A DNA origami fiducial for accurate 3D AFM imaging

Kolbeck, Pauline J.; Dijk-Moes, Relinde van; Brouwer, Kelly J H; Blaaderen, Alfons van; Vanderlinden, Willem; Liedl, Tim; Lipfert, Jan

doi:10.1101/2022.11.11.516090

Cited by 4 publications

(2 citation statements)

References 64 publications

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“…As an example of the rst case, we demonstrate upright positioning of DNA origami barrels. Our DNA origami barrel is a donut-shaped structure designed previously [9] and constructed from horizontally aligned, circular DNA duplexes. The barrel has a diameter of 60 nm and a height of 27 nm (Fig.…”

Section: Mainmentioning

confidence: 99%

“…Replacing top-down lithography in parts or entirely through selfassembly processes could help to reduce production times and energy costs. Structural DNA nanotechnology and in particular DNA origami self-assembly 1,2 has proven useful in the bottom-up fabrication of well-de ned complex designer two-dimensional and three-dimensional nanostructures with single-nanometre feature resolution 3,4,5,6,7,8,9 . DNA origami-assisted lithographic methods can successfully transfer spatial information of discrete DNA origami shapes 10,11,12,13,14,15 or extended 3D periodic DNA lattices 16 into inorganic substrates.…”

Section: Introductionmentioning

confidence: 99%

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Site-directed placement of three-dimensional DNA origami

Martynenko,

Erber,

Ruider

et al. 2023

Nat. Nanotechnol.

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Assembling hybrid substrates with nanometer-scale precision and molecular addressability enables advances in such distant elds as material research and biosensing. As such, the combination of lithographic methods with 2D DNA origami self-assembly has led, among others, to the development of photonic crystal cavity arrays and the exploration of sensing nanoarrays where molecular devices are patterned on the sub-micron scale. Here we extend this concept to the third dimension through mounting 3D DNA origami onto nano-patterned substrates followed by silici cation to provide mechanical and chemical stability. Our versatile and scalable method relying on self-assembly at ambient temperatures offers the potential to 3D-position any inorganic and organic components that are compatible with DNA architectures. This way, complex and 3D-patterend surfaces designed on the molecular level while reaching macroscopic dimensions could supersede energy-intensive manufacturing steps in substrate processing.

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Section: Mainmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Site-directed placement of three-dimensional DNA origami

Martynenko,

Erber,

Ruider

et al. 2023

Nat. Nanotechnol.

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Cooperative dynamics of DNA grafted magnetic nanoparticles optimize magnetic biosensing and coupling to DNA origami

Lak¹,

Wang²,

Kolbeck

et al. 2023

Preprint

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Magnetic nanoparticles (MNPs) enable unique capabilities for biosensing and actuation via coupling to DNA origami, yet how DNA grafting density affects their dynamics and accessibility remains poorly understood. Here, we demonstrate functionalization of MNPs with single-stranded DNA (ssDNA) via click chemistry conjugation with tunable grafting density. Several complementary methods show that particle translational and rotational dynamics exhibit a sigmoidal dependence on ssDNA grafting density. At low densities ssDNA strands are coiled and cause small changes to particle dynamics, while at high densities they form polymer brushes that cooperatively change particle dynamics. Intermediate ssDNA densities show the highest magnetic biosensing sensitivity for detection of target nucleic acids. Finally, we demonstrate that MNPs with high grafting densities are required to efficiently couple them to DNA origami. These results together establish ssDNA grafting density as a critical parameter for functionalization of MNPs for use in a broad range of applications.

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Topology-dependent DNA binding

Kolbeck,

Tišma,

Analikwu

et al. 2023

Preprint

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DNA stores our genetic information and is ubiquitous in biological and biotechnological applications, where it interacts with binding partners ranging from small molecules to large macromolecular complexes. Binding is modulated by mechanical strains in the molecule and, in turn, can change the local DNA structure. Frequently, DNA occurs in closed topological forms where topology and supercoiling add a global constraint to the interplay of binding-induced deformations and strain-modulated binding. Here, we present a quantitative model of how the global constraints introduced by DNA topology modulate binding and create a complex interplay between topology and affinity. We focus on fluorescent intercalators, which unwind DNA and enable direct quantification via fluorescence detection. Using bulk measurements, we show that DNA supercoiling can increase or decrease intercalation relative to an open topology depending on ligand concentration and the initial topology. Our model quantitatively accounts for observations obtained using psoralen for UV-induced DNA crosslinking, which is frequently used to quantify supercoiling in vivo. Finally, we observe topology-dependent binding in a single-molecule assay, which provides direct access to binding kinetics and DNA supercoil dynamics. Our results have broad implications for the detection and quantification of DNA and for the modulation of DNA binding in cellular contexts.

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A DNA origami fiducial for accurate 3D AFM imaging

Cited by 4 publications

References 64 publications

Site-directed placement of three-dimensional DNA origami

Site-directed placement of three-dimensional DNA origami

Cooperative dynamics of DNA grafted magnetic nanoparticles optimize magnetic biosensing and coupling to DNA origami

Topology-dependent DNA binding

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