Multi‐Mode Reconfigurable DNA‐Based Chemical Reaction Circuits for Soft Matter Computing and Control

Tang, Qian; Lai, Wei; Wang, Peipei; Xiong, Xiewei; Xiao, Mingshu; Li, Li; Fan, Chunhai; Pei, Hao

doi:10.1002/anie.202102169

Cited by 34 publications

(23 citation statements)

References 57 publications

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“…Considering that using large molecules such as DNA and proteins to actuate DNA devices is relatively slow kinetically, and often requires minutes to hours to complete the actuation (the rate constant of a TMSD reaction ranges from 10 to 10 6 M −1 •s −1 [57], while the folding of an acidic pH-triggered i-motif has a rate constant of~8.35 min -1 [73], or takes only~100 ms time [74]), environmental factors such as pH [75][76][77][78][79][80], light [81,82], temperature [83,84], and ionic concentration [85][86][87] are also used to trigger DNA devices, and have the advantages of being rapidly and remotely controllable. For instance, i-motifs [76,78] and Hoogsteen base pairing [79,80] (Figure 2E) can be used to design devices that are responsive to changes in pH [75,88] (Figure 2F). Light-actuating DNA devices have been created by attaching azobenzene [89] to the DNA backbone, since the azobenzene undergoes isomerization from the trans to cis conformation upon exposure to UV light and returns to the trans when exposed to visible light.…”

Section: Dynamic Dna Nanotechnologymentioning

confidence: 99%

Obtaining Precise Molecular Information via DNA Nanotechnology

Tang

Han

2021

Membranes

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Precise characterization of biomolecular information such as molecular structures or intermolecular interactions provides essential mechanistic insights into the understanding of biochemical processes. As the resolution of imaging-based measurement techniques improves, so does the quantity of molecular information obtained using these methodologies. DNA (deoxyribonucleic acid) molecule have been used to build a variety of structures and dynamic devices on the nanoscale over the past 20 years, which has provided an accessible platform to manipulate molecules and resolve molecular information with unprecedented precision. In this review, we summarize recent progress related to obtaining precise molecular information using DNA nanotechnology. After a brief introduction to the development and features of structural and dynamic DNA nanotechnology, we outline some of the promising applications of DNA nanotechnology in structural biochemistry and in molecular biophysics. In particular, we highlight the use of DNA nanotechnology in determination of protein structures, protein–protein interactions, and molecular force.

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Section: Dynamic Dna Nanotechnologymentioning

confidence: 99%

Obtaining Precise Molecular Information via DNA Nanotechnology

Tang

Han

2021

Membranes

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“…Dynamic DNA nanotechnology utilizes a non‐equilibrium nucleic acid system based on TMSD [ 21 ] or enzymatic reactions, to develop DNA nanomechanical devices, [ 22 ] and molecular logic networks. [ 23–28 ] 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.…”

Section: Introductionmentioning

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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“…The base sequences, composed of nucleic acids, provide considerable structural and functional information to biopolymers. The functional information of nucleic acid coding and the switchable trigger function has been extensively applied in various aspects of developing DNA nanotechnology [ 15 , 16 ], involving the development of DNA-based circuit pathways [ 17 ], DNA machines [ 18 ], nucleic acid-based sensors [ 19 ], and carriers used for controlled drug release [ 20 ]. Seeman completed the first work using DNA as building block in nanotechnology by assembling DNAs into four-arm Holliday junction and lattice [ 21 ], proving that DNA could be designed into artificial structures.…”

Section: Introductionmentioning

confidence: 99%