DNA Nanotechnology-based Biocomputing

Yin, Jue; Wang, Junke; Niu, Renjie; Ren, Shaokang; Wang, Dexu; Chao, Jie

doi:10.1007/s40242-020-9086-5

Cited by 23 publications

(15 citation statements)

References 99 publications

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“…This work demonstrates that molecular self-assembly could be a reliable algorithmic element within programmable chemical systems. Considering that Chao's group has made a review on static/dynamic DNA assemblies-based DNA computing, [8] we herein just outline in detail the developments of the first three subjects in this section. Reproduced with permission.…”

Section: D/3d Dna Nanostructuresmentioning

confidence: 99%

“…However, according to the quantum physics theory prediction, the miniaturization technology will hit its physical limit before long. [8] Under this background, molecular engineers aim at searching for novel and promising substitutes for logic computing to surmount above limitations, which thereby conduces to the emergence of "molecular logic." As molecular-level functional mimics of silicon logic counterparts, "molecular logic" has attracted broad interests and paved unique horizons for implementing diverse smart applications.…”

Section: Introductionmentioning

confidence: 99%

“…Moreover, the combination of Boolean logic's stringency with DNAs' excellent biocompatibility also stimulated smartly designed bio-applications of DNA computing to bioanalysis/diagnostics, bioimaging, drug load/release, and so on. [8,9,16] In this review, we first systematically classify diverse logic devices into different categories (from common logic gates to versatile logic library and so on, See Table 1), and then illustrate the operating principles and functions of these logic devices. After that, emphasis is put on state-of-the-art DNA computing systems using varieties of materials as building components, including representative functional DNA motifs (aptamer, metalion dependent DNAzyme/DNA nanostructure, G-quadruplex, imotif, triplex, molecular beacon (MB), etc.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

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

Fan

Wang

et al. 2020

Advanced Science

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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.

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Section: D/3d Dna Nanostructuresmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Fan

Wang

et al. 2020

Advanced Science

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“…Finally, we constructed a phase diagram by investigating how the addition of the linker changed the phase-separation pattern. While this work only focused on the formation of phase-separated hydrogel capsules on a droplet interface, DNA nanotechnology provides various functional DNA devices, capable of computing (34), sensing (35), and actuating (36), that can be incorporated in the hydrogel capsules. Therefore, our results will serve as the means to design and construct functional microcapsules for artificial cell studies.…”

Section: Main Text Introductionmentioning

confidence: 99%

Pattern Regulation of DNA Hydrogels Formed by Lateral Phase Separation of DNA Nanostructures on Water-in-Oil Droplet Interfaces

Sato

Takinoue²

2021

Preprint

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<p>Phase separation is a key phenomenon in artificial cell construction. Recent studies have shown that the liquid-liquid phase separation of designed-DNA nanostructures induces the formation of liquid-like condensates that eventually become hydrogels by lowering the solution temperature. As a compartmental capsule is an essential artificial cell structure, many studies have focused on the lateral phase separation of artificial lipid vesicles. However, controlling phase separation using a molecular design approach remains challenging. Here, we present the lateral liquid-liquid phase separation of DNA nanostructures that leads to the formation of phase-separated capsule-like hydrogels. We designed three types of DNA nanostructures (two orthogonal and a linker nanostructure) that were adsorbed onto an interface of water-in-oil droplets via electrostatic interactions. The phase separation of DNA nanostructures led to the formation of hydrogels of bicontinuous, patch, and mix patterns, due to the immiscibility of liquid-like DNA during the self-assembly process. The frequency of appearance of these patterns was regulated by designing DNA sequences and altering the mixing ratio of the nanostructures. We constructed a phase diagram for the capsule-like DNA hydrogels by investigating pattern formation under various conditions. Our results provide a method for the design and control of phase-separated hydrogel capsules using sequence-designed DNAs. We envision that by incorporating various DNA nanodevices into DNA hydrogel capsules, the capsules will gain molecular sensing, chemical-information processing, and mechano-chemical actuating functions, allowing the construction of functional molecular systems.</p>

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“…Bio-computing implies the construction of computations and logical operations based on biocomponents: DNA, RNA, enzymes and cells [ 2 ]. Thus, a lot of work has already been done to create logical operations involving DNA [ 3 , 4 ], RNA [ 5 ], DNAzymes [ 6 , 7 , 8 ] and enzymes [ 9 , 10 ]. These systems can perform basic arithmetic operations, such as addition and subtraction [ 11 , 12 ], calculate the square root [ 13 ], play logic games [ 14 , 15 ] and simulate keyboard lock [ 16 , 17 ].…”

Section: Introductionmentioning

confidence: 99%

Logic Gates Based on DNA Aptamers

Andrianova

Kuznetsov

2020

Pharmaceuticals

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DNA bio-computing is an emerging trend in modern science that is based on interactions among biomolecules. Special types of DNAs are aptamers that are capable of selectively forming complexes with target compounds. This review is devoted to a discussion of logic gates based on aptamers for the purposes of medicine and analytical chemistry. The review considers different approaches to the creation of logic gates and identifies the general algorithms of their creation, as well as describes the methods of obtaining an output signal which can be divided into optical and electrochemical. Aptameric logic gates based on DNA origami and DNA nanorobots are also shown. The information presented in this article can be useful when creating new logic gates using existing aptamers and aptamers that will be selected in the future.

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DNA Nanotechnology-based Biocomputing

Cited by 23 publications

References 99 publications

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

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

Pattern Regulation of DNA Hydrogels Formed by Lateral Phase Separation of DNA Nanostructures on Water-in-Oil Droplet Interfaces

Logic Gates Based on DNA Aptamers

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