ATP-Triggered, Allosteric Self-Assembly of DNA Nanostructures

Li, Qian; Liu, Longfei; Mao, Dake; Yu, Yuyan; Li, Weili; Zhao, Xinfeng; Mao, Chengde

doi:10.1021/jacs.9b10272

Cited by 35 publications

(34 citation statements)

References 29 publications

(35 reference statements)

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“…In living systems, some highly complicated and hierarchical machines have been evolved to perform significant biological processes with remarkable precision and efficiency. [1][2][3] Inspired by natural ingenuity, diverse DNA-based nanodevices have been created to convert chemical energy into mechanical motion, [4][5][6][7][8] holding great promises for intelligent drug delivery, [9][10][11][12] disease diagnosisand [13][14][15][16] and biosensing analysis. [17][18][19][20] Recently, the three-dimensional (3D) DNA nanomachines based on gold nanoparticles (AuNPs) [21][22][23][24] have attracted extensive attention due to the improved abilities in simulating complex biological operation compared with one-dimensional (1D) 25,26 or two-dimensional (2D) DNA nanomachines.…”

Section: Introductionmentioning

confidence: 99%

A core–brush 3D DNA nanostructure: the next generation of DNA nanomachine for ultrasensitive sensing and imaging of intracellular microRNA with rapid kinetics

et al. 2021

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Section: Introductionmentioning

confidence: 99%

A core–brush 3D DNA nanostructure: the next generation of DNA nanomachine for ultrasensitive sensing and imaging of intracellular microRNA with rapid kinetics

et al. 2021

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“…[131] Another important aspect is to use ATP to trigger allosteric self-assembly of DNA nanostructures self-assemblies, whereby ATP induces conformational changes of the device to trigger secondary responses. [132,133,134] Aside from the allosteric control in equilibrium self-assemblies, ATP-triggered allosteric self-assembly in non-equilibrium systems has been recently reported by Ricci and co-workers, [135] where ATP was not used as a fuel but rather used as a co-assembling component when the system was running out of fuel.…”

Section: Atp Regenerationmentioning

confidence: 99%

ATP‐Responsive and ATP‐Fueled Self‐Assembling Systems and Materials

2020

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his/her body weight in ATP each day, which is enabled through a very efficient ADP/ATP recycling system. [7] Aside of the fascinating non-equilibrium succeeded by exploiting ATP/GTP as chemical fuels to drive structures and functions, it is also important to realize that ATP and other nucleoside phosphates can be used as biological and chemical signals. [8-10] Lots of biological processes such as chromatin remodeler activation, [11] inflammatory signaling, [12] and cell differentiation [13] are mediated by ATP signaling. Additionally, cancer cells have a higher concentration of ATP, [14] which in turn provides a handle to develop new types of molecular therapies. This of course requires to develop sophisticated carriers or self-assembling structures that highly specifically react to ATP and potentially even to its concentration, ideally without any interference from other nucleoside phosphates. [15-20] For such cases, it is also important to realize that ATP is used as a chemical signal rather than a chemical fuel, as the primary objective may not be to harvest its energy from hydrolysis for functions, but just to use its chemical structure for a change of function. Overall, it becomes clear that the use of ATP (and similarly GTP) as a trigger or as a chemical fuel is of high relevance to interact with living systems and also to be able to create active devices in long term that can create work and allow for active communication in a biological environment using the fuels available therein. [21] In the scope of this review on ATP-dependent systems, and being set at the interface of near-equilibrium responsive materials versus non-equilibrium active materials, it is useful to begin Adenosine triphosphate (ATP) is a central metabolite that plays an indispensable role in various cellular processes, from energy supply to cell-tocell signaling. Nature has developed sophisticated strategies to use the energy stored in ATP for many metabolic and non-equilibrium processes, and to sense and bind ATP for biological signaling. The variations in the ATP concentrations from one organelle to another, from extracellular to intracellular environments, and from normal cells to cancer cells are one motivation for designing ATPtriggered and ATP-fueled systems and materials, because they show great potential for applications in biological systems by using ATP as a trigger or chemical fuel. Over the last decade, ATP has been emerging as an attractive co-assembling component for man-made stimuli-responsive as well as for fuel-driven active systems and materials. Herein, current advances and emerging concepts for ATP-triggered and ATP-fueled self-assemblies and materials are discussed, shedding light on applications and highlighting future developments. By bringing together concepts of different domains, that is from supramolecular chemistry to DNA nanoscience, from equilibrium to nonequilibrium self-assembly, and from fundamental sciences to applications, the aim is to cross-fertilize current approaches with the ultimate aim to bring ...

