Programmable Aptamer-Controlled Fibrinogenesis Using Dynamic DNA Networks and Synthetic Transcription Machineries

Conspectus: Fibrinogenesis─the transformation of fibrinogen to fibrin─is one of the most significant physiological pathways regulating hemostasis by promoting clot formation at vascular injury sites. Thrombin is the key catalyst driving fibrinogenesis, and thus the control of its activity is of utmost medical significance. While diverse auxiliary therapies exist to regulate blood coagulation and thrombin activity, the temporal, dose-controlled, transient, and periodic control of thrombin and fibrinogenesis remains highly desirable. Antithrombin aptamers─biopolymers that bind to and inhibit thrombin─are ideal for achieving such precise regulation of thrombin activity.The present Account introduces dynamic DNA networks, machineries, and reaction modules involving antithrombin aptamers for the temporal modulation of thrombin activity. Constitutional dynamic networks (CDNs), dissipative DNA reaction circuits, and dynamic transcription machineries are introduced as functional frameworks to control fibrinogenesis. Phototriggered reconfiguration of CDNs containing thrombin-inhibitory constituents leads to orthogonal dynamic regulatory frameworks, resulting in upregulated or downregulated fibrinogenesis. Coupling CDNs to transient reaction modules generates orthogonal transient upregulation or downregulation of fibrinogenesis. Moreover, transcription machineries are implemented for transient control of fibrinogenesis. This is achieved via the temporal activation and inhibition of thrombin: a transcription machinery transcribes an RNA antidote that displaces the antithrombin DNA aptamer from the thrombin/aptamer complex, while RNase H mediates the dissipative inhibition of thrombin by hydrolytically depleting the RNA antidote in the RNA/DNA aptamer duplex. Additionally, integrating split thrombin aptamers into the phototriggered, oscillatory transcription machinery, in combination with a counter dynamic transcription machinery, guides the transient and oscillatory inhibition of thrombin (via the T7 RNA polymerase/RNase H system). This enables phototriggered transient inhibition and oscillatory modulation of fibrinogenesis, which shows promising potential for spatiotemporal control of blood coagulation. Finally, future perspectives on dynamically guided nucleic acid frameworks for regulating blood clotting are discussed.