Design and bioanalytical applications of stochastic DNA walkers

Abstract

Synthetic DNA walkers that are inspired by the walking behaviors of naturally occurring motor proteins have emerged into an important subfield of DNA nanotechnology. While early DNA walkers were designed...

The rate-limiting procedure of 3D DNA walkers and their applications in tandem technology

“…In the 3D walkers, typically, only the track DNA is firmly anchored to the nanoparticle while the free-walking DNA is stochastically dissociated in a homogeneous solution, which can randomly move along the functionalized-track substrates and extends the walking range to improve amplification ability. 44,45 In fact, the magnification ability of free 3D walkers has been limited by many factors.…”

Antibody-Bridged DNAzyme Walker for Sensitive Detection of Small Molecules

“…28,35−37 Aptamers often serve as recognition elements in DNAzyme-based DNA walkers for detections of a variety of targets, relying on aptamer binding-induced structure switch or assembly. 17,18,22,38 Antibodies have been available for many SM targets with high affinity and specificity, but immunoassays using DNAzyme walker for SM detection are still rare. S1.…”

“…As one of the attractive DNA molecular machines, DNA walkers exhibit high processivity and quick walking kinetics and have attracted increasing attentions in various fields. − A typical DNA walker usually is composed of the track element, the walking strand element, and the driving element. − It can move autonomously and progressively along predesigned tracks to carry out the task of rapid payload release by pH changes, strand exchange reactions, and DNA cleavage with the assistance of DNAzymes or protein enzymes. − It is noted that the DNA walker can be well assembled into multiple exquisite nanostructures by changing the structure of its components, enabling it to be utilized in a variety of applications. − Benefiting from efficient signal amplification, flexible programmability, and adaptable design involving simple strand hybridization or enzymatic cleavage reactions, DNA walker has become a promising strategy for target detection. − Among different types of DNA walkers, the DNA walker powered by the metal ion-dependent DNAzyme catalytic reaction shows remarkable prospects as a protein enzyme-free signal amplification strategy, − harnessing benefits of RNA cleavage DNAzyme in easy synthesis, low cost, simple design, and facile modification and molecular engineering. ,− Aptamers often serve as recognition elements in DNAzyme-based DNA walkers for detections of a variety of targets, relying on aptamer binding-induced structure switch or assembly. ,,, Antibodies have been available for many SM targets with high affinity and specificity, but immunoassays using DNAzyme walker for SM detection are still rare.…”

Programmably engineered stochastic RNA nanowalker for ultrasensitive miRNA detection

“…Stochastic walkers present a novel approach to addressing this issue. 19–22 The stochastic walker is a molecular device that moves randomly on two-dimensional and three-dimensional tracks, navigating through the interface in an unscripted manner. In comparison to DNA walkers that adhere to predetermined paths, the unpredictable movement of stochastic walkers could significantly boost speed and the ability to process information.…”

“…This makes it a promising option for enhancing analytical and diagnostic abilities. 19 For example, the Ellington group demonstrated 3D trajectories on DNA-coated microparticle surfaces by guiding DNA movement across the surface using catalytic hairpin assembly (CHA). 23 We previously developed an EXO III-powered DNA walker that travels along stochastic paths on gold nanoparticles (AuNPs), recognized for their rapid and sensitive DNA detection capabilities.…”