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

doi:10.6023/A24110357

Acta Chimica Sinica ›› 2025, Vol. 83 ›› Issue (3): 309-318.DOI: 10.6023/A24110357 Previous Articles

Review

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)

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

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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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Fig. & Tab. 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]

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

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]

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]

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]

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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