An aptamer-enabled DNA nanobox for protein sensing

Tang, Marco S. L.; Shiu, Simon Chi‐Chin; Godonoga, M; Cheung, Yiu-ming; Liang, Shuailong; Dirkzwager, Roderick M.; Kinghorn, Andrew B.; Fraser, Lewis A.; Heddle, Jonathan G.; Tanner, Julian A.

doi:10.1016/j.nano.2018.01.018

Cited by 50 publications

(29 citation statements)

References 57 publications

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“…developed a DNA origami nanobox with a logic‐gate lock system that uses a DNA aptamer targeting the malaria biomarker protein PfLDH, which acts as the “key” ( Figure A). [ 86 ] The group demonstrated that this box can be opened specifically by PfLDH, based on both TEM and FRET. PfLDH showed the highest reduction in FRET, whereas the structurally related human LDH‐subunit B (hLDH‐B) produced no FRET response, which demonstrated that placing the aptamer on the origami box did not impede aptamer specificity (Figure 15A, left).…”

Section: Higher Complexity Aptamer Switches In Dna Nanotechnologymentioning

confidence: 99%

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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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Section: Higher Complexity Aptamer Switches In Dna Nanotechnologymentioning

confidence: 99%

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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“…The device was demonstrated to open on exposure to MUC-1-containing cell lysate [88]. Other aptamers used in relation to disease treatment or detection include the PfLDH aptamer [60] which has been shown to work as part of a malaria biosensor/protype therapeutic delivery system whereby the aptamers control the opening of a DNA origami box [77]. In this work, two pairs of aptamer lock with partially complementary strands were integrated between the lid and the main box.…”

Section: Aptamers For Controlling Dna Origami Structural Changesmentioning

confidence: 99%

DNA Aptamers for the Functionalisation of DNA Origami Nanostructures

Sakai

Islam

Adamiak

et al. 2018

Genes

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DNA origami has emerged in recent years as a powerful technique for designing and building 2D and 3D nanostructures. While the breadth of structures that have been produced is impressive, one of the remaining challenges, especially for DNA origami structures that are intended to carry out useful biomedical tasks in vivo, is to endow them with the ability to detect and respond to molecules of interest. Target molecules may be disease indicators or cell surface receptors, and the responses may include conformational changes leading to the release of therapeutically relevant cargo. Nucleic acid aptamers are ideally suited to this task and are beginning to be used in DNA origami designs. In this review, we consider examples of uses of DNA aptamers in DNA origami structures and summarise what is currently understood regarding aptamer-origami integration. We review three major roles for aptamers in such applications: protein immobilisation, triggering of structural transformation, and cell targeting. Finally, we consider future perspectives for DNA aptamer integration with DNA origami.

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“…Finally, cell targeting aptamers enable specificity of drug delivery by DNA origami carriers. As listed in Table 1, the majority of the research relies on a limited number of established aptamers to demonstrate feasibility of designs while some have utilised DNA origami to expand the applications of newly developed aptamers [50,70,76,78]. There are more aptamers, both well-characterised or novel that are potentially useful for functionalisation of DNA origami structures with various potential applications.…”

Section: Conclusion and Perspectivementioning

confidence: 99%

DNA Aptamers for Functionalisation of DNA Origami Nanostructures

Sakai¹,

Islam²,

Adamiak³

et al. 2018

Preprint

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DNA origami has emerged in recent years as a powerful technique for designing and building 2D and 3D nanostructures. While the breadth of structures that have been produced is impressive, one of the remaining challenges, especially for DNA origami structures intended to carry out useful biomedical tasks in vivo, is to endow them with the ability to detect and respond to molecules of interest. Target molecules may be disease indicators or cell surface receptors, and the responses may include conformational changes leading to release of therapeutically relevant cargo. Nucleic acid aptamers are ideally suited to this task and are beginning to be used in DNA origami designs. In this review we consider examples of uses of DNA aptamers in DNA origami structures and summarise what is currently understood regarding aptamer-origami integration. We review three major roles for aptamers in such applications: protein immobilisation, triggering of structural transformation, and cell targeting. Finally, we consider future perspectives for DNA aptamer integration with DNA origami.

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An aptamer-enabled DNA nanobox for protein sensing

Cited by 50 publications

References 57 publications

Engineering Aptamer Switches for Multifunctional Stimulus‐Responsive Nanosystems

Engineering Aptamer Switches for Multifunctional Stimulus‐Responsive Nanosystems

DNA Aptamers for the Functionalisation of DNA Origami Nanostructures

DNA Aptamers for Functionalisation of DNA Origami Nanostructures

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