Asumadu Precious, Guo Zhuowen, Qi Shuo, Liu Chang, Li Yaqi, Shi Qiaoqiao, Kong Dezhao, Ye Hua, Fu Caili, Wang Zhouping
School of Grain Science and Technology, Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Jiangsu University of Science and Technology, Zhenjiang, 212003, China.
Biomedical and Health Technology Platform, National University of Singapore (Suzhou) Research Institute, Suzhou, 215123, China.
Anal Bioanal Chem. 2025 Jul 10. doi: 10.1007/s00216-025-05982-1.
DNA aptamer-based logic gates represent significant advances in molecular computing, enabling complex biological computations at the nanoscale. These systems leverage the unique programmable properties of DNA aptamers-short, single-stranded oligonucleotides with high specificity and binding affinity for diverse applications across fields such as clinical diagnostics, food/environmental monitoring, and targeted therapeutic delivery, garnering significant research interest in the past few decades. In this review, we first expand on the fundamentals of aptamers, including its SELEX process and post-SELEX modifications. We systematically examine the design principles and operation mechanisms of DNA aptamer-based logic gates, mainly AND, OR, INHIBIT and NOT as reported by researchers. Then, we highlight various logic gates based on different oligonucleotides spanning from intact and split aptamers to DNA origami architectures, DNA nanorobots, and G-quadruplex structural switches, bringing to light their applications across various fields. Recent innovations in multi-input/output gate cascades, CRISPR-Cas-integrated systems and signal amplification approaches are highlighted as key developments in DNA aptamer-based logic gates. Finally, we elucidate challenges relating to DNA aptamer-based systems such as aptamer performance, cross-reactivity in complex multi-input systems and the complexities of merging other systems to amplify output readability, among others, to the end that in addressing these challenges, we will be able to unlock the full potential of this system.
基于DNA适配体的逻辑门代表了分子计算领域的重大进展，能够在纳米尺度上进行复杂的生物计算。这些系统利用了DNA适配体独特的可编程特性，DNA适配体是短的单链寡核苷酸，对临床诊断、食品/环境监测和靶向治疗递送等领域的各种应用具有高特异性和结合亲和力，在过去几十年中引起了广泛的研究兴趣。在这篇综述中，我们首先详细阐述了适配体的基本原理，包括其指数富集的配体系统进化技术（SELEX）过程和SELEX后修饰。我们系统地研究了基于DNA适配体的逻辑门的设计原则和操作机制，主要是研究人员报道的与、或、非抑制和非逻辑门。然后，我们重点介绍了基于不同寡核苷酸的各种逻辑门，从完整和拆分的适配体到DNA折纸结构、DNA纳米机器人和G-四链体结构开关，揭示了它们在各个领域的应用。多输入/输出门级联、CRISPR-Cas集成系统和信号放大方法的最新创新被强调为基于DNA适配体的逻辑门的关键发展。最后，我们阐明了基于DNA适配体的系统所面临的挑战，如适配体性能、复杂多输入系统中的交叉反应性以及合并其他系统以提高输出可读性的复杂性等，以期通过应对这些挑战，充分发挥该系统的潜力。
