Transcription factors are essential regulators of various physiological and pathological processes. However, detecting transcription factor-DNA binding activities is often time-consuming and labor-intensive. Homogeneous biosensors that are compatible with mix-and-measure protocols have the potential to simplify the workflow for therapeutic screening and disease diagnostics. In this study, we apply a combined computational-experimental approach to investigate the design of a sticky-end probe biosensor, where the transcription factor-DNA complex stabilizes the fluorescence resonance energy transfer signal of the donor-acceptor pair. We design a sticky-end biosensor for the SOX9 transcription factor based on the consensus sequence and characterize its sensing performance. A systems biology model is also developed to investigate the reaction kinetics and optimize the operating conditions. Taken together, our study provides a conceptual framework for the design and optimization of sticky-end probe biosensors for homogeneous detection of transcription factor-DNA binding activity.

转录因子是各种生理和病理过程的重要调节因子。然而，检测转录因子-DNA 结合活性通常既耗时又费力。与混合和测量方案兼容的同质生物传感器有可能简化治疗筛选和疾病诊断的工作流程。在这项研究中，我们应用计算实验相结合的方法来研究粘端探针生物传感器的设计，其中转录因子-DNA复合物稳定了供体-受体对的荧光共振能量转移信号。我们根据共有序列设计了 SOX9 转录因子的粘端生物传感器，并表征了其传感性能。还开发了系统生物学模型来研究反应动力学并优化操作条件。总而言之，我们的研究为粘端探针生物传感器的设计和优化提供了一个概念框架，用于均匀检测转录因子-DNA 结合活性。