Propelling DNA Computing with Materials’ Power: Recent Advancements in Innovative DNA Logic Computing Systems and Smart Bio‐Applications

Abstract

DNA computing is recognized as one of the most outstanding candidates of next-generation molecular computers that perform Boolean logic using DNAs as basic elements. Benefiting from DNAs' inherent merits of low-cost, easy-synthesis, excellent biocompatibility, and high programmability, DNA computing has evoked substantial interests and gained burgeoning advancements in recent decades, and also exhibited amazing magic in smart bio-applications. In this review, recent achievements of DNA logic computing systems using multifarious materials as building blocks are summarized. Initially, the operating principles and functions of different logic devices (common logic gates, advanced arithmetic and non-arithmetic logic devices, versatile logic library, etc.) are elaborated. Afterward, state-of-the-art DNA computing systems based on diverse "toolbox" materials, including typical functional DNA motifs (aptamer, metal-ion dependent DNAzyme, G-quadruplex, i-motif, triplex, etc.), DNA tool-enzymes, non-DNA biomaterials (natural enzyme, protein, antibody), nanomaterials (AuNPs, magnetic beads, graphene oxide, polydopamine nanoparticles, carbon nanotubes, DNA-templated nanoclusters, upconversion nanoparticles, quantum dots, etc.) or polymers, 2D/3D DNA nanostructures (circular/interlocked DNA, DNA tetrahedron/polyhedron, DNA origami, etc.) are reviewed. The smart bio-applications of DNA computing to the fields of intelligent analysis/diagnosis, cell imaging/therapy, amongst others, are further outlined. More importantly, current "Achilles' heels" and challenges are discussed, and future promising directions of this field are also recommended.

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.…”

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

“…The use of DNA as a functional material for logic gate operations and computational circuitry has attracted substantial research efforts in the past two decades. [1][2][3][4] Data storage, retrieval and random access of information by DNA strands, [5][6][7][8] and the use of DNA assemblies as functional in vivo operating computing circuitry, were extensively discussed. [9][10][11] The structural and functional information encoded in the base sequences of nucleic acids, and the possibility to recongure nucleic acid structures by auxiliary input triggers such as pH, [12][13][14] metal ions, [15][16][17] fuel strands, 18,19 molecular or macromolecular ligands 20,21 and DNA machines 22,23 enabled the design of logic gates of variable complexities.…”

Graphene Oxide Based Fluorescent DNA Aptasensor for Liver Cancer Diagnosis and Therapy

“…DNA tetrahedrons (DNA-tetra), [15][16] consisting of four ssDNA sequences by complementary self-assembly, have been recognized as an effective drug carrier for intracellular imaging and tumor treatment, benefiting from that DNA-tetra can rapidly across the cell membrane through caveolin-dependent pathway without being hydrolyzed. [17][18] Although aptamer modified DNA-tetra has been recently utilized for fluorescent in vitro and in vivo applications, [19][20][21] the targeting selectivity and signal-to-noise ratio remain to be further improved. To this end, locating of fluorescent DNA-tetra on GO surface could be a brilliant approach to achieve in vivo diagnosis and treatment.…”