scholarly journals Programming Self-Assembly of DNA Tiles

2016 ◽  
Vol 143 (1-2) ◽  
pp. 35-49
Author(s):  
Marco Bellia ◽  
M. Eugenia Occhiuto
Keyword(s):  
Self Assembly ◽  
Dna Tiles

scholarly journals Constructing Large 2D Lattices Out of DNA-Tiles

Molecules ◽  
2021 ◽  
Vol 26 (6) ◽  
pp. 1502
Author(s):  
Johannes M. Parikka ◽  
Karolina Sokołowska ◽  
Nemanja Markešević ◽  
J. Jussi Toppari
Keyword(s):  
Self Assembly ◽  
Dna Nanotechnology ◽  
Building Blocks ◽  
High Yield ◽  
Dna Nanostructures ◽  
Liquid Interfaces ◽  
Basic Principles ◽  
Dna Tiles ◽  
One Step ◽  
Solid Liquid

The predictable nature of deoxyribonucleic acid (DNA) interactions enables assembly of DNA into almost any arbitrary shape with programmable features of nanometer precision. The recent progress of DNA nanotechnology has allowed production of an even wider gamut of possible shapes with high-yield and error-free assembly processes. Most of these structures are, however, limited in size to a nanometer scale. To overcome this limitation, a plethora of studies has been carried out to form larger structures using DNA assemblies as building blocks or tiles. Therefore, DNA tiles have become one of the most widely used building blocks for engineering large, intricate structures with nanometer precision. To create even larger assemblies with highly organized patterns, scientists have developed a variety of structural design principles and assembly methods. This review first summarizes currently available DNA tile toolboxes and the basic principles of lattice formation and hierarchical self-assembly using DNA tiles. Special emphasis is given to the forces involved in the assembly process in liquid-liquid and at solid-liquid interfaces, and how to master them to reach the optimum balance between the involved interactions for successful self-assembly. In addition, we focus on the recent approaches that have shown great potential for the controlled immobilization and positioning of DNA nanostructures on different surfaces. The ability to position DNA objects in a controllable manner on technologically relevant surfaces is one step forward towards the integration of DNA-based materials into nanoelectronic and sensor devices.

Directed Self-Assembly of DNA Tiles into Complex Nanocages

2014 ◽  
Vol 126 (31) ◽  
pp. 8179-8182 ◽  
Author(s):  
Cheng Tian ◽  
Xiang Li ◽  
Zhiyu Liu ◽  
Wen Jiang ◽  
Guansong Wang ◽  
...  
Keyword(s):  
Self Assembly ◽  
Dna Tiles

The Design and Application of Exclusive OR Logical Computation Based on DNA 3-Arm Sub-Tile Self-Assembly

2020 ◽  
Vol 15 (11) ◽  
pp. 1327-1334
Author(s):  
Chun Huang ◽  
Ying-Jie Han ◽  
Jun-Wei Sun ◽  
Wei-Jun Zhu ◽  
Yan-Feng Wang ◽  
...  
Keyword(s):  
Integrated Circuits ◽  
Self Assembly ◽  
Dna Computing ◽  
Vital Role ◽  
Model Design ◽  
Dna Encoding ◽  
Computing Model ◽  
Dna Tiles ◽  
Half Adder ◽  
Exclusive Or

DNA algorithmic self-assembly plays a vital role in DNA computing, which is applied to create new DNA tiles and then guides these tiles into an algorithmic lattice. However, the larger the logical calculation scale is, the more tile sets will be needed, so that computing model design and experiment will be increasingly difficult. This paper presents a new DNA ‘3-arm sub-tile strategy’ that constructs XOR and half-adder logical circuits. The types of DNA tile corresponding to the logical values is unified in DNA XOR and half-adder logical circuits, which have only three kinds of DNA tiles: logic ‘0’, logic ‘1’ and fixation tile. Compared with the previous references, the amount of DNA tile types has been greatly reduced. Moreover, the half-adder molecular circuit has a distinctive feature, which is an application of the expansion of the XOR logic circuit. Meanwhile, a set of DNA 3-arm sub-tiles suitable for half-adder logical computation is designed on the NUPACK online server. The simulated experiments show that the correct rate of base pairing of the designed DNA encoding is high and the structures are stable. The DNA 3-arm sub-tile self-assembly methods provide a new way to form DNA logical circuits, and has a great potential in the expansion of the integrated circuits.

