scholarly journals DNA Origami Model for Simple Image Decoding

2020 ◽  
Vol 2020 ◽  
pp. 1-8
Author(s):  
Risheng Wang ◽  
Zhixiang Yin ◽  
Jianzhong Cui ◽  
Jing Yang ◽  
Zhen Tang ◽  
...  
Keyword(s):  
Self Assembly ◽  
Molecular Beacon ◽  
Important Application ◽  
Dna Origami ◽  
Hairpin Structure ◽  
Hybridization Chain Reaction ◽  
Chain Reaction ◽  
Reaction Solution ◽  
Application Methods ◽  
Image Decoding

DNA origami is the application of self-assembly in nanotechnology. The combination of DNA origami and hybridization chain reaction is one of the important application methods of DNA origami. In this paper, DNA origami is used to design the cipher pattern on the base of origami. The cipher chain, which is put into the reaction solution, hybridizes with the molecular beacon and the hairpin structure that form the cipher pattern to build a DNA origami model that can decode the pattern. The cipher chain consists of the starting chain and the intermediate chain. When the cipher is correct, the cipher chain can open the molecular beacon and the hairpin structure to display the cipher pattern on the origami base in the solution.

Lab in a tube: a fast-assembled colorimetric sensor for highly sensitive detection of oligonucleotides based on a hybridization chain reaction

RSC Advances ◽  
2015 ◽  
Vol 5 (55) ◽  
pp. 44714-44721 ◽  
Author(s):  
Siqi Zhang ◽  
Kun Wang ◽  
Zhenyu Li ◽  
Zhongmin Feng ◽  
Ting Sun
Keyword(s):  
Complex Formation ◽  
Dna Sequence ◽  
Self Assembly ◽  
The Self ◽  
Hybridization Chain Reaction ◽  
Chain Reaction ◽  
Highly Sensitive ◽  
G Quadruplex ◽  
Colored Product ◽  
Highly Sensitive Detection

Upon adding THBV, the self-assembly of THBV with H1 allows the rest of the DNA sequence of H1 to accelerate H1–H2 complex formation. The G-quadruplex at the end of the H1–H2 complex could catalyze TMB into a colored product.

DNA Computing Model for Satisfiability Problem Based on Hybridization Chain Reaction

2020 ◽  
pp. 2159010
Author(s):  
Zhixiang Yin ◽  
Jing Yang ◽  
Qiang Zhang ◽  
Zhen Tang ◽  
Guoqiang Wang ◽  
...  
Keyword(s):  
Dna Computing ◽  
Dna Origami ◽  
Satisfiability Problem ◽  
Hybridization Chain Reaction ◽  
Chain Reaction ◽  
Computing Device ◽  
Computing Model ◽  
Novel Method ◽  
Np Complete ◽  
The Given

Satisfiability problem is a famous nondeterministic polynomial-time complete (NP-complete) problem, which has always been a hotspot in artificial intelligence. In this paper, by combining the advantages of DNA origami with hybridization chain reaction, a computing model was proposed to solve the satisfiability problem. For each clause in the given formula, a DNA origami device was devised. The device corresponding to the clause was capable of searching for assignments that satisfied the clause. When all devices completed the search in parallel, the intersection of these satisfying assignments found must satisfy all the clauses. Therefore, whether the given formula is satisfiable or not was decided. The simulation results demonstrated that the proposed computing model was feasible. Our work showed the capability of DNA origami in architecting automatic computing device. The paper proposed a novel method for designing functional nanoscale devices based on DNA origami.

scholarly journals Elucidation of leak-resistance DNA hybridization chain reaction with universality and extensibility

2020 ◽  
Vol 48 (5) ◽  
pp. 2220-2231 ◽  
Author(s):  
Shaofei Li ◽  
Pan Li ◽  
Meihong Ge ◽  
Hongzhi Wang ◽  
Yizhuang Cheng ◽  
...  
Keyword(s):  
Self Assembly ◽  
Signal Amplification ◽  
Clinical Medicine ◽  
Surface Enhanced Raman Spectroscopy ◽  
Careful Consideration ◽  
Hybridization Chain Reaction ◽  
Chain Reaction ◽  
Dna Hairpins ◽  
Surface Enhanced Raman ◽  
Thermodynamics And Dynamics

