AFM Imaging of Hybridization Chain Reaction Mediated Signal Transmission between Two DNA Origami Structures

2017 ◽  
Vol 129 (44) ◽  
pp. 13821-13824 ◽  
Author(s):  
Sarah Helmig ◽  
Kurt Vesterager Gothelf
Keyword(s):  
Signal Transmission ◽  
Dna Origami ◽  
Hybridization Chain Reaction ◽  
Chain Reaction ◽  
Afm Imaging

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.

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.

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.

A new method for the in situ assay of α-glucosidase activity and inhibitor screening through an enzyme substrate-mediated DNA hybridization chain reaction

2019 ◽  
Vol 43 (24) ◽  
pp. 9458-9465
Author(s):  
Xiquan Yue ◽  
Lihong Su ◽  
Xu Chen ◽  
Junfeng Liu ◽  
Longpo Zheng ◽  
...  
Keyword(s):  
Small Molecule ◽  
Dna Hybridization ◽  
New Method ◽  
Hybridization Chain Reaction ◽  
Chain Reaction ◽  
Inhibitor Screening ◽  
Glucosidase Activity ◽  
Enzyme Substrate ◽  
In Situ Assay

The strategy is based on small molecule-mediated hybridization chain reaction.

Ultrasensitive ratiometric detection of Pb2+ using DNA tetrahedron-mediated hyperbranched hybridization chain reaction

2021 ◽  
Vol 1147 ◽  
pp. 170-177
Author(s):  
Pingping Ji ◽  
Guimei Han ◽  
Yan Huang ◽  
Hongxin Jiang ◽  
Qiwen Zhou ◽  
...  
Keyword(s):  
Hybridization Chain Reaction ◽  
Chain Reaction ◽  
Ratiometric Detection ◽  
Dna Tetrahedron

scholarly journals Spatiotemporally programmable cascade hybridization of hairpin DNA in polymeric nanoframework for precise siRNA delivery

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Feng Li ◽  
Wenting Yu ◽  
Jiaojiao Zhang ◽  
Yuhang Dong ◽  
Xiaohui Ding ◽  
...  
Keyword(s):  
Steric Effect ◽  
Sirna Delivery ◽  
Dna Nanotechnology ◽  
Hybridization Chain Reaction ◽  
Dna Nanostructures ◽  
Chain Reaction ◽  
Dna Hairpins ◽  
In Vivo Experiments ◽  
Dna And Rna

AbstractDNA nanostructures have been demonstrated as promising carriers for gene delivery. In the carrier design, spatiotemporally programmable assembly of DNA under nanoconfinement is important but has proven highly challenging due to the complexity–scalability–error of DNA. Herein, a DNA nanotechnology-based strategy via the cascade hybridization chain reaction (HCR) of DNA hairpins in polymeric nanoframework has been developed to achieve spatiotemporally programmable assembly of DNA under nanoconfinement for precise siRNA delivery. The nanoframework is prepared via precipitation polymerization with Acrydite-DNA as cross-linker. The potential energy stored in the loops of DNA hairpins can overcome the steric effect in the nanoframework, which can help initiate cascade HCR of DNA hairpins and achieve efficient siRNA loading. The designer tethering sequence between DNA and RNA guarantees a triphosadenine triggered siRNA release specifically in cellular cytoplasm. Nanoframework provides stability and ease of functionalization, which helps address the complexity–scalability–error of DNA. It is exemplified that the phenylboronate installation on nanoframework enhanced cellular uptake and smoothed the lysosomal escape. Cellular results show that the siRNA loaded nanoframework down-regulated the levels of relevant mRNA and protein. In vivo experiments show significant therapeutic efficacy of using siPLK1 loaded nanoframework to suppress tumor growth.

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