Research on DNA Nanostructures Based on the Hybrid Chain Reaction for the Assignment Problem

Nanostructures with information processing play an important role in many fields. It is an excellent approach to the application that DNA nanostructures represented by DNA origami molecules combine with the hybrid chain reaction. In this paper, the assignment problem is mapped to a combinatorial graph on the DNA origami substrate. The graph has several modules corresponding to the time efficiency matrix of the assignment problem. The starting chain of the corresponding module is hybridized with the hairpin structure of the starting point, and the corresponding module is opened to emit light. The feasible solution to the problem can be obtained by observing the light-emitting fluorescent numbers of the opened modules. The fluorescent numbers of all the opened modules are added up on the same origami substrate, then different opening methods in different test tubes are compared, and the optimal solution is obtained.

[1]  Hao Yan,et al.  Reconfigurable DNA origami to generate quasifractal patterns. , 2012, Nano letters.

[2]  Jie Chao,et al.  Molecular logic gates on DNA origami nanostructures for microRNA diagnostics. , 2014, Analytical chemistry.

[3]  John Reif,et al.  Improved Optical Multiplexing with Temporal DNA Barcodes. , 2019, ACS synthetic biology.

[4]  Harry M. T. Choi,et al.  Programming DNA Tube Circumferences , 2008, Science.

[5]  Jie Chao,et al.  Solving mazes with single-molecule DNA navigators , 2018, Nature Materials.

[6]  Harry M. T. Choi,et al.  Programming biomolecular self-assembly pathways , 2008, Nature.

[7]  Rong Zhou,et al.  Nonlinear hybridization chain reaction-based functional DNA nanostructure assembly for biosensing, bioimaging applications. , 2020, Biosensors & bioelectronics.

[8]  Mao Ye,et al.  DNA-Based Dynamic Reaction Networks. , 2018, Trends in biochemical sciences.

[9]  Thomas H. LaBean.  Nanotechnology: Another dimension for DNA art , 2009, Nature.

[10]  Arvind Murugan,et al.  Temporal Pattern Recognition through Analog Molecular Computation. , 2018, ACS synthetic biology.

[11]  Erik Winfree,et al.  Self-assembly of carbon nanotubes into two-dimensional geometries using DNA origami templates. , 2010, Nature nanotechnology.

[12]  P. Rothemund.  Folding DNA to create nanoscale shapes and patterns , 2006, Nature.

[13]  Hanadi F. Sleiman,et al.  DNA Nanostructures at the Interface with Biology , 2018 .

[14]  Lulu Qian,et al.  Fractal assembly of micrometre-scale DNA origami arrays with arbitrary patterns , 2017, Nature.

[15]  Ulrich F. Keyser,et al.  Nanopore-Based DNA Hard Drives for Rewritable and Secure Data Storage. , 2020, Nano letters.

[16]  Fatima Benbouzid-Si Tayeb,et al.  An efficient hybrid multi-objective memetic algorithm for the frequency assignment problem , 2020, Eng. Appl. Artif. Intell..

[17]  Jing Yang,et al.  DNAzyme-Based Logic Gate-Mediated DNA Self-Assembly. , 2015, Nano letters.

[18]  Hao Yan,et al.  Scaffolded DNA origami of a DNA tetrahedron molecular container. , 2009, Nano letters.

[19]  Zhao Zhang,et al.  Placing and shaping liposomes with reconfigurable DNA nanocages. , 2017, Nature chemistry.

[20]  Arun Richard Chandrasekaran,et al.  Rationally Engineered Nucleic Acid Architectures for Biosensing Applications. , 2019, Chemical reviews.

[21]  J. Reif,et al.  DNA-Templated Self-Assembly of Protein Arrays and Highly Conductive Nanowires , 2003, Science.

[22]  J. Reif,et al.  Nucleic Acid Databases and Molecular-Scale Computing. , 2019, ACS nano.

[23]  Robert M. Dirks,et al.  Triggered amplification by hybridization chain reaction. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[24]  Wael Mamdouh,et al.  Single-molecule chemical reactions on DNA origami. , 2010, Nature nanotechnology.

[25]  Juan Dong,et al.  Amplified detection of nucleic acid by G-quadruplex based hybridization chain reaction. , 2012, Biosensors & bioelectronics.

[26]  Yanan Tang,et al.  Emerging bioanalytical applications of DNA walkers , 2018, TrAC Trends in Analytical Chemistry.

[27]  P. Yin,et al.  Complex shapes self-assembled from single-stranded DNA tiles , 2012, Nature.

[28]  Yonggang Ke,et al.  Visualization of the Cellular Uptake and Trafficking of DNA Origami Nanostructures in Cancer Cells. , 2018, Journal of the American Chemical Society.

[29]  Lauro T. Kubota,et al.  Supramolecular DNA origami nanostructures for use in bioanalytical applications , 2018, TrAC Trends in Analytical Chemistry.

[30]  Georg Seelig,et al.  A spatially localized architecture for fast and modular DNA computing. , 2017, Nature nanotechnology.

[31]  Huangxian Ju,et al.  Multiplexed chemiluminescence imaging assay of protein biomarkers using DNA microarray with proximity binding-induced hybridization chain reaction amplification. , 2018, Analytica chimica acta.