Dissipative, programmable, and functional DNA systems

Unlike most man-made materials, life operates far from thermodynamic equilibrium, continuously consuming chemical fuels, exploiting concentration gradients, and orchestrating complex enzymatic networks to sustain its dynamic organization, autonomy, and responsiveness. These dissipative processes enable biological systems to perform temporally regulated, adaptable functions and interact with their environment. DNA, with its predictable base pairing, functional secondary structures and high degree of programmability, has become a compelling building block for designing such life-like systems. Chapter 1 provides the scientific context for this work by introducing the foundational principles of static DNA nanotechnology and the biomolecular tools employed for sequence-specific DNA modification, amplification, and degradation. It also offers an overview of dissipative processes in biological systems and highlights the current state of DNA-based out-of-equilibrium assemblies. Chapter 2 establishes a foundational dissipative control strategy for enzyme activity using exonuclease-mediated degradation. Distinct regulatory strategies were employed to transiently control the activity of an amino acid-based enzyme and a nucleic acid-based DNAzyme in response to synthetic DNA fuel strands. The transient behavior emerged from the controlled degradation of a functionality-inducing DNA fuel, enabling autonomous cycles of activation and deactivation. In addition to external control over the system’s lifetime, a novel internal strategy to modulate the system’s kinetics is introduced by harnessing the intrinsic toe-hold-dependent digestion kinetics of the employed exonucleases. Chapter 3 extends this principle to intercommunicating DNA networks, in which two individually operating cycles are coupled to transiently guide information flow from a transiently activated DNAzyme, which subsequently enabled the temporal activation of a protein enzyme. This setup allows for the propagation of signals across modular subsystems and represents a significant step toward more advanced dynamic, concatenated, and programmable control within synthetic DNA-based networks. Chapter 4 introduces an ATP-powered enzymatic reaction network to regulate DNAzyme activity through the antagonistic action of nucleic acid cleaving and ligating enzymes. The result was a tunable, autonomous cycle that allowed precise control over the lifetime of DNAzyme functionality, introducing nicking enzymes as regulatory elements within synthetic enzymatic reaction networks. Chapter 5 applies a similar ERN, built on the enzymatic interplay of two antagonistic enzymes, to soft matter systems, demonstrating ATP-fueled programming of degradation kinetics in DNA hydrogels. The ability to autonomously modulate the mechanical stability of a material via a built-in enzymatic cycle exemplifies how dissipative processes can govern the structural autonomy of responsive materials. Together, these chapters showcase how chemical fuels and molecular design principles can be combined to construct dissipative, programmable, and functionally rich DNA-based systems, adding to the groundwork for future developments in adaptive nanotechnology.