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“…[ 68 ] Possible dynamic modes for response including extension‐contraction, [ 69 ] opening‐closing, [ 70 ] and reversible rotations. [ 71 ] The range of useful inputs for such systems has subsequently expanded to include restriction enzyme reactions, [ 72 ] pH changes, [ 73 ] small‐molecule triggers, [ 74 ] and even light [ 75 ] or electrical signals. [ 76 ]…”

Section: Higher Complexity Aptamer Switches In Dna Nanotechnologymentioning

confidence: 99%

“…Finally, a number of research groups have been exploring the generation of 2D and 3D DNA‐based “logic gates” (e.g., OR, YES, and AND) that exploit aptamer‐substrate binding as inputs. [ 89 ] These have been built around a variety of structural frameworks, including pattern‐based DNA origami, [ 90 ] contractile three‐way junctions, [ 91 ] dimer and trimer origami frames, [ 74b,92 ] 3D DNA nanotetrahedra, [ 78e ] and DNA icosahedrons. [ 93 ] These dynamic logic systems, which can undergo geometric reconfigurations in a controllable and programmable manner in response to specific small‐molecule, DNA strand, or other triggers, have great potential applications for biosensing and molecular computing.…”

Section: Higher Complexity Aptamer Switches In Dna Nanotechnologymentioning

confidence: 99%

Engineering Aptamer Switches for Multifunctional Stimulus‐Responsive Nanosystems

et al. 2020

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specific and strong recognition of molecular targets (i.e., aptamers), catalyze biochemical reactions (i.e., ribozymes), or form sophisticated and dynamic "smart materials" or even 3D constructs (i.e., DNA origami). [2] There is particular interest in the use of nucleic acids for the construction of molecular switches, which undergo a function-altering structural change in response to an external stimulus. [3] Many such examples exist in nature, where switches enable organisms to sense physiological changes and selectively control biological functions in response. For example, riboswitches exist naturally as domains within messenger RNA (mRNA) transcripts that can bind to specific metabolites with high specificity in order to stabilize a secondary structure that prevents subsequent translation. [4] Synthetic, engineered molecular switches based on nucleic acids can achieve even greater diversity of function. Such designs make use of aptamersnucleic acid-based affinity reagents isolated via an in vitro process of systematic evolution by exponential enrichment (SELEX), in which DNA or RNA sequences with specific ligand binding are isolated from a large pool of random sequences. [5] Aptamers have proven to be robust recognition elements due to their thermal stability, ease of synthesis, and capacity to undergo ready modification with a broad array of functional groups. Importantly, traditional selection methods can be expanded upon by innovative engineering techniques to enable the incorporation of additional functions that further extend the utility of aptamers. Aptamers can adopt various 2-and 3-D structures such as duplexes, hairpins, and G-quadruplexes, and the inducible formation and disruption of these configurations can be exploited to enable complex functions besides simple biosensing. Consequently, aptamers have been incorporated into many intricate configurations, such as logic gates and dynamic nanomachines. Various research groups have also described aptamer-based switches that undergo conformational changes in response to triggers such as shifts in pH, stimulation with light, or the presence of a specific ligand. [6] Although still a relatively young area of research, these efforts could prove highly useful for materials research-conferring even greater and more selective control over devices based on functionalized nucleic acids. Aptamers are becoming increasingly integrated with various organic and inorganic molecules in order to control the assembly and operation of novel functional Although RNA and DNA are best known for their capacity to encode biological information, it has become increasingly clear over the past few decades that these biomolecules are also capable of performing other complex functions, such as molecular recognition (e.g., aptamers) and catalysis (e.g., ribozymes). Building on these foundations, researchers have begun to exploit the predictable base-pairing properties of RNA and DNA in order to utilize nucleic acids as functional materials that can undergo a molecular "switching" ...

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ATP-Triggered, Allosteric Self-Assembly of DNA Nanostructures

Cited by 35 publications

References 29 publications

A core–brush 3D DNA nanostructure: the next generation of DNA nanomachine for ultrasensitive sensing and imaging of intracellular microRNA with rapid kinetics

A core–brush 3D DNA nanostructure: the next generation of DNA nanomachine for ultrasensitive sensing and imaging of intracellular microRNA with rapid kinetics

ATP‐Responsive and ATP‐Fueled Self‐Assembling Systems and Materials

Engineering Aptamer Switches for Multifunctional Stimulus‐Responsive Nanosystems

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