基于大环主体分子的核酸探针设计策略及生物应用

doi:10.6023/A24110357

化学学报 ›› 2025, Vol. 83 ›› Issue (3): 309-318.DOI: 10.6023/A24110357 上一篇

综述

基于大环主体分子的核酸探针设计策略及生物应用

郭煜静^a, 张梦盼^a, 巩子彤^a, 赵云莉^a, 石康琦^a^,^b^,^*(), 何磊良^a^,^*()

a 郑州大学公共卫生学院郑州 450001
b 开封市疾病预防控制中心开封 475000

投稿日期:2024-11-26 发布日期:2025-01-24

作者简介:

郭煜静, 2000年8月出生, 河南焦作人, 自2022年9月起加入郑州大学公共卫生学院何磊良课题组从事硕士研究工作, 研究涉及主客体化学, 超分子自组装.

张梦盼, 2002年2月出生, 河北邢台人, 自2023年9月起加入郑州大学公共卫生学院何磊良课题组从事硕士研究工作, 研究涉及核酸纳米探针设计及生物传感.

巩子彤, 2001年10月出生, 山东济宁人, 自2023年9月起加入郑州大学公共卫生学院何磊良课题组从事硕士研究工作, 研究涉及超分子自组装探针用于膜受体成像.

赵云莉, 2001年1月出生, 安徽芜湖人, 自2023年9月起加入郑州大学公共卫生学院何磊良课题组从事硕士研究工作, 研究涉及荧光编码核酸纳米探针设计及多元成像.

石康琦, 1996年12月出生, 河南开封人, 自2021年9月起加入郑州大学公共卫生学院何磊良课题组从事硕士研究工作, 研究涉及主客体介导的超分子自组装探针设计及成像应用.

何磊良, 教授, 2015年于湖南大学获博士学位, 目前在郑州大学公共卫生学院进行研究工作, 主要研究兴趣包括肿瘤液体活检及单细胞分析与调控.

基金资助:
国家自然科学基金(82373630); 国家自然科学基金(82073606)

Design and Biological Application of Macrocyclic Host Molecules-based Nucleic Acid Probes

Yujing Guo^a, Mengpan Zhang^a, Zitong Gong^a, Yunli Zhao^a, Kangqi Shi^a^,^b(), Leiliang He^a()

a College of Public Health, Zhengzhou University, Zhengzhou 450001, China
b Kaifeng Center for Disease Control and Prevention, Kaifeng 475000, China

Received:2024-11-26 Published:2025-01-24
Contact: ^*E-mail: skq961228@163.com; hell2015@zzu.edu.cn
Supported by:
National Natural Science Foundations of China(82373630); National Natural Science Foundations of China(82073606)

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摘要/Abstract

大环主体分子由于其独特的空腔结构及可灵活设计的主客体作用而得到广泛应用, 然而大环主体分子本身缺少靶向性, 因此在复杂的生物环境中很难对靶标进行特异性检测. 联合核酸探针可特异性识别生物靶标的优势, 设计基于大环主体分子的新型核酸探针, 可显著提高探针灵敏度、特异性和抗复杂环境干扰等性能. 本文系统综述了基于大环主体分子的核酸探针设计及其在生物传感和生物成像中的应用, 最后对该领域面临的挑战及未来的发展方向进行了展望, 通过整合多个响应元件增加基于大环主体分子的核酸探针的智能性和逻辑性, 构建智能响应材料, 可使其更好地适应体内环境的复杂性.

关键词: 大环主体分子, 核酸探针, 主客体相互作用, 生物传感, 生物成像

The rapid development of macrocyclic host molecules, with their unique cavity structures of various sizes, allows them to serve as molecular recognition sites for recognition and functional regulation mediated by host-guest interactions. Additionally, macrocyclic host molecules possess characteristics such as fluorescence enhancement, high biocompatibility, and ease of derivatization, which have led to their widespread application across various fields. However, macrocyclic host molecules inherently lack targeting ability, making specific detection of targets in complex biological environments challenging. The derivatization of macrocyclic molecule compounds can be used to adjust their recognition, physical, and biological properties on one hand; on the other hand, they can form macrocyclic polymers through covalent linkages. Moreover, they can spontaneously form supramolecular self-assemblies through non-covalent interactions. Leveraging these characteristics of macrocyclic host compounds, and combining the advantages of nucleic acid probes that can specifically recognize biological targets, the design and preparation of new nucleic acid probes based on macrocyclic host molecules often exhibit superior performance in terms of high sensitivity, high specificity, and resistance to interference from complex environments. This article systematically reviews the design strategies of nucleic acid probes based on both monomeric and aggregated forms of macrocyclic host molecules, which can be applied to the detection of genes, other targets, as well as cellular and in vivo imaging. Especially, nucleic acid probes based on monomeric macrocyclic host molecules, such as molecular beacons, aptamer probes, and adjacent nucleic acid probes, can target different targets and show broad application potential. Finally, the article looks forward to the challenges and future development directions in this field, suggesting that by integrating multiple responsive elements, the intelligence and logic of nucleic acid probes based on macrocyclic host molecules can be enhanced, and the construction of smart responsive materials can better adapt to the complexity of the in vivo environment.

Key words: macrocyclic host molecules, nucleic acid probe, host-guest interactions, bio-sensing, bio-imaging

引用此文

郭煜静, 张梦盼, 巩子彤, 赵云莉, 石康琦, 何磊良. 基于大环主体分子的核酸探针设计策略及生物应用[J]. 化学学报, 2025, 83(3): 309-318.

