Photomodulated Transient Catalytic Constitutional Dynamic Networks and Reaction Circuits

A method to photomodulate dynamically transient DNA-based reaction circuits and networks is introduced. The method relies on the integration of photoresponsive o-nitrobenzyl-phosphate ester-caged DNA hairpin with a "mute" reaction module. Photodeprotection (λ=365 nm) of the hairpin structure separates a fuel strand triggering the dynamic, transient, operation of the DNA circuit/network. By temporal photocleavage of the hairpin within the course of transient operation of the circuit, photomodulation of the systems are demonstrated. The modulation amplitude and rhythms are controlled by the time-interval and cycle numbers of photo-deprotecting the hairpin structure. The method is applied to transiently photomodulate the catalytic activities of a DNAzyme, enabling the photomodulation of the transient assembly of a constitutional dynamic network (CDN) and the transient reconfiguration of the CDN framework. The different systems are supported by computational kinetic models allowing to predict, and experimentally validate, the behavior of the systems under variable auxiliary conditions. Moreover, the photomodulated transient CDNs are implemented as functional frameworks guiding the thrombin-catalyzed coagulation of fibrinogen to fibrin (fibrinogenesis) and photomodulated operation of a biocatalytic cascade.