Recent progress of frame nucleic acids studies towards atomic fabrications

Yang Bei; Li Qian; Liu Hua-Jie; Fan Chun-Hai

doi:10.7498/aps.70.20201437

Abstract

In recent years, the technology of traditional integrated circuit fabrication is facing a huge challenge. As the top-down lithography gradually approaches to its size limit, the development of atomic-scale precise fabrication for functional devices has already become a major scientific issue at present and might become a breakthrough in the development of information technology in the future. With the reference of the bottom-up self-assembly, which is the basic principle of constructing various advanced structures in living systems, the integrated assembly of atoms can be gradually constructed through a series of operations such as capturing, positioning, and moving atoms. The advent of framework nucleic acids (FNAs) happens to provide a new platform for manipulating single atom or integrating multiple atoms. As is well known, the nucleic acids are not only the carriers of genetic information, but also biological building blocks for constructing novel microscopic and macroscopic materials. The FNAs represent a new type of framework with special properties and features, constructed by nucleic acids’ bottom-up self-assembly. With the improvement of chemical synthesis and modification method of nucleic acids, various molecules and materials, such as fluorophores, nanoparticles, proteins, and lipids, can be spatially organized on FNAs with atomic precision, and these functionalized FNAs have been widely explored in the fields of biosensing, biocomputing, nano-imaging, information storage, nanodevices, etc. Based on the features of precise addressability, superior programmability and tailorable functionality, FNAs can be used for implementing the artificial self-assembly of objects with atomic precision to realize the precise arrangement in spatial and functional integration of basic assembly units, and even prompt the development of device fabrication from atomic scale to macroscopic scale. This review focuses on the intersection of FNAs and atomic fabrication, giving a systematically description of the feasibility and advantages of precisely atomic fabrication with FNAs from three aspects. First, the DNA/RNA nanoarchitectures from static state to dynamic state and general strategies for programmable functionalization of FNAs are briefly introduced. Then the applications of FNAs in device fabrication are highlighted, including single molecule reactors, single molecule sensors, nanodevices for cargo loading and transporting, nanophotonics, nanoelectronics and information processing devices. Finally, an outlook of the future development of atomic fabrication with FNAs is given as well.

Keywords:

Authors and contacts

1.
Key Laboratory of Advanced Civil Engineering Materials of Ministry of Education, Shanghai Research Institute for Intelligent Autonomous Systems, School of Chemical Science and Engineering, Tongji University, Shanghai 200092, China
2.
School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China

Corresponding author: Liu Hua-Jie, liuhuajie@tongji.edu.cn ; Fan Chun-Hai, fanchunhai@sjtu.edu.cn

Funds: Project supported by the National Key Research and Development Program of China (Grant Nos. 2016YFA0400900, 2016YFA0201200), the National Natural Science Foundation of China (Grant Nos. 21722310, 21834007, 21873071, 91953106), and the Fundamental Research Funds for the Central Universities of China

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图 1 典型框架核酸结构: DNA瓦块和DNA折纸结构　(a) DNA瓦块组装成的二维晶格^[28]; (b) DNA四面体^[20]; (c) 类富勒烯结构^[21]; (d) DNA折纸设计图及几种二维平面折纸结构^[22]; (e) 球形^[40]、花鸟图案^[42]和兔子^[41]线框DNA折纸结构; (f) DNA纳米花瓶结构^[43]; (g) 16个折纸模块组成的蒙娜丽莎图案^[50]

Figure 1. Typical FNAs: DNA tile and DNA origami: (a) DNA four-way junction^[28]; (b) DNA tetrahedron^[20]; (c) DNA buckyball self-assembled by three-point-star DNA tiles^[21]; (d) 2D DNA origami structures^[22]; (e) sphere^[40], flower-and-bird pattern^[42] and bunny-shape^[41] wireframe DNA origami structures; (f) nanoflask DNA origami structure with complex curvatures^[43]; (g) a Mona Lisa pattern self-assembled by 16 DNA origami tiles^[50].

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图 2 框架核酸介导纳米颗粒组装　(a) DNA瓦块介导AuNPs组装成二维阵列^[60]; (b) 三角形DNA纳米管封装的AuNP线^[62]; (c) DNA折纸模块介导AuNPs形成平面阵列^[63]; (d) DNA单链编码的AuNPs组装成分支状类分子结构^[65]

Figure 2. FNAs-directed nanoparticles assembly: (a) 2D AuNP arrays self-assembled by DNA tiles ^[60]; (b) AuNP lines size-selective encapsulated within triangular DNA nanotubes^[62]; (c) 2D AuNP arrays directed by DNA origami tiles^[63]; (d) branched molecule-like structures self-assembled by single-stranded DNA encoded AuNPs^[65].

