Nucleic Acid Based Constitutional Dynamic Networks: From Basic Principles to Applications

Abstract

Inspired by nature where intracellular dynamic interactions between DNA, RNA and proteins processed within complex networks leading to programmed reaction patterns, extensive research efforts are directed to mimic these processes by chemical means, "Systems Chemistry". The present perspective introduces nucleic acids as functional modules to construct constitutional dynamic networks, CDNs, mimicking natural networks. The base sequences comprising nucleic acids provide a rich "tool box" to assemble signal-triggered reconfigurable CDNs revealing adaptive and hierarchically adaptive properties, intercommunication between CDNs, and feedback-driven reaction pathways similar to natural systems. Pathways for the evolution of CDNs and the formation of networks of enhanced complexities are discussed. Different applications of constitutional dynamic networks are introduced including programmed catalysis, CDN-guided optical and catalytic functions of nanoparticle aggregates, and CDN-dictated stiffness and self-healing functions of hydrogels. Future perspectives of the field in designing dissipative transient CDNs, CDNs-guided transcription/translation synthesis of selective proteins, and the challenging integration of CDNs into cell-like containments aiming to assemble "artificial cells" are addressed.

DNA Assembly‐Based Stimuli‐Responsive Systems

“…For example, DNA assemblybased nanomachines that perform sensitive tests of physical quantities [132,[379][380][381] or track biological behavior, [380] have been emerging as valuable biophysical tools to investigate physical and biological mechanisms at the nanoscale or single-molecule level. [380] Furthermore, DNA assembly-based stimuli-responsive systems in logic gates [272,289,338,378,382] and constitutional dynamic networks [52,239,277,278,[284][285][286][287][288][383][384][385][386] recently attract substantial research efforts, such orthogonal dynamic control provides additional dimensions for spatiotemporal control, and holds great application potential in the field of DNA computing, DNA information storage and biological interaction networks.…”

“…The stimuli‐triggered constitutional dynamic network is a recently rapidly developing topic, which is aiming to assemble “artificial cells” by stimuli‐responsive DNA modules to mimic intracellular dynamic interactions between DNA, RNA, and proteins. [ 277 ] The DNA‐based stimuli‐responsive system provides various communication pathways for constitutional dynamic networks. At present, different stimuli‐responsive DNA systems have been used to control the constitutional dynamic network.…”

DNA-based constitutional dynamic networks as functional modules for logic gates and computing circuit operations

“…Nucleic acid-based constitutional dynamic networks, CDNs, attract substantial research efforts as a means to mimic biological networks. 48 The simplest [2 × 2] CDN consists of four two-component equilibrated constituents AA ′, AB ′, BA ′ and BB ′. 49,50 The stabilization of one of the constituents, e.g.…”

Computational studies of a DNA-based aptasensor: toward theory-driven transduction improvement.

“…The intensity of the recorded signal depends on the refraction index and on the capacitance of the thin solution layer close to the surface, respectively. These techniques have already shown their relevance in the field of aptasensors 6,7 . However, the inherent lack of affinity of aptamers selected against low molecular weight targets, with affinity constants usually in the µM range, requires innovative amplification strategies to reach lower limits of detection.…”

“…Recent advances in designing functional DNA architectures 7,8 allow to consider a new class of highly sensitive aptasensors that switch their entire conformation even if only few bases are involved in a target binding process. In most of the cases, the aptamer sequence is introduced inside a host matrix (scaffold) participating in its overall 3Dstructure.…”