3D DNA Self-Assembly Algorithmic Model to Solve the Hamiltonian Path Problem

2021 ◽  
Vol 16 (5) ◽  
pp. 731-737
Author(s):  
Jingjing Ma
Keyword(s):  
Self Assembly ◽  
Dna Computing ◽  
Computing Time ◽  
Hamiltonian Path ◽  
Experimental Methods ◽  
Deterministic Algorithm ◽  
Assembly Algorithm ◽  
Hamiltonian Path Problem ◽  
Dna Tiles ◽  
Algorithmic Model

Self-assembly reveals the innate character of DNA computing, DNA self-assembly is regarded as the best way to make DNA computing transform into computer chip. This paper introduces a strategy of DNA 3D self-assembly algorithm to solve the Hamiltonian Path Problem. Firstly, I introduced a non-deterministic algorithm. Then, according to the algorithm I designed the types of DNA tiles which the computing process needs. Lastly, I demonstrated the self-assembly process and the experimental methods which can get the final result. The computing time is linear, and the number of the different tile types is constant.

Analysis of the Self-Assembly of 4×4 DNA Tiles by Temperature-Dependent FRET Spectroscopy

ChemPhysChem ◽  
2009 ◽  
Vol 10 (18) ◽  
pp. 3239-3248 ◽  
Author(s):  
Barbara Saccà ◽  
Rebecca Meyer ◽  
Christof M. Niemeyer
Keyword(s):  
Self Assembly ◽  
The Self ◽  
Temperature Dependent ◽  
Dna Tiles

Characterization and modulation of the hierarchical self-assembly of nanostructured DNA tiles into supramolecular polymers

2006 ◽  
Vol 4 (18) ◽  
pp. 3427 ◽  
Author(s):  
Marco Brucale ◽  
Giampaolo Zuccheri ◽  
Luca Rossi ◽  
Armando Bazzani ◽  
Gastone Castellani ◽  
...  
Keyword(s):  
Self Assembly ◽  
Supramolecular Polymers ◽  
Dna Tiles

Directed Self-Assembly of DNA Tiles into Complex Nanocages

2014 ◽  
Vol 53 (31) ◽  
pp. 8041-8044 ◽  
Author(s):  
Cheng Tian ◽  
Xiang Li ◽  
Zhiyu Liu ◽  
Wen Jiang ◽  
Guansong Wang ◽  
...  
Keyword(s):  
Self Assembly ◽  
Dna Tiles

The Application of DNA Self-Assembly Model for Bin Packing Problem

2012 ◽  
Vol 3 (1) ◽  
pp. 1-15
Author(s):  
Yanfeng Wang ◽  
Xuewen Bai ◽  
Donghui Wei ◽  
Weili Lu ◽  
Guangzhao Cui
Keyword(s):  
Self Assembly ◽  
Bin Packing ◽  
Formal Model ◽  
Linear Time ◽  
Packing Problem ◽  
Assembly Model ◽  
Dna Tiles ◽  
Bin Packing Problem ◽  
Complete Problems ◽  
Np Complete

Bin Packing Problem (BPP) is a classical combinatorial optimization problem of graph theory, which has been proved to be NP-complete, and has high computational complexity. DNA self-assembly, a formal model of crystal growth, has been proposed as a mechanism for the bottom-up fabrication of autonomous DNA computing. In this paper, the authors propose a DNA self-assembly model for solving the BPP, this model consists of two units: grouping based on binary method and subtraction system. The great advantage of the model is that the number of DNA tile types used in the model is constant and it can solve any BPP within linear time. This work demonstrates the ability of DNA tiles to solve other NP-complete problems in the future.

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