Exploration of the Kinetics of Toehold-Mediated Strand Displacement <i>via</i> Plasmon Rulers

Li, Meixing; Xu, Conghui; Zhang, Nan; Qian, Guangsheng; Zhao, Wei; Xu, Jing‐Juan; Chen, Hong‐Yuan

doi:10.1021/acsnano.7b08673

Cited by 82 publications

(86 citation statements)

References 46 publications

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“…Considering the versatility of aptamers and peptides as recognition ligands, 34,35 and various nucleic acids involved in signal amplification (strand displacement reaction, hybrid chain reaction, rolling circle amplification, etc. ), [36][37][38][39] the proposed CVG-AFS/ICP-MS-based bioassay platform is expected to have a broad spectrum of applications in bioanalysis (enzyme, cancer cell, etc.) with improved analytical performance.…”

Section: Discussionmentioning

confidence: 99%

Sensitive CVG-AFS/ICP-MS label-free nucleic acid and protein assays based on a selective cation exchange reaction and simple filtration separation

Chen

Huang

Dai

et al. 2019

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Section: Discussionmentioning

confidence: 99%

Sensitive CVG-AFS/ICP-MS label-free nucleic acid and protein assays based on a selective cation exchange reaction and simple filtration separation

Chen

Huang

Dai

et al. 2019

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“…Nanoparticle assemblies were also used to study DNA interaction mechanisms such as toe-hold exchange, [97] DNA hybridization, [98][99][100][101] and protein-DNA interactions [102] (Figure 5). The dynamics of these reactions can be followed over time using, e.g., core-satellite constructs where large core particles are linked to small satellite particles through single-stranded DNA.…”

Section: Molecular Sensingmentioning

confidence: 99%

Plasmonic Assemblies for Real‐Time Single‐Molecule Biosensing

Armstrong

Horáček

Zijlstra

2020

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and bound states in the continuum, [27,28] and have been used in applications like biosensing [29] and color printing. [30] Plasmonic assemblies have proven particularly powerful in the field of biosensing. The presence of a biomarker results in, e.g., the (dis-)assembly of solution-phase plasmonic particles, or to changes in the particle-spacing in an assembly. Both result in strong changes in the far-field optical response of the plasmonic assemblies that is most often monitored using spectroscopy in a UV-vis spectrometer. In solution-based sensors, clustering of metal nanoparticles can be induced by target molecules, shifting the optical extinction spectrum of the nanoparticle solution (Figure 1d). [31] Such clustering assays based on particle (dis-) assembly have resulted in colorimetric assays for a range of analytes including proteins, DNA/RNA sequences, heavy ions, and toxic compounds. [31,32] Single-molecule biosensors, on the other hand, detect analytes by probing the optical response of a single nanoparticle. An important advantage of single-molecule sensing is the ability to construct histograms of sensor properties at the single-molecule level, e.g., the induced plasmon shift and statistical parameters like the waiting-time between events. Single-molecule biosensing using plasmonic sensors has been demonstrated in 2012 by Figure 1. Reported applications of nanoparticle assemblies. a) Left: Calculated SERS enhancement factors for a sphere dimer with a 2 nm gap spacing. Right: A Raman spectra of methylene blue dispersed on a monolayer (black) and bilayer (red) of gold nanoparticles. Adapted with permission. [11] Copyright 2019, American Chemical Society. (https://pubs.acs.org/doi/10.1021/acsnano.9b04224) Further permissions related to this material should be directed to the ACS. b) Non-linear emission spectrum of noncentrosymmetric patterned gold nanorods. The third-harmonic generation (THG) peak is in green and the second-harmonic generation (SHG) is in orange. Top inset-scheme of the assembly's THG (green) and SHG (orange) stemming from the red excitation wavelength (ω). Bottom inset-electron microscopy image of the nanoassembly (scale bar 200 nm). Adapted with permission. [16] Copyright 2019, American Chemical Society. c) Examples of metamaterials comprised of plasmonic assemblies (scale bars are 500 nm). Reproduced with permission. [25] Copyright 2014, Springer Nature. d) Left: A cluster assay biosensor in which nanoparticle assembly is induced by a target molecule. Right: An example UV-vis spectrum of the gold nanoparticle monomers (red) and subsequent assemblies upon addition of target molecules (blue).

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“…The kinetics of TMSD are largely dependent on the sequence and length of the toehold. In theory, the rate of the strand‐displacement reaction of TMSD can be quantitatively controlled over 10 6 ‐fold …”

Section: Introductionmentioning

confidence: 99%

Applications of Catalytic Hairpin Assembly Reaction in Biosensing

Liu

Zhang

Xie

et al. 2019

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Nucleic acids are considered as perfect programmable materials for cascade signal amplification and not merely as genetic information carriers. Among them, catalytic hairpin assembly (CHA), an enzyme‐free, high‐efficiency, and isothermal amplification method, is a typical example. A typical CHA reaction is initiated by single‐stranded analytes, and substrate hairpins are successively opened, resulting in thermodynamically stable duplexes. CHA circuits, which were first proposed in 2008, present dozens of systems today. Through in‐depth research on mechanisms, the CHA circuits have been continuously enriched with diverse reaction systems and improved analytical performance. After a short time, the CHA reaction can realize exponential amplification under isothermal conditions. Under certain conditions, the CHA reaction can even achieve 600 000‐fold signal amplification. Owing to its promising versatility, CHA is able to be applied for analysis of various markers in vitro and in living cells. Also, CHA is integrated with nanomaterials and other molecular biotechnologies to produce diverse readouts. Herein, the varied CHA mechanisms, hairpin designs, and reaction conditions are introduced in detail. Additionally, biosensors based on CHA are presented. Finally, challenges and the outlook of CHA development are considered.

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Exploration of the Kinetics of Toehold-Mediated Strand Displacement via Plasmon Rulers

Cited by 82 publications

References 46 publications

Sensitive CVG-AFS/ICP-MS label-free nucleic acid and protein assays based on a selective cation exchange reaction and simple filtration separation

Sensitive CVG-AFS/ICP-MS label-free nucleic acid and protein assays based on a selective cation exchange reaction and simple filtration separation

Plasmonic Assemblies for Real‐Time Single‐Molecule Biosensing

Applications of Catalytic Hairpin Assembly Reaction in Biosensing

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