The enzyme-free catalytic
hairpin assembly (CHA) process
is introduced
as a functional reaction module for guided, high-throughput, emergence,
and evolution of constitutional dynamic networks, CDNs, from a set
of nucleic acids. The process is applied to assemble networks of variable
complexities, functionalities, and spatial confinement, and the systems
provide possible mechanistic pathways for the evolution of dynamic
networks under prebiotic conditions. Subjecting a set of four or six
structurally engineered hairpins to a promoter P1leads
to the CHA-guided emergence of a [2 × 2] CDN or the evolution
of a [3 × 3] CDN, respectively. Reacting of a set of branched
three-arm DNA-hairpin-functionalized junctions to the promoter strand
activates the CHA-induced emergence of a three-dimensional (3D) CDN
framework emulating native gene regulatory networks. In addition,
activation of a two-layer CHA cascade circuit or a cross-catalytic
CHA circuit and cascaded driving feedback-driven evolution of CDNs
are demonstrated. Also, subjecting a four-hairpin-modified DNA tetrahedron
nanostructure to an auxiliary promoter strand simulates the evolution
of a dynamically equilibrated DNA tetrahedron-based CDN that undergoes
secondary fueled dynamic reconfiguration. Finally, the effective permeation
of DNA tetrahedron structures into cells is utilized to integrate
the four-hairpin-functionalized tetrahedron reaction module into cells.
The spatially localized miRNA-triggered CHA evolution and reconfiguration
of CDNs allowed the logic-gated imaging of intracellular RNAs. Beyond
the bioanalytical applications of the systems, the study introduces
possible mechanistic pathways for the evolution of functional networks
under prebiotic conditions.