DNA nanotechnology and synthetic biology

doi:10.12211/2096-8280.2021-063

Abstract

Abstract:

Conventional biology investigates and examines life for knowledge and explanations. Synthetic biology, however, breaks through this paradigm and opens a new research era that relies on the reconstruction or creation of biological/bionic elements towards new properties and applications. As a multidisciplinary field, synthetic biology benefits from system biology, molecular biology, structural biology, bio-design and engineering and cutting-edge biological techniques. It reveals the law of life, and makes breakthroughs. DNA nanotechnology, using DNA as building materials to make self-assembled nanostructure, has become a significant support technique for synthetic biology. Besides the remarkable biological affinity of nucleic acids, DNA nanotechnology shows unique advantages of the precise designability, addressability, controllability and modular assembly. In this article, we reviewed the current progresses in how to use DNA nanostructure to direct the arrangement and assembly of other biomolecules (e.g. nucleic acids, proteins and lipids) and to construct or mimic novel cell elements (e.g. DNA nuclear pore, DNA membrane-spanning channel and DNA clathrin-mimic networks), biological reactions (e.g. membrane fusion, lipid transfer and vesicle tubulation), and biochemical systems (e.g. RNA-extruding nanofactories, in situ assembly of viral protein and coagulation system). We also introduced the attempts of employing DNA nano-robots for drug delivery and tumor therapy. However, further studies are expected to better synthesize, simulate and regulate biological systems by using DNA nanostructures. For example, how to recover the property of DNA to carry genetic/artificial information; how to balance the complexity and simplicity towards high efficient performance; how to expand the production scale and reduce the cost; how to produce functional structures in cells. Meanwhile, medical applications ask for more improvements, such as increasing drug loading efficiency, enhancing targeting specificity, maintaining structure stability invivo, lowering the immunogenicity and modifying adjuvant for immune therapy. In summary, DNA nanotechnology presents a broad application prospect in synthetic biology, which will help understanding the essence of life, simulating the process of life, establishing artificial systems and developing future technologies.

Key words: synthetic biology, DNA nanotechnology, artificial systems, orderly assembly, healthcare

摘要：

合成生物学突破了经典生物学“格物致知”的研究范式，开启了“建物致知”“建物致用”的研究时代。合成生物学是以系统生物学为基础，结合工程学设计，运用现代生物学技术方法，通过构建新的生物体系以揭示生命规律和开发颠覆性技术的交叉学科。以DNA为主要建筑材料进行纳米尺度结构自组装的DNA纳米技术，具有高度可设计性、精确可寻址性、生物亲和性、模块化组装等独特优势，已经成为合成生物学重要的支持技术。本文介绍了利用DNA纳米结构实现核酸、蛋白质、磷脂等生物大分子的有序装配；构建仿生细胞元件（例如核孔、人工膜通道、网格蛋白），生物过程（例如膜融合、脂质转移、成管过程）和生化体系（例如RNA挤出纳米工厂、体外病毒衣壳蛋白合成和凝血系统）；及其在药物递送、肿瘤治疗等领域的应用。此外，未来的研究有望通过DNA纳米结构来更好地合成、模拟和调节天然生物体系。例如，如何一定程度恢复和利用DNA纳米结构携载遗传信息的能力；如何提高结构设计复杂性的同时，兼顾人工体系的简单性和生产的高效性；如何扩大生产规模，降低成本；如何在细胞中生产结构并组装。同时，临床应用层面仍有许多亟待解决的问题，比如增加药物的搭载效率，增强结构的靶向性，维持机体中结构稳定性，以及通过修饰进行免疫治疗。DNA纳米技术在合成生物学具有广泛的应用前景，将有助于认识生命本质、模拟生命过程、建立人工体系、开发改变未来的技术。

关键词: 合成生物学, DNA纳米技术, 有序装配, 人工体系, 医疗健康

CLC Number:

Q 81

Qian SHI, Yuanyuan WU, yang YANG. DNA nanotechnology and synthetic biology[J]. Synthetic Biology Journal, 2022, 3(2): 302-319.

施茜, 吴园园, 杨洋. DNA纳米技术与合成生物学[J]. 合成生物学, 2022, 3(2): 302-319.

Figures/Tables 8

Fig. 1 Schematic diagrams showing the relationship and key concepts of classical biology and synthetic biology

Fig. 2 Basic principle of DNA origami and its development (Scale bar: 50 nm)(a) Principle for the 2D assembly of DNA origami[9]; (b) 3D structure assembly with the bending control[11]; (c) Design for curved surface and DNA gridiron[12-13]

Fig. 3 Assembly and applications of nucleic acid molecules(a) RNA recognition array[34];(b) DNA machines and molecular handling[46]

Tab. 1 Classification of protein assembly

	根据结合方式分类	DNA修饰	蛋白修饰	优点	缺点
非共价偶联	生物素-链亲和素^[47]	生物素	链亲和素	①具有可逆性；	结合不稳定
	Ni-NTA-Histag^[48]	NTA	Histag	②可进行定点定位修饰
	抗体-抗原^[49]	抗原	抗体	②可进行定点定位修饰
	核酸适配体-蛋白^[50]	核酸适配体	—
	DNA结合蛋白^[51]	特异的dsDNA	锌指蛋白
	RNA-病毒蛋白^[52]	RNA	病毒蛋白
	DNA-衣壳蛋白^[53]	—	衣壳蛋白
共价偶联	√非特异性			①结合较稳定；	结合位点不易控制
	SPDP^[54]	氨基	半胱氨酸残基	②反应温和，步骤简单	结合位点不易控制
	Sulfo-SMCC^[55]	氨基	半胱氨酸残基
	√特异性
	SNAP-tag^[56]	O6-烷基鸟嘌呤	SNAP-tag	①结合较稳定；	需要进行蛋白质工程
	Halo-tag^[57]	5-氯已烷	Halo-tag	②可控制结合位点	操作较复杂

Fig. 4 DNA nanoframe-directed assembly of proteins and phospholipids(a) DNA swing arm and regulation on cascade enzymatic reactions[61]; (b) Vesicles with controllable sizes [62]; (c) Two-dimensional lipid bilayer assembly[64]

Fig. 5 Mimic and construction of cell elements(a) Simulation of the nuclear pore complex [55]; (b) Simulation of cytoskeleton protein and network [70]

Fig. 6 Mimic king biological reactions and biochemical systems(a) Simulation of SNAREs protein-induced membrane fusion[71]; (b) Mimicking BAR protein-induced membrane tubulation [74]; (c) Producing RNA in a nanofactory[75]; (d) Assembly TMV capsid protein on the DNA template [52]; (e) Autonomous regulation of the thrombin dependent coagulation [77]; (f) Simulation of the G-actin movement [78]

Fig. 7 Applications in biomedicines(a) Logic-gate controlled DNA nanorobot[81]; (b) Viral capsid protein modified DNA nanostructure[104]; (c) Virus-inspired membrane-coated DNA nanostructure[105]

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