Engineering high-robustness DNA molecular circuits by utilizing nucleases

Fu, Shengnan; Li, Na; Li, Junjie; Deng, Yingnan; Xu, Libin; Chen, Yu; Su, Xin

doi:10.1039/c9nr09979d

Cited by 20 publications

(15 citation statements)

References 41 publications

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“…While it appears generally straightforward to couple most DNA-processing enzymes to a DNA based molecular program 48 , we note that natural 49 or synthetic 50 strategies also exist to connect the presence of various small molecules, and thus the corresponding enzymes, to nucleic regulatory processes and circuits.…”

Section: Discussionmentioning

confidence: 99%

Directed Evolution of Enzymes based on in vitro Programmable Self-Replication

Dramé-Maigné

Espada

McCallum

et al. 2021

Preprint

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High-throughput directed evolution, implemented in well-controlled in vitro conditions, provides a powerful route for enzyme engineering. Most existing technologies are based on activity screening and require the sequential observation and sorting of each individual variant. By contrast, approaches based on autonomous feedback loops, linking phenotype to genotype replication, enable autonomous selection without screening. However, these approaches are only possible in vivo, or applicable to very specific activities, such as polymerases or ligases. Here, we leverage synthetic molecular networks to create a programmable in vitro feedback loop linking a target enzymatic activity to gene amplification. After encapsulation and lysis of up to 10^7 transformed variants, the genes present in each droplet are amplified according to the activity of the encoded enzyme, resulting in the autonomous enrichment of interesting sequences. Applied to a nicking enzyme with thermal or kinetic selection pressures, this method reveals detailed mutational landscapes and provides improved variants.

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Section: Discussionmentioning

confidence: 99%

Directed Evolution of Enzymes based on in vitro Programmable Self-Replication

Dramé-Maigné

Espada

McCallum

et al. 2021

Preprint

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“…Some DNA related enzymes show strong specificity and high catalytic efficiency which are beneficial for designing DNA circuits. [ 95 ] We provide some typical cases of using enzymes to construct DNA logic circuits.…”

Section: Design Of Dna Molecular Logic Circuitsmentioning

confidence: 99%

“…[ 100–102 ] As shown in Figure 3c, Su and co‐workers used λ exonuclease (λ exo) to construct a highly robust DNA molecular circuit. [ 95 ] Compared with the TMSD circuit, it has advanced features such as leakage suppression, hundreds of times faster, and simple structure. This circuit can also be used to detect small molecules and proteins.…”

Section: Design Of Dna Molecular Logic Circuitsmentioning

confidence: 99%

DNA Logic Circuits for Cancer Theranostics

Chen

Zhang

et al. 2022

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solutions for precise cancer theranostics based on tumor microenvironment (TME) and biomarkers. [3][4][5][6][7] Nano-drugs such as liposomes, [8] polymer nanoparticles, [9] and inorganic nanoparticles [10] have been approved by Food and Drug Administration for the clinical treatment of cancer. However, current nanomedicine technologies lack intelligence which is the capability of autonomous computing in biological samples. Owing to the basepairing language and dynamic assembly of DNA strands, DNA-based logic devices/ circuits hold great potential to enhance the intelligence of nanomedicine.DNA nanotechnology began with the DNA four-arm junction structure proposed by Seeman in the 1980s. [11] On the basis of the Watson-Crick base pairing principle, such nanotechnology creates a variety of controllable nanoscale structures based on self-assembly of nucleic acid, and then built up static DNA nano structures such as DNA tiles and DNA origami by bottom-up approach. [12] The development of static DNA nanotechnology creates highly stable and variable DNA nanostructures showing the applications in nanomedicine including molecular imaging, drug delivery, biosensors, and the revolution of data storage. [13][14][15][16][17][18] Because nucleic acid materials have excellent structural controllability, biosafety, and functional diversity, they have emerged as excellent materials for the early diagnosis and timely treatment of cancer. [19] DNA nanotechnology had been further developed by Yurke et al. They constructed the first DNA molecular machine and proposed the concept of toehold-mediated strand displacement (TMSD) for the first time, [20] which opened a new era of dynamic DNA nanotechnology. Dynamic DNA nanotechnology utilizes a nonequilibrium nucleic acid system based on TMSD [21] or enzymatic reactions, to develop DNA nanomechanical devices, [22] and molecular logic networks. [23][24][25][26][27][28] Through the cascade and integration of multiple DNA reaction modules, DNA logic circuit is developed for cancer theranostics. [29,30] The basic DNA logic circuit can be conceptualized as a black box, which accepts the DNA strand as input and implements signal conversion by performing modular circuit elements such as TMSD and enzymatic reaction, [31] finally releases the DNA strand as output. [32] In cancer theranostics, DNA logic circuits can respond to the microenvironment or specific biomarkers of tumor, through signal transduction, logical judgment, signal amplification, Cancer diagnosis and therapeutics (theranostics) based on the tumor microenvironment (TME) and biomarkers has been an emerging approach for precision medicine. DNA nanotechnology dynamically controls the self-assembly of DNA molecules at the nanometer scale to construct intelligent DNA chemical reaction systems. The DNA logic circuit is a particularly emerging approach for computing within the DNA chemical systems. DNA logic circuits can sensitively respond to tumor-specific markers and the TME through logic operations and signal amplification, to genera...

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“…Su's group incorporated TMSD reaction, dual-site binding approach and -exonuclease into one system and operated multi-layer cascaded circuit (AND-OR-AND), Figure 9C. [75] In addition, Shapiro's group constructed an autonomous molecular computer which could achieve logical control of gene expression, in which the restriction nuclease was used as hardware molecules. [76] This molecular computer could logically analyze the levels of messenger RNA species, and generate a molecule capable of changing gene expression.…”

Section: Dna Tool-enzymesmentioning

confidence: 99%

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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Engineering high-robustness DNA molecular circuits by utilizing nucleases

Abstract: We utilized site-specific and sequence-independent nucleases to engineer high-robustness DNA molecular circuits.

Cited by 20 publications

References 41 publications

Directed Evolution of Enzymes based on in vitro Programmable Self-Replication

Directed Evolution of Enzymes based on in vitro Programmable Self-Replication

DNA Logic Circuits for Cancer Theranostics

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

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