involving fluorescent hybridization probes (including electrochemical 18–20 and quantitative real-time polymerase chain reaction (qPCR) 21 approaches) and MS2 RNA binding protein-fluorescent protein systems, 22–27 have limitations in terms of probe degradation, delivery challenges, complex kinetics, 21–24 and inability to visualize multiple miRNA targets in a single cell, hindering their effectiveness. 28 Besides, the presence of homologous sequences and the low expression levels of miRNAs in living cells pose challenges to their detection.…”