The path towards functional nanoparticle-DNA origami composites

Johnson, Joshua A.; Dehankar, Abhilasha; Robbins, Ariel; Kabtiyal, Prerna; Jergens, Elizabeth; Lee, Kil Ho; Johnston-Halperin, Ezekiel; Poirier, Michael G.; Castro, Carlos E.; Winter, Jessica O.

doi:10.1016/j.mser.2019.06.003

Cited by 18 publications

(17 citation statements)

References 479 publications

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“…Likewise, the process can be varied with more steps and preparations adjusted for advanced design strategies such as when the target system has decorated staples with nanoparticles [46]- [48], is hybridized with polymers [13], [49]- [52], functions as actuators [53]- [55] or has additional design complexities [45], [56], [57].…”

Section: Basic Design Principlesmentioning

confidence: 99%

Design Approaches and Computational Tools for DNA Nanostructures

Koh¹,

Lee²,

Lee³

et al. 2021

IEEE Open J. Nanotechnol.

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Designing a structure in nanoscale with desired shape and properties has been enabled by structural DNA nanotechnology. Design strategies in this research field have evolved to interpret various aspects of increasingly more complex nanoscale assembly and to realize molecular-level functionality by exploring static to dynamic characteristics of the target structure. Computational tools have naturally been of significant interest as they are essential to achieve a fine control over both shape and physicochemical properties of the structure. Here, we review the basic design principles of structural DNA nanotechnology together with its computational analysis and design tools.

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Section: Basic Design Principlesmentioning

confidence: 99%

Design Approaches and Computational Tools for DNA Nanostructures

Koh¹,

Lee²,

Lee³

et al. 2021

IEEE Open J. Nanotechnol.

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“…There are some workarounds, however, to achieve lattice structures where all lattices have the same arrangement. However, well-defined support for this kind of design is missing, despite this being a topic for many researchers [ 39 , 40 , 41 , 42 ]. In contrast, UNF was designed with a multi-component design in mind, naturally supporting such structures.…”

Section: Use Casesmentioning

confidence: 99%

Unified Nanotechnology Format: One Way to Store Them All

et al. 2021

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The domains of DNA and RNA nanotechnology are steadily gaining in popularity while proving their value with various successful results, including biosensing robots and drug delivery cages. Nowadays, the nanotechnology design pipeline usually relies on computer-based design (CAD) approaches to design and simulate the desired structure before the wet lab assembly. To aid with these tasks, various software tools exist and are often used in conjunction. However, their interoperability is hindered by a lack of a common file format that is fully descriptive of the many design paradigms. Therefore, in this paper, we propose a Unified Nanotechnology Format (UNF) designed specifically for the biomimetic nanotechnology field. UNF allows storage of both design and simulation data in a single file, including free-form and lattice-based DNA structures. By defining a logical and versatile format, we hope it will become a widely accepted and used file format for the nucleic acid nanotechnology community, facilitating the future work of researchers and software developers. Together with the format description and publicly available documentation, we provide a set of converters from existing file formats to simplify the transition. Finally, we present several use cases visualizing example structures stored in UNF, showcasing the various types of data UNF can handle.

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“…Nucleic acid-modified nanoparticles have led to ribonucleic acid (RNA) vaccines, small interfering RNA (siRNA) therapeutics, and deoxyribonucleic acid (DNA) and RNA diagnostics in healthcare [1]. Similarly, nanoparticles modified with DNA have been used to construct complex nanostructured materials for energy applications [2]. Nanoparticle clusters [3] or arrays [4] can enable emergent behaviours, like surface plasmon resonance (SPR) or Förster Resonance Energy Transfer (FRET) [2].…”

Section: Introductionmentioning

confidence: 99%

“…Emerging bio-orthogonal approaches with higher yields (e.g., click chemistry [10]) require the addition of unusual functional groups that still necessitate use of standard chemistries. For this reason, most DNA composite materials, including those assembled using short ssDNAs [3] or DNA nanotechnologies [2], employ gold nanoparticles that are easily modified via thiol binding to their surfaces. Very few examples exist of DNA materials incorporating other nanoparticle types (e.g., quantum dots, magnetic nanoparticles, catalysts) [13][14][15], despite potential advantages of such structures in biomedical imaging, optoelectronic, and energy applications.…”

Section: Introductionmentioning

confidence: 99%

DNA-caged Nanoparticles via Electrostatic Self-Assembly

Jergens¹,

Fernandes-Junior

Cui

et al. 2022

Preprint

Self Cite

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DNA-modified nanoparticles enable DNA sensing and therapeutics in nanomedicine and are also crucial for nanoparticle self-assembly with DNA-based materials. However, methods to conjugate DNA to nanoparticle surfaces are limited, inefficient, and lack control. Inspired by DNA tile nanotechnology, we demonstrate a new approach to nanoparticle modification based on electrostatic attraction between negatively charged DNA tiles and positively charged nanoparticles. This approach does not disrupt nanoparticle surfaces and leverages the programmability of DNA nanotechnology to control DNA presentation. We demonstrated this approach using a variety of nanoparticles, including polymeric micelles, polystyrene beads, gold nanoparticles, and superparamagnetic iron oxide nanoparticles with sizes ranging from 5-20 nm in diameter. DNA cage formation was confirmed through transmission electron microscopy (TEM), neutralization of zeta potential, and a series of fluorescence experiments. DNA cages present “handle” sequences that can be used for reversible target attachment or self-assembly. Handle functionality was verified in solution, at the solid-liquid interface, and inside fixed cells, corresponding to applications in biosensing, DNA microarrays, and erasable immunocytochemistry. These experiments demonstrate the versatility of the electrostatic DNA caging approach and provide a new pathway to nanoparticle modification with DNA that will empower further applications of these materials in medicine and materials science.

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The path towards functional nanoparticle-DNA origami composites

Cited by 18 publications

References 479 publications

Design Approaches and Computational Tools for DNA Nanostructures

Design Approaches and Computational Tools for DNA Nanostructures

Unified Nanotechnology Format: One Way to Store Them All

DNA-caged Nanoparticles via Electrostatic Self-Assembly

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