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图 3 框架核酸介导原位生长　(a) 三角形DNA折纸上定点金属化形成银纳米簇^[69]; (b) DNA折纸上选择性金属化构建8字形图案^[70]; (c) DNA-二氧化硅复合材料的制备^[71]; (d) DNA折纸上定点合成“i”形二氧化硅纳米结构^[72]

Figure 3. FNAs-directed in-situ growth of nanomaterials: (a) Silver nanoclusters synthesized on DNA origami^[69]; (b) selective DNA condensation and metallization on DNA origami for fabricating a digit 8 pattern^[70]; (c) DNA origami silicification diatom-mimicking structures^[71]; (d) site-specific synthesis of “i-pattern” silica nanostructure on DNA origami^[72].

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图 4 框架核酸构建单分子反应器　(a) DNA 折纸上单分子化学键断裂反应^[74]; (b) DNA折纸上光诱导多巴胺聚合反应^[77]; (c) DNA折纸上酶通路调控系统^[78]; (d) DNA纳米管中GO_x和HRP的酶级联反应^[79]; (e) DNA机器可逆调控酶级联反应^[80]

Figure 4. FNAs used for single molecule reactors: (a) Single-molecule chemical cleavage reactions on DNA origami^[74]; (b) light-triggered polydopamine formation on DNA origami^[77]; (c) enzyme pathway regulation system on a rectangular DNA origami platform^[78]; (d) bienzyme cascade of GO_x and HRP in a DNA origami nanotube^[79]; (e) reversible regulation of enzyme cascade reaction by a DNA machine^[80].

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图 5 框架核酸构建单分子传感器　(a) DNA 折纸上设计的V形探针检测目标RNA^[84]; (b) 字母图案的DNA折纸用于SNP检测^[85]; (c) DNA四面体探针检测目标DNA^[87]; (d) AuNP二聚体检测染料分子的SERS信号^[88]; (e) AuNP四聚体对SERS信号的单分子水平定点、定量检测^[89]

Figure 5. FNAs used for single molecule sensing: (a) Detection of the target RNA by hybridization with V-shaped probe stretched from a DNA origami^[84]; (b) SNP detection with alphabetic patterned origami structures ^[85]; (c) recognition of the target DNA with a DNA tetrahedral structured probe ^[87]; (d) DNA origami-templated AuNP dimers for SERS^[88]; (e) DNA origami-templated tetrameric Au nanoclusters for quantizing single-molecule SERS^[89].

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图 6 框架核酸用于分子装载和输运　(a) DNA 折纸上的分子装配线^[93]; (b) 电场驱动DNA纳米机械臂旋转并使金纳米棒运动^[95]; (c) 凝血酶功能化的DNA纳米机器人^[97]; (d) 3种用于经皮给药的DNA四面体结构^[98]

Figure 6. FNAs used for cargos loading and transporting: (a) Molecular assembly line on DNA origami^[93]; (b) electrically actuated rotation of a nanorobotic arm, moving a gold nanorod^[95]; (c) DNA origami nanocapsule actuated by changing pH^[97]; (d) 3DNA tetrahedrons for transdermal drug delivery^[98].

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图 7 框架核酸的纳米光学应用　(a) 基于DNA四面体的光流体激光器实验装置^[101]; (b) DNA-PAINT^[102]; (c) DNA折纸上线性排列的AuNPs产生光波导^[103]; (d) AuNPs在DNA折纸上的左旋和右旋排列^[104]; (e) 四面体DNA折纸组装的金纳米棒手性超分子^[105]; (f) 金纳米棒在DNA折纸上的动态行走^[106]

Figure 7. FNAs used for nanophotonics: (a) Optofluidic lasers based on a DNA tetrahedron^[101]; (b) DNA-PAINT ^[102]; (c) waveguide on the line of AuNPs arranged by a DNA origami^[103]; (d) AuNP helices on DNA origami^[104]; (e) tetrahedral DNA origami-templated plasmonic metamolecules^[105]; (f) Au nanorod walking on DNA origami^[106].

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图 8 框架核酸构建纳电子器件　(a) DNA折纸到SiO₂基底的直接图案转移^[114]; (b) 聚合物线在DNA折纸上形成的“U”形图案^[115]; (c) DNA瓦块组装AuNP构建单电子晶体管^[116]; (d) DNA折纸模板制备高度致密的CNT平行阵列^[117]

Figure 8. FNAs used for nanoelectronics: (a) Pattern transferring from DNA origami into SiO₂^[114]; (b) polymer binding to the DNA origami with a “U” shaped pattern^[113]; (c) DNA tile-templated single electron nanoelectronics^[116]; (d) CNT alignment based on trench-like DNA templates^[117].

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图 9 框架核酸构建信息处理器件　(a) DNA 折纸分子计算器^[122]; (b) DNA单分子巡航机器人解迷宫^[123]; (c) DNA折纸加密系统^[124]; (d) DNA折纸多米诺阵列编码信息^[125]

Figure 9. FNAs used for information processing: (a) DNA origami calculator^[122]; (b) single-molecule DNA navigator for solving maze on the 2 D origami^[123]; (c) DNA origami cryptography system^[124]; (d) DNA origami domino array for coding information^[125].

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