Structural stability of DNA origami nanostructures in the presence of chaotropic agents

Ramakrishnan, Saminathan; Krainer, Georg; Grundmeier, Guido; Schlierf, Michael; Keller, Adrian

doi:10.1039/c6nr00835f

Cited by 65 publications

(99 citation statements)

References 43 publications

(51 reference statements)

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“…The formation of crystalline ice during freezing can largely be suppressed by the addition of cryoprotectants. [ 16 ] However, since DNA origami nanostructures are often more sensitive toward chemical denaturation than genomic DNA, [ 17 ] it is important to carefully choose a cryoprotectant that does not inflict any damage on the DNA origami nanostructures at the concentration required to induce vitrification. Therefore, we investigated the stability of the DNA origami triangles in the presence of different concentrations of glycerol, which is one of the most widely used cryoprotectants for biological systems.…”

Section: Resultsmentioning

confidence: 99%

Cryopreservation of DNA Origami Nanostructures

Yang

Kielar

Zhu

et al. 2020

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Although DNA origami nanostructures have found their way into numerous fields of fundamental and applied research, they often suffer from rather limited stability when subjected to environments that differ from the employed assembly conditions, that is, suspended in Mg2+‐containing buffer at moderate temperatures. Here, means for efficient cryopreservation of 2D and 3D DNA origami nanostructures and, in particular, the effect of repeated freezing and thawing cycles are investigated. It is found that, while the 2D DNA origami nanostructures maintain their structural integrity over at least 32 freeze–thaw cycles, ice crystal formation makes the DNA origami gradually more sensitive toward harsh sample treatment conditions. Whereas no freeze damage could be detected in 3D DNA origami nanostructures subjected to 32 freeze–thaw cycles, 1000 freeze–thaw cycles result in significant fragmentation. The cryoprotectants glycerol and trehalose are found to efficiently protect the DNA origami nanostructures against freeze damage at concentrations between 0.2 × 10−3 and 200 × 10−3 m and without any negative effects on DNA origami shape. This work thus provides a basis for the long‐term storage of DNA origami nanostructures, which is an important prerequisite for various technological and medical applications.

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Section: Resultsmentioning

confidence: 99%

Cryopreservation of DNA Origami Nanostructures

Yang

Kielar

Zhu

et al. 2020

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“…In addition to the addressability of the DNA nanostructures, the stability of these structures is another major advantage in their use for the fabrication of enzymatic cascades. DNA origami nanostructures have been shown to be stable against nuclease digestion and cell lysate, several physical (temperature and UV light exposure) and chemical (alkaline solution and a range of organic solvents) treatments and chaotropic denaturing agents (such as urea and guanidinium chloride), and they can also be lyophilized, stored and reused or concentrated when required. The stability of DNA nanostructures can be enhanced by photo‐crosslinking and graphene encapsulation .…”

Section: Scaffolded Dna Origami Templatesmentioning

confidence: 99%

Nucleic‐Acid‐Templated Enzyme Cascades

et al. 2017

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Cellular metabolism involves complex sequences of organized enzymatic reactions, known as metabolic pathways, that convert substrates into readily usable materials. In nature, these enzymatic complexes are organized in a well-defined manner so that the cascade reactions are more rapid and efficient than they would be if the enzymes were randomly distributed in the cytosol. Development of artificial enzyme cascades that resemble nature's organization of sequentially assembled enzymes is of current interest due to its potential applications, from diagnostics to the production of high-value chemicals. Nucleic acids and their nanostructures have been used to organize enzyme cascades and have been shown to enhance the efficiencies and rates of sequential reactions. Here we summarize the recent progress in the development of artificial enzyme cascades and sequential reactions by arranging enzymes on various DNA/RNA templates and discuss the future directions of this research endeavour.

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“…The ST,o nt he other hand, is ap seudo-double-layer structure and degradation usually starts from the upperl ayer and subsequently proceeds to the second layer,u ntil the remaining ST fragments eventually detach ( Figure 2B). [32] Some structures may thus be partially damaged during sample preparation and handling, therebyp roviding a startingp oint for DNase Ia ttack. In other RTs, DNase I rather seems to attack the vertices,r esulting in disintegration and subsequent digestion of the individual trapezoids (Figure 2C).…”

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Real‐Time Observation of Superstructure‐Dependent DNA Origami Digestion by DNase I Using High‐Speed Atomic Force Microscopy

et al. 2019

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GuidoG rundmeier, [a] AdrianK eller,* [a] andV eikkoL inko* [a, b, c] DNA nanostructures have emerged as intriguing tools for numerous biomedical applications. However, in many of those applicationsa nd most notably in drug delivery,t heir stability and function may be compromised by the biological media. A particularly important issue for medicala pplications is their interaction with proteins such as endonucleases, which may degrade the well-defined nanoscale shapes.H erein, fundamental insights into this interaction are provided by monitoring DNase Id igestion of four structurally distinct DNA origami nanostructures (DONs) in real time and at as ingle-structure level by using high-speed atomic force microscopy.T he effect of the solid-liquidi nterface on DON digestioni sa lso assessed by comparison with experiments in bulk solution. It is shown that DON digestion is strongly dependentoni ts superstructure and flexibility and on the local topology of the individual structure.The rapidly evolvingf ield of DNA nanotechnology enables custom fabrication of various nanoscale shapes with unprecedented addressability; [1] these have found some fascinating implementations in materials science and especiallyi nm any biochemicala nd biophysical systems. [2][3][4][5] In recenty ears, programmable DNA origami nanostructures (DONs) [6][7][8][9][10] have been considered promising candidates for the development of tailored and multifunctional drug-delivery vehicles. [11][12][13][14] For therapeutic in vivo applications, the DON vehicles should preferably be compatible with the immunes ystem, resistant to nucleases, have as ufficiently long circulation half-life, and be able to maintain their shape at the ionic strengths of the biological fluids. [15] However,c oncerns have been raised regarding the stabilityo fD ONs and their performance in biological media. [16, 17] Although it has been shown that DONs can survive under low-cation conditions, [18,19] stability studies performedi n serum or cell culture media have yielded somewhat controversial and quite distinct results. [8,15,[19][20][21] Therefore, significant efforts have been madei nto coating ands tabilizing DONs under biologically relevant conditions. [17,[22][23][24][25] Herein, we study DON digestion by endonucleases (DNase I) in dependence of DON superstructure. DNase Ii sw idely present in serum and varioust issues,w hich makes it one of the most relevantt hreatst ot he stability of DONs in vivo. Previously,D ON cleavage by endonucleases was studied by employing ratherl ong timescales. [8,16] Therefore, thesea pproaches can only resolve the time points at which the whole or most of the nanostructure has been digested. Moreover,t hese experiments could neither reveals patial variations of DNase Is usceptibility within as ingle DON, nor facilitate parallel comparison of different structures under the same conditions. Herein, we thus employ high-speed atomicf orce microscopy (HS-AFM) [26] to study the degradation of four well-established and structurally disti...

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Structural stability of DNA origami nanostructures in the presence of chaotropic agents

Cited by 65 publications

References 43 publications

Cryopreservation of DNA Origami Nanostructures

Cryopreservation of DNA Origami Nanostructures

Nucleic‐Acid‐Templated Enzyme Cascades

Real‐Time Observation of Superstructure‐Dependent DNA Origami Digestion by DNase I Using High‐Speed Atomic Force Microscopy

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