UNIQUIMER 3D, a software system for structural DNA nanotechnology design, analysis and evaluation

Proteins and DNA exhibit key physical chemical properties that make them advantageous for building nanostructures with outstanding features. Both DNA and protein nanotechnology have growth notably and proved to be fertile disciplines. The combination of both types of nanotechnologies is helpful to overcome the individual weaknesses and limitations of each one, paving the way for the continuing diversification of structural nanotechnologies. Recent studies have implemented a synergistic combination of both biomolecules to assemble unique and sophisticate protein–DNA nanostructures. These hybrid nanostructures are highly programmable and display remarkable features that create new opportunities to build on the nanoscale. This review focuses on the strategies deployed to create hybrid protein–DNA nanostructures. Here, we discuss strategies such as polymerization, spatial directing and organizing, coating, and rigidizing or folding DNA into particular shapes or moving parts. The enrichment of structural DNA nanotechnology by incorporating protein nanotechnology has been clearly demonstrated and still shows a large potential to create useful and advanced materials with cell-like properties or dynamic systems. It can be expected that structural protein–DNA nanotechnology will open new avenues in the fabrication of nanoassemblies with unique functional applications and enrich the toolbox of bionanotechnology.

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Hybrid Nanoassemblies from Viruses and DNA Nanostructures

Nanomaterials ◽

10.3390/nano11061413 ◽

2021 ◽

Vol 11 (6) ◽

pp. 1413

Author(s):

Sofia Ojasalo ◽

Petteri Piskunen ◽

Boxuan Shen ◽

Mauri A. Kostiainen ◽

Veikko Linko

Keyword(s):

Cell Activation ◽

Immune Cell ◽

Dna Nanotechnology ◽

Biological Properties ◽

Dna Nanostructures ◽

Dna Structures ◽

Nanoscale Structures ◽

Immune Cell Activation ◽

Wide Range ◽

Structural Dna Nanotechnology

Viruses are among the most intriguing nanostructures found in nature. Their atomically precise shapes and unique biological properties, especially in protecting and transferring genetic information, have enabled a plethora of biomedical applications. On the other hand, structural DNA nanotechnology has recently emerged as a highly useful tool to create programmable nanoscale structures. They can be extended to user defined devices to exhibit a wide range of static, as well as dynamic functions. In this review, we feature the recent development of virus-DNA hybrid materials. Such structures exhibit the best features of both worlds by combining the biological properties of viruses with the highly controlled assembly properties of DNA. We present how the DNA shapes can act as “structured” genomic material and direct the formation of virus capsid proteins or be encapsulated inside symmetrical capsids. Tobacco mosaic virus-DNA hybrids are discussed as the examples of dynamic systems and directed formation of conjugates. Finally, we highlight virus-mimicking approaches based on lipid- and protein-coated DNA structures that may elicit enhanced stability, immunocompatibility and delivery properties. This development also paves the way for DNA-based vaccines as the programmable nano-objects can be used for controlling immune cell activation.

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The Helicity of a DNA-2’-Fluoro DNA Hybrid Duplex Structure

International Journal of Nanotechnology and Nanomedicine ◽

10.33140/ijnn/02/01/00005 ◽

2017 ◽

Vol 2 (1) ◽

Keyword(s):

Double Helix ◽

Dna Nanotechnology ◽

Helical Structure ◽

Hydrogen Atoms ◽

Atomic Force ◽

Hybrid Duplex ◽

Dna Backbone ◽

Helical Turn ◽

Dna 2 ◽

Structural Dna Nanotechnology

Structural DNA nanotechnology is a system whereby branched DNA molecules are fashioned into objects, or 1D, 2D and 3D lattices, as well as nanomechanical devices. Normally, one is dealing with the usual B-form DNA molecule, but variations on this theme can lead to alterations in both the structures and the properties of the constructs. 2’-Fluoro DNA (FDNA), wherein one of the hydrogen atoms of the 2’ carbon is replaced by a fluorine atom, is a minimal steric perturbation on the structure of the DNA backbone. The helical structure of this duplex is of great interest for applications in structural DNA nanotechnology, because the DNA-FDNA hybrid assumes an A-form double helix, without the instabilities associated with RNA. Here we have used an atomic force microscopic method to estimate the helicity of DNA-FDNA hybrids, and we find that the structure contains 11.8 nucleotide pairs per helical turn with an error of ± 0.6 nucleotide pairs, similar to other A-form molecules.

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