Dissipative DNA nanotechnology

Abstract

DNA nanotechnology has emerged as a powerful tool to precisely design and control molecular circuits, machines, and nanostructures. A major goal in this field is to build devices with life-like properties such as directional motion, transport, communication and adaptation. In this Review, we provide an overview of the nascent field of dissipative DNA nanotechnology, which aims at developing life-like systems by combining programmable nucleic acid reactions with energy dissipating processes. We first delineate the notions, terminology and characteristic features of dissipative DNA-based systems and then we survey DNA-based circuits, devices and materials whose functions are controlled by chemical fuels. We emphasize how energy consumption enables these systems to perform work and cyclical tasks, in contrast with DNA devices that operate without dissipative processes. The ability to take advantage of chemical fuel molecules brings dissipative DNA systems closer to active molecular devices in nature, and points to the transformative potential of dissipative DNA nanotechnology toward the synthesis of living matter.

Autoinhibited transient, gated, and cascaded dynamic transcription of RNAs

“…Enzyme-based DNA machines relying on polymerization/endonucleases/nickases were used to assemble out-of-equilibrium circuits, revealing oscillatory behaviors ( 39 , 40 ), gated and cascaded transient operations ( 41 ), or dissipative reconfiguration of constitutional dynamic networks ( 42 ). In addition, enzyme-guided transient release and uptake of loads and DNA ligation ( 43 , 44 ) and transient enzyme-driven aggregation of nanoparticles and control over their optical properties were demonstrated ( 45 ). All-DNA DNAzyme-driven transient systems and gated transient networks and control over transient catalytic processes were reported ( 46 ).…”

Shape-shifting microgel automata controlled by DNA sequence instructions

“…Biomolecules have unique advantages as signals: they can be produced in astonishing variety, diffuse through three-dimensional media, and react with high specificity (8). Biomolecules can provide energy to drive chemical reactions and can also become structural components of material (9,10). In contrast, light or electronic signals require batteries or external power sources to store energy and line-of-sight access, wires, or tubes that direct signals to a specific location, where they interact with limited specificity (11)(12)(13).…”

Orthogonal Enzyme-Driven Timers for DNA Strand Displacement Reactions

“…Predictable base-pairing, low-cost production, and chemical versatility make synthetic DNA an optimal material to build nanoscale objects and devices that can find applications in fields like sensing, drug delivery, and therapeutics. − The majority of these systems rely on simple programmable reactions between synthetic DNA strands that allow us to create well-defined static and dynamic two-dimensional or three-dimensional structures. − Several strategies have been proposed to date to make such DNA-based systems responsive to different molecular and environmental inputs that include proteins, small molecules, pH, and temperature. − Spatial reconfigurations and precise input-induced conformational changes have also been demonstrated to control the functionality of the DNA-based systems. − Beyond this, significant efforts have been devoted to establish reaction networks that can carry out signal processing and dynamic signal generation in analogy to biological systems. − Living systems and cellular pathways are not only precisely controlled by environmental and molecular cues but are also temporally programed using elaborate positive and negative feedback mechanisms that typically operate through out-of-equilibrium, dissipative, or delayed reactions. − Inspired by this, several DNA-based reaction systems have been reported to date whose dynamics can be controlled in a programmable way, for example, by altering the energy landscapes of the process, − by implementing negative/positive feedback loops, , and by employing dissipative reaction steps. − This allowed us to set up synthetic reaction networks with a complex time-dependent behavior that in parallel can modulate the functionality and/or assembly of DNA downstream systems. − …”