Wireframe Orbit-Accelerated Bipedal DNA Walker for Electrochemiluminescence Detection of Methyltransferase Activity

Abstract

In spite of the DNA walkers executing the signal accumulation task in the process of moving along the predetermined paths, the enhancement of walking dynamics and walking path controllability are still challenging due to the unprogrammed arrangements of DNA orbits. Taking these dilemmas into account, a bipedal DNA walker was designed skillfully by the virtue of wireframe orbits assembled by DNA cubes in order, which improved the efficiency and the continuity of walking. It could be attributed to the fact that both the contact chance and the dynamic interaction between walking strands and designated orbits were beneficial to minimize the possibility of derailment and improve the accumulation of signal. In addition, the hollow titanium dioxide nanospheres coated with rubrene (Rub@TiO2 NSs) were prepared by the etching of inner silicon dioxide nanoparticles (SiO2 NPs) to regulate the distribution pattern of rubrene (Rub) molecules and expose more electrochemically active sites for high-efficient electrochemiluminescence (ECL). Benefiting by the pore confinement-enhanced ECL, the electron and mass transfer was significantly accelerated because of the hollow structure of Rub@TiO2 NSs. Subsequently, endogenous dissolved oxygen as the coreactant and palladium nanoparticles (Pd NPs) as the coreaction accelerator were employed to constitute a ternary ECL system with explosive signal response. Combining with this ECL platform, the bipedal walker activated by the target can autonomously and directionally move on the DNA wireframe orbits to release the quenching probes continuously. In this way, the biosensor displayed a low detection limit (2.30 × 10–8 U·mL–1) and a wide linear range (1.0 × 10–7 to 1.0 × 10–1 U·mL–1) for the sensitive detection of Dam methyltransferase (Dam MTase) activity. Therefore, a novel strategy for the accurate quantification of epigenetic targets was developed by virtue of improving the walking dynamics of DNA walker and amplifying the ECL of Rub molecules.

Controllable Three-Dimensional DNA Nanomachine-Mediated Electrochemical Biosensing Platform for Rapid and Ultrasensitive Detection of MicroRNA

“…DNA nanomachine as an effective molecular machine has been widely concerned for constructing nucleic acid signal amplification strategies, owing to the properties of highly programmable self-assembly and accelerated target-recycling kinetics of it. − Currently, according to different DNA nanostructures, DNA nanomachines can be divided into one-dimensional (1D) DNA nanomachines, , two-dimensional (2D) DNA nanomachines, , and three-dimensional (3D) DNA nanomachines. , Although 1D and 2D DNA nanomachines possess low steric hindrance, these DNA nanomachines have also suffered from easy derailment of the DNA leg and shortly successive walking duration. − In light of the above drawbacks, 3D DNA nanomachines can operate more effectively due to their efficient loading capacity and continuous walking capacity, , thus achieving amplification ability of the electrochemical signal. Nevertheless, the walking rate of existing 3D DNA nanomachines is still limited by the weak driving force from the single particle size of the nanomachine core and the large steric hindrance of the distance between the nanomachine core and the catalytic region of the walking arm.…”

“…DNA nanomachine as an effective molecular machine has been widely concerned for constructing nucleic acid signal amplification strategies, owing to the properties of highly programmable self-assembly and accelerated target-recycling kinetics of it. 10−13 Currently, according to different DNA nanostructures, DNA nanomachines can be divided into onedimensional (1D) DNA nanomachines, 14,15 two-dimensional (2D) DNA nanomachines, 16,17 and three-dimensional (3D) DNA nanomachines. 18,19 Although 1D and 2D DNA nanomachines possess low steric hindrance, these DNA nanomachines have also suffered from easy derailment of the DNA leg and shortly successive walking duration.…”

Dual-Signal Integrated Aptasensor for Microcystin-LR Detection via In Situ Generation of Silver Nanoclusters Induced by Circular DNA Strand Displacement Reactions

“…To enhance the signal amplification performance of the dual-signal integrated sensing strategy, co-reaction acceleration strategies and CRISPR-Cas12a nucleases were utilized. Co-reaction acceleration strategies have attracted extensive research by promoting the oxidation or reduction reactions of co-reactants, thereby enhancing the basal signal of luminophores. – Precious metals such as silver nanoparticles (AgNPs), gold nanoparticles (AuNPs), platinum nanoflowers (Pt NFs), and silver–platinum (Ag–Pt) alloys are able to accelerate the electron transfer between luminophores and co-reactants by virtue of their excellent electronic properties . Therefore, the synthesis of AgPtAu with three elements of Ag, Pt, and Au as a co-reaction accelerator for the AgNCs/S 2 O 8 2– system is more likely to yield a satisfactory ECL signal.…”

Target-Driven Annular DNA Walker Coupled with Electrochemiluminescent Silicon Quantum Dots for APE1 Bioanalysis

“…Traditionally, walking legs are programmed to hybridize with preset orbits that are randomly self-assembled on the nanoparticles (e.g., gold nanoparticles, AuNPs). However, due to the less ordered assembly of the orbits, cumulative multistep base complementary pairing increases the operating time and derailment probability of the walking legs. , Recently, we developed a bipedal walker that was able to continuously move along the wireframe orbits which were assembled by DNA cube orderly . Nevertheless, due to the exposure of the 5′ and 3′ ends of the walking legs, it was prone to premature exhaustion when applied in actual physiological samples, limiting the lifespan and detection reliability of the DNA walker.…”