Yujing Guo, Mengpan Zhang, Zitong Gong, Yunli Zhao, Kangqi Shi, Leiliang He. Design and Biological Application of Macrocyclic Host Molecules-based Nucleic Acid Probes[J]. Acta Chimica Sinica, 2025, 83(3): 309-318.

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图/表 5

不同类型	设计策略	应用范围	优点	局限性	参考文献
基于大环主体分子单体的分子信标	通过共价或非共价作用使分子信标与大环主体分子单体耦合	应用于核酸检测等	提高检测灵敏度等	大环主体分子类型有待拓展、主客体结合能力有待提高	[37-38,40]
基于大环主体分子单体的核酸适配体探针	通过共价或非共价作用使核酸适配体与大环主体分子单体耦合	可以用于检测特定的生物分子、蛋白质等多种靶标	改善靶标识别特异性及复杂环境稳定性等	核酸适配体筛选效率有待改善	[50]
基于大环主体分子单体的相邻探针	通过共价或非共价作用使相邻探针与大环主体分子单体耦合	适用于小分子等靶标检测	改善检测信背比、提高检测灵敏度等	探针的选择性、多目标物检测有待提高	[58]
基于大环主体分子聚集体的核酸探针	核酸探针与大环主体分子聚集体耦合	适用于非病毒载体的靶向基因传递与释放等	降低细胞毒性、增强基因转染效率等	制备的可控性、精确性有待提高	[61⇓-63]

表1. 基于大环主体分子的核酸探针设计策略对比

Table 1. A comparison of nucleic acid probe design strategies based on macrocyclic host molecules

图1. 基于大环主体分子单体的分子信标 (a)基于γ-CD/芘的主客体作用构建结构稳定、高选择性和高灵敏度的分子信标[37]; (b)环糊精超分子包络物介导的芘二聚体开关用于血清中生物硫醇的时间分辨荧光检测[38]; (c)主客体相互作用稳定的三茎分子信标用于核酸杂交的可逆调控[40]

Figure 1. Molecular beacons based on monomeric macrocyclic host molecules (a) A molecular beacon based on γ-CD/pyrene host-guest interaction for structural stability, high selectivity, and high sensitivity[37]; (b) Cyclodextrin supramolecular envelope-mediated pyrene dimer switches for time-resolved fluorescence detection of biological thiols in serum[38]; (c) Triple stem molecular beacon stabilized by host-guest interactions for reversible regulation of nucleic acid hybridization[40]

图2. 基于大环主体分子单体的核酸适配体探针 (a)环状二价核酸适配体的构建[49]; (b) β-CD功能化环状二价核酸适配体用于增强蛋白质的胞内运输效率[50]; (c)葫芦脲介导的超分子传感策略用于成像细胞表面μ-阿片受体(μORs)二聚化[51]; (d) DNA-小分子嵌合体(DC)转换器以实现将ATP输入转化为CB[7]释放CA-II抑制剂1[56]

Figure 2. Aptamer probes based on monomeric macrocyclic host molecules (a) Construction of cyclic divalent aptamers[49]; (b) β-CD functionalized cyclic divalent aptamers for enhancing the intracellular transport efficiency of proteins[50]; (c) Cucurbituril-mediated supramolecular sensing strategy for imaging the dimerization of μ-opioid receptors (μORs) on the cell surface[51]; (d) DNA-small molecule chimera (DC) converter to achieve the conversion of ATP input to CB[7] release of CA-II inhibitor 1[56]

图3. 基于大环主体分子聚集体的核酸探针设计策略 (a)基于α-CD分子聚集体的非病毒基因递送系统设计[62]; (b)衍生化γ-CD介导的分子聚集体用于靶向基因传递[63]; (c)调控主客体相互作用构筑SFNP用于肺腺癌和炎症区分[64]

Figure 3. Design strategies for nucleic acid probes based on macrocyclic host molecule aggregates (a) Design of non-viral gene delivery systems based on α-CD molecular aggregates[62]; (b) Derivatized γ-CD mediated molecular aggregates for targeted gene delivery[63]; (c) Regulation of host-guest interactions to construct SFNPs for distinguishing lung adenocarcinoma from inflammation[64]

图4. 基于大环主体分子的核酸探针用于生物传感和生物成像 (a)基于三茎分子信标(TMB)的纳米孔传感策略用于DNA或蛋白质检测[70]; (b)基于链置换反应和γ-CD荧光增敏实现T4 PNK活性检测[71]; (c)基于α-CD的金/DNA纳米机器实现肿瘤选择性诊断和治疗[72]; (d) AzoR激活的MRET探针实现体内特异和敏感的肿瘤成像[73]

Figure 4. Nucleic acid probes based on macrocyclic host molecules for biosensing and bioimaging (a) Nanopore sensing strategy based on triple-stem molecular beacons (TMB) for DNA or protein detection[70]; (b) Detection of T4 PNK activity based on strand displacement reaction and γ-CD fluorescence enhancement[71]; (c) α-CD-based gold/DNA nanomachines for selective tumor diagnosis and therapy[72]; (d) AzoR-activated MRET probes for specific and sensitive in vivo tumor imaging[73]

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基于大环主体分子的核酸探针设计策略及生物应用

Design and Biological Application of Macrocyclic Host Molecules-based Nucleic Acid Probes

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