合成生物学 ›› 2022, Vol. 3 ›› Issue (2): 302-319.DOI: 10.12211/2096-8280.2021-063
施茜, 吴园园, 杨洋
收稿日期:
2021-06-04
修回日期:
2021-10-24
出版日期:
2022-04-30
发布日期:
2022-05-11
通讯作者:
杨洋
作者简介:
基金资助:
Qian SHI, Yuanyuan WU, yang YANG
Received:
2021-06-04
Revised:
2021-10-24
Online:
2022-04-30
Published:
2022-05-11
Contact:
yang YANG
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。
中图分类号:
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.
Qian SHI, Yuanyuan WU, yang YANG. DNA nanotechnology and synthetic biology[J]. Synthetic Biology Journal, 2022, 3(2): 302-319.
图2 DNA折纸术基本原理及其发展(标尺:50 nm)(a)DNA折纸术原理及二维组装[9];(b)三维组装与弯曲控制[11];(c)曲面设计与网状编织[12-13]
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]
图3 核酸分子装配及应用(a)RNA识别阵列[34];(b)DNA机器与分子搬运[46]
Fig. 3 Assembly and applications of nucleic acid molecules(a) RNA recognition array[34];(b) DNA machines and molecular handling[46]
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[ | 生物素 | 链亲和素 | ①具有可逆性; | 结合不稳定 |
Ni-NTA-Histag[ | NTA | Histag | ②可进行定点定位修饰 | ||
抗体-抗原[ | 抗原 | 抗体 | |||
核酸适配体-蛋白[ | 核酸适配体 | — | |||
DNA结合蛋白[ | 特异的dsDNA | 锌指蛋白 | |||
RNA-病毒蛋白[ | RNA | 病毒蛋白 | |||
DNA-衣壳蛋白[ | — | 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[ | 氨基 | 半胱氨酸残基 | ②反应温和,步骤简单 | ||
Sulfo-SMCC[ | 氨基 | 半胱氨酸残基 | |||
√特异性 | |||||
SNAP-tag[ | 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[ | 5-氯已烷 | Halo-tag | ②可控制结合位点 | 操作较复杂 |
表1 蛋白装配的分类
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[ | 生物素 | 链亲和素 | ①具有可逆性; | 结合不稳定 |
Ni-NTA-Histag[ | NTA | Histag | ②可进行定点定位修饰 | ||
抗体-抗原[ | 抗原 | 抗体 | |||
核酸适配体-蛋白[ | 核酸适配体 | — | |||
DNA结合蛋白[ | 特异的dsDNA | 锌指蛋白 | |||
RNA-病毒蛋白[ | RNA | 病毒蛋白 | |||
DNA-衣壳蛋白[ | — | 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[ | 氨基 | 半胱氨酸残基 | ②反应温和,步骤简单 | ||
Sulfo-SMCC[ | 氨基 | 半胱氨酸残基 | |||
√特异性 | |||||
SNAP-tag[ | 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[ | 5-氯已烷 | Halo-tag | ②可控制结合位点 | 操作较复杂 |
图4 蛋白组装与磷脂组装(a)酶促反应介导与调控[61];(b)可控尺寸囊泡组装[62];(c)二维磷脂膜组装[64]
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]
图5 构建仿生细胞元件(a)模拟核孔复合体[55];(b)模拟细胞骨架蛋白[70]
Fig. 5 Mimic and construction of cell elements(a) Simulation of the nuclear pore complex [55]; (b) Simulation of cytoskeleton protein and network [70]
图6 模拟生物过程和生化体系(a)模拟蛋白锚定和膜融合[71];(b)囊泡成管[74];(c)RNA挤出纳米工厂[75];(d)自组装合成衣壳蛋白[52];(e)自主调控凝血系统[77];(f)肌动蛋白运动[78]
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]
图7 在生物医学领域应用(a)逻辑门控DNA纳米机器人[81];(b)病毒衣壳蛋白修饰DNA纳米结构[104];(c)仿病毒磷脂膜包裹DNA纳米结构[105]
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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