A label-free light-scattering method to resolve assembly and disassembly of DNA nanostructures

Ijäs, Heini; Liedl, Tim; Linko, Veikko; Posnjak, Gregor

doi:10.1016/j.bpj.2022.10.036

Cited by 10 publications

(6 citation statements)

References 36 publications

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“…One of the common reagents to remove divalent ions like Ni 2+ is ethylenediaminetetraacetic acid (EDTA). 35,36 We utilized dynamic light scattering (DLS) analysis 44 combined with AFM imaging and gel electrophoresis to assess the kinetics of the formation and disassembly of the ribbons. In DLS analysis, we first monitored STs in the annealing buffer as a control experiment.…”

Section: Resultsmentioning

confidence: 99%

Creation of ordered 3D tubes out of DNA origami lattices

et al. 2023

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Section: Resultsmentioning

confidence: 99%

Creation of ordered 3D tubes out of DNA origami lattices

et al. 2023

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“…A noteworthy finding related to digestion assays is that in order to obtain molecular insights of such processes, one should preferentially use complementary analysis techniques and combine the results with microscopy imaging. As an example, in the work by Ijäs et al., [ 88 ] the authors used both light scattering and EtBr‐stained gel electrophoresis to study global and local effects of DNA origami digestion by DNase I. With scattering, the authors were able to follow the global decrease of the DNA origami size/molecular mass during digestion, while the EtBr fluorescence intensity indicated the amount of intercalated dye in the accessible hybridized strands that could have also been partially detached from the structure.…”

Section: Discussionmentioning

confidence: 99%

“…As a continuation of the abovementioned work, Ijäs et al investigated the DNase I digestion of different 2D (triangle, bowtie, and Z-shape) and 3D DNA origami ("capsule" and 24HB) either alone or when loaded with the DNA-intercalating chemotherapeutic drug doxorubicin (DOX) in a more quantitative manner. [23] Here, it was possible to resolve both the digestion and drug release profiles spectroscopically by following changes in DNA absorbance (can also be achieved by following changes in light-scattering intensity) [88] and DOX fluorescence emission intensity (Figure 3b). The fastest digestion was obtained for the plain 2D triangles, similarly as in the work by Ramakrishnan et al, [84] where the digestion profiles obtained on mica were also compared to the ones recorded in bulk solution.…”

Section: Dnase Imentioning

confidence: 99%

Stability of DNA Origami Nanostructures in Physiological Media: The Role of Molecular Interactions

Linko

Keller

2023

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Programmable, custom‐shaped, and nanometer‐precise DNA origami nanostructures have rapidly emerged as prospective and versatile tools in bionanotechnology and biomedicine. Despite tremendous progress in their utilization in these fields, essential questions related to their structural stability under physiological conditions remain unanswered. Here, DNA origami stability is explored by strictly focusing on distinct molecular‐level interactions. In this regard, the fundamental stabilizing and destabilizing ionic interactions as well as interactions involving various enzymes and other proteins are discussed, and their role in maintaining, modulating, or decreasing the structural integrity and colloidal stability of DNA origami nanostructures is summarized. Additionally, specific issues demanding further investigation are identified. This review – through its specific viewpoint – may serve as a primer for designing new, stable DNA objects and for adapting their use in applications dealing with physiological media.

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“…1 Similarly, recent work on DLS has shown that in addition to providing particle size distributions, DLS can be used to monitor and characterize changes in morphology due to melting and formation as well as degradation events. 41 Importantly, while DLS has emerging capabilities and is amenable to high-throughput measurement, the high instrument cost may limit its accessibility.…”

Section: Introductionmentioning

confidence: 99%

Capacitance measurements for assessing DNA origami nanostructures

Walawalkar

Sajal

Gilpin

et al. 2023

Preprint

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Nanostructures fabricated with DNA are emerging as a practical approach for applications ranging from advanced manufacturing to therapeutics. To support the strides made in improving accessibility and facilitating commercialization of DNA nanostructure applications, we identify the need for a rapid characterization approach that aids nanostructure production. In our work, we introduce a low-fidelity characterization approach that provides an interdependent assessment of DNA origami formation, concentration and morphology using capacitance sensing. Change in charge is one of the transduction methods to determine capacitive loading on a substrate. It is known that cations in the solution stabilize DNA origami nanostructures. So, we hypothesized that the presence of cations and nanostructures in a buffer solution can induce capacitance change that is distinctive of the nanostructure present. In this study we were able to detect a change in the capacitance when the nanostructure solution was deposited on our capacitance sensor, and we could distinguish between pre-annealed and annealed structures at concentrations less than 15 nM. The capacitance measurements were affected by the concentration of Mg2+ions in the solution, the staple-to-scaffold stoichiometric ratio of the nanostructure and the nanostructure morphology. Maintaining a 12.5 mM Mg2+concentration in the nanostructure buffer, we discover a linear relationship between the relative capacitance change and the nanostructure concentration from 5 nM to 20 nM, which we call the characteristic curve. We find distinct characteristic curves for our three nanostructures with distinct morphologies but similar molecular weight - a rectangular plate, a sphere and a rod. Given that we can distinguish nanostructure formation, concentration and morphology, we expect that capacitance measurement will emerge as an affordable and rapid approach for quality control for nanostructure production.

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A label-free light-scattering method to resolve assembly and disassembly of DNA nanostructures

Cited by 10 publications

References 36 publications

Creation of ordered 3D tubes out of DNA origami lattices

Creation of ordered 3D tubes out of DNA origami lattices

Stability of DNA Origami Nanostructures in Physiological Media: The Role of Molecular Interactions

Capacitance measurements for assessing DNA origami nanostructures

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