Direct Visualization of Transient Thermal Response of a DNA Origami

Song, Jie; Arbona, Jean-Michel; Zhang, Zhao; Liu, Lei; Xie, Erqing; Elezgaray, Juan; Aimé, Jean‐Pierre; Gothelf, Kurt V.; Besenbacher, Flemming; Dong, Mingdong

doi:10.1021/ja3017939

Cited by 76 publications

(93 citation statements)

References 27 publications

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“…Answering these questions may be important for understanding the mechanism through which 3D DNA box origami can develop resistance to serum. The mica surface may have a stabilizing role for the bottom side of box origami [29]. However, it is worth noting that the damage to box origami in serum solution may be due to the hollow structure.…”

Section: Resultsmentioning

confidence: 99%

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Serum-induced degradation of 3D DNA box origami observed with high-speed atomic force microscopy

et al. 2015

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3D DNA origami holds tremendous potential for the encapsulation and selective release of therapeutic drugs. Observations of the real-time performance of these structures in physiological environments will contribute to the development of future applications. We investigated the degradation kinetics of 3D DNA box origami in serum by using high-speed atomic force microscope optimized for imaging 3D DNA origami in real time. The time resolution allowed to characterize the stages of serum effects on individual 3D DNA boxes origami with nanometer resolution. Our results indicate that the digestion process is a combination of rapid collapse and slow degradation phases. Damage to box origami occurs mainly in the collapse phase. Thus, the structural stability of 3D DNA box origami should be improved, especially in the collapse phase, before these structures are used in clinical applications.

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Section: Resultsmentioning

confidence: 99%

“…AFM evaluates the stability of DNA origami to various stimuli basing its morphologic evolution in situ. [28,29]. However, detailed evidence of the structural stability of the origami, direct visualization of the degradation process, and real-time analyses cannot be achieved with standard AFM because of its slow innate scan speed [30].…”

Section: Introductionmentioning

confidence: 99%

Serum-induced degradation of 3D DNA box origami observed with high-speed atomic force microscopy

et al. 2015

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“…A cooling water fluid circuit refrigerates the piezo-scanner. Before the acquisition of every image, a dwell time of 5 min was allowed to equilibrate the temperature 17 . AFM image acquisition was carried out in tapping mode in air (probes: OMCL-AC160TS-C2, Olympus, Japan).…”

Section: Methodsmentioning

confidence: 99%

“…Here we use thermally controlled AFM (TC-AFM) 17,18 to directly investigate both the structure and in situ dynamics of water condensation on mica (hydrophilic surface) in both the hydrophobic-hydrophilic interface (graphene and mica) and the hydrophilic-hydrophilic interface (MoS 2 and mica). By carefully monitoring the whole dynamic water growth process, the water interaction within the hydrophobic-hydrophilic interface was investigated.…”

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confidence: 99%

Evidence of Stranski–Krastanov growth at the initial stage of atmospheric water condensation

Song

Wang

et al. 2014

Nat Commun

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The precipitation products (rain, snow and so on) of atmospheric water vapour are widely prevalent, and yet the map of its initial stage at a surface is still unclear. Here we investigate the condensation of water vapour occurring in both the hydrophobic-hydrophilic interface (graphene/mica) and the hydrophilic-hydrophilic interface (MoS 2 /mica) by in situ thermally controlled atomic force microscopy. By monitoring the dynamic dewetting/rewetting transitions process, the ice-like water adlayers, at the hydrophobic-hydrophilic interface and not at the hydrophilic-hydrophilic interface, stacked on top of each other up to three ice-I h layers (each of height 3.7 ± 0.2 Å), and the transition from layers to droplets was directly visualized experimentally. Compared with molecular dynamics simulation, the Stranski-Krastanov growth model is better suited to describe the whole water condensation process at the hydrophobic-hydrophilic interface. The initial stage of the hydrometeor is rationalized, which potentially can be utilized for understanding the boundary condition for water transport and the aqueous interfacial chemistry.

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“…Staples bind to the scaffold only, not to other staples, and can hybridize to the same number of scaffold domains at any stage of assembly. Arbona et al [22,26] have presented a model of origami folding in which cooperativity arises from two effects.…”

Section: Introductionmentioning

confidence: 99%

Modelling DNA origami self-assembly at the domain level

Dannenberg

Dunn

Bath

et al. 2015

The Journal of Chemical Physics

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We present a modelling framework, and basic model parameterization, for the study of DNA origami folding at the level of DNA domains. Our approach is explicitly kinetic and does not assume a specific folding pathway. The binding of each staple is associated with a free-energy change that depends on staple sequence, the possibility of coaxial stacking with neighbouring domains, and the entropic cost of constraining the scaffold by inserting staple crossovers. A rigorous thermodynamic model is difficult to implement as a result of the complex, multiply connected geometry of the scaffold: we present a solution to this problem for planar origami. Coaxial stacking of helices and entropic terms, particularly when loop closure exponents are taken to be larger than those for ideal chains, introduce interactions between staples. These cooperative interactions lead to the prediction of sharp assembly transitions with notable hysteresis that are consistent with experimental observations. We show that the model reproduces the experimentally observed consequences of reducing staple concentration, accelerated cooling and absent staples. We also present a simpler methodology that gives consistent results and can be used to study a wider range of systems including non-planar origami.

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Direct Visualization of Transient Thermal Response of a DNA Origami

Cited by 76 publications

References 27 publications

Serum-induced degradation of 3D DNA box origami observed with high-speed atomic force microscopy

Serum-induced degradation of 3D DNA box origami observed with high-speed atomic force microscopy

Evidence of Stranski–Krastanov growth at the initial stage of atmospheric water condensation

Modelling DNA origami self-assembly at the domain level

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