Abstract Hybridization chain reaction (HCR) was a significant discovery for the development of nanoscale materials and devices. One key challenge for HCR is the vulnerability to background leakage in the absence of the initiator. Here, we systematically analyze the sources of leakage and refine leak-resistant rule by using molecular thermodynamics and dynamics, biochemical and biophysical methods. Transient melting of DNA hairpin is revealed to be the underlying cause of leakage and that this can be mitigated through careful consideration of the sequence thermodynamics. The transition threshold of the energy barrier is proposed as a testing benchmark of leak-resistance DNA hairpins. The universal design of DNA hairpins is illustrated by the analysis of hsa-miR-21-5p as biomarker when used in conjunction with surface-enhanced Raman spectroscopy. We further extend the strategy for specific signal amplification of miRNA homologs. Significantly, it possibly provides a practical route to improve the accuracy of DNA self-assembly for signal amplification, and that could facilitate the development of sensors for the sensitive detection of interest molecules in biotechnology and clinical medicine.

DNA logic assembly powered by a triplex-helix molecular switch for extracellular pH imaging

2018 ◽  
Vol 54 (61) ◽  
pp. 8498-8501 ◽  
Author(s):  
Hongjie Qi ◽  
Shuzhen Yue ◽  
Sai Bi ◽  
Caifeng Ding ◽  
Weiling Song
Keyword(s):  
Self Assembly ◽  
Molecular Switch ◽  
Extracellular Ph ◽  
The Self ◽  
Hybridization Chain Reaction ◽  
Dna Nanostructures ◽  
Chain Reaction ◽  
Molecular Logic ◽  
Ph Imaging ◽  
Logic Operations

A strategy is rationally designed to finely control the hybridization chain reaction (HCR) for the self-assembly of DNA nanostructures by simply changing the pH, which is successfully applied to molecular logic operations and extracellular pH imaging.

Triggered and catalyzed self-assembly of hyperbranched DNA structures for logic operations and homogeneous CRET biosensing of microRNA

2016 ◽  
Vol 52 (31) ◽  
pp. 5455-5458 ◽  
Author(s):  
Sai Bi ◽  
Shuzhen Yue ◽  
Qiang Wu ◽  
Jiayan Ye
Keyword(s):  
Self Assembly ◽  
Hybridization Chain Reaction ◽  
Strand Displacement ◽  
Chain Reaction ◽  
Dna Structures ◽  
Catalytic Hairpin Assembly ◽  
Displacement Based ◽  
Logic Operations

Toehold-mediated strand displacement-based nanocircuits are developed by integrating catalytic hairpin assembly with hybridization chain reaction, achieving self-assembly of hyperbranched DNA structures and amplified homogeneous CRET detection of microRNA.

scholarly journals A sensitive platform for DNA detection based on organic electrochemical transistor and nucleic acid self-assembly signal amplification

RSC Advances ◽  
2021 ◽  
Vol 11 (60) ◽  
pp. 37917-37922
Author(s):  
Chaohui Chen ◽  
Qingyuan Song ◽  
Wangting Lu ◽  
Zhengtao Zhang ◽  
Yanhua Yu ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Self Assembly ◽  
Signal Amplification ◽  
Dna Detection ◽  
New Method ◽  
Hybridization Chain Reaction ◽  
Chain Reaction ◽  
Electrochemical Transistor ◽  
First Time

A new method has been developed for DNA detection by integrating hybridization chain reaction signal amplification with organic electrochemical transistor device for the first time.

Visual solution to minimum spanning tree problem based on DNA origami

2021 ◽  
Vol 11 (10) ◽  
pp. 1700-1706
Author(s):  
Jing Yang ◽  
Zhixiang Yin ◽  
Zhen Tang ◽  
Xue Pang ◽  
Jianzhong Cui ◽  
...  
Keyword(s):  
Spanning Tree ◽  
Minimum Spanning Tree ◽  
Calculation Model ◽  
Dna Origami ◽  
Fluorescence Labeling ◽  
Hybridization Chain Reaction ◽  
Chain Reaction ◽  
Gold Particles ◽  
Visual Computing ◽  
Nano Gold

DNA origami is a highly precise nanometer material based on DNA molecular. In the current study, we present a visual computing model of minimum spanning tree that combines advantages of DNA origami, hybridization chain reaction and nano-gold particles. Nano-gold particles were used to represent vertices and molecular beacons with fluorescent labels were used as anchor strands, which were fixed on origami substrate with staple strands according to the shape in graph. We then induced hybridization chain reaction using initiator strands and fuel strands. Lastly the problem was detected using fluorescence. The model provides a visualized calculation model of minimum spanning tree by using hybridization chain reaction and fluorescence labeling on origami bases. This model utilizes their advantages and demonstrates effectiveness of the model through case simulation. It also reduces computational complexity of the problem and improve the way of solution reading.

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