Tang Decui, He Shuoyao, Yang Yani, Zeng Yuqi, Xiong Mengyi, Ding Ding, Wei Weijun, Lyu Yifan, Zhang Xiao-Bing, Tan Weihong
Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, China.
Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
Nat Commun. 2025 Jan 22;16(1):923. doi: 10.1038/s41467-025-56219-9.
Multiple receptor analysis-based DNA molecular computation has been developed to mitigate the off-target effect caused by nonspecific expression of cell membrane receptors. However, it is quite difficult to involve nanobodies into molecular computation with programmed recognition order because of the "always-on" response mode and the inconvenient molecular programming. Here we propose a spatial segregation-based molecular computing strategy with a shielded internal computing layer termed DNA nano-phage (DNP) to program nanobody into DNA molecular computation and build a series of kinetic models to elucidate the mechanism of microenvironment-confinement. We explain the contradiction between fast molecular diffusion and effective DNA computation using a "diffusion trap" theory and comprehensively overcome the kinetic bottleneck of DNP by determining the rate-limiting step. We predict and verify that identifying trace amount of target cells in complex cell mixtures is an intrinsic merit of microenvironment-confined DNA computation. Finally, we show that DNP can efficiently work in complex human blood samples by shielding the interference of erythrocytes and enhance phagocytosis of macrophages toward target cells by blocking CD47-SIRPα pathway.
基于多受体分析的DNA分子计算技术已被开发出来，以减轻细胞膜受体非特异性表达所引起的脱靶效应。然而，由于纳米抗体的“始终开启”响应模式和不便的分子编程，将其纳入具有编程识别顺序的分子计算中相当困难。在此，我们提出一种基于空间隔离的分子计算策略，即具有屏蔽内部计算层的DNA纳米噬菌体（DNP），将纳米抗体编程到DNA分子计算中，并建立一系列动力学模型来阐明微环境限制的机制。我们用“扩散陷阱”理论解释了快速分子扩散与有效DNA计算之间的矛盾，并通过确定限速步骤全面克服了DNP的动力学瓶颈。我们预测并验证，在复杂细胞混合物中识别痕量靶细胞是微环境限制的DNA计算的固有优点。最后，我们表明，DNP可以通过屏蔽红细胞的干扰在复杂的人类血液样本中有效工作，并通过阻断CD47-SIRPα途径增强巨噬细胞对靶细胞的吞噬作用。
