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DNA-Based Nanostructures: Emerging Trends and Applications

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A special issue of Nanomaterials (ISSN 2079-4991). This special issue belongs to the section "Biology and Medicines".

Deadline for manuscript submissions: closed (30 June 2021) | Viewed by 15946

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Special Issue Editor

Prof. Dr. Leonid Gurevich

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Guest Editor

Department of Materials and Production, Aalborg University, DK-9220 Aalborg, Denmark
Interests: nanotechnology; self-assembly; DNA; AFM; drug delivery; biosensors; molecular electronics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Various aspects of DNA-based nanostructures belong to some of most exciting topics in nanotechnology, benefitting from the intrinsic ability of DNA to self-assemble and store information. The use of DNA structures in nanotechnology, pioneered by Ned Seeman, has now expanded from simple 2D-arrays to complex 3D moveable structures and currently spans a broad range of fields, from nanomedicine and drug delivery to biosensors, plasmonics, and nanoelectronics. In this Special Issue, we aim to cover recent advances in this fast-growing field and invite manuscripts related to all aspects of DNA-based nanostructures.

Prof. Leonid Gurevich
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Nanomaterials is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2900 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

DNA nanostructures
DNA robots
DNA origami
DNA self-assembly
DNA nanoelectronics

Published Papers (4 papers)

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Research

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24 pages, 12135 KiB

Open AccessArticle

Membrane-Interacting DNA Nanotubes Induce Cancer Cell Death

by Samet Kocabey, Aslihan Ekim Kocabey, Roger Schneiter and Curzio Rüegg

Nanomaterials 2021, 11(8), 2003; https://0-doi-org.brum.beds.ac.uk/10.3390/nano11082003 - 04 Aug 2021

Cited by 8 | Viewed by 2849

Abstract

DNA nanotechnology offers to build nanoscale structures with defined chemistries to precisely position biomolecules or drugs for selective cell targeting and drug delivery. Owing to the negatively charged nature of DNA, for delivery purposes, DNA is frequently conjugated with hydrophobic moieties, positively charged polymers/peptides and cell surface receptor-recognizing molecules or antibodies. Here, we designed and assembled cholesterol-modified DNA nanotubes to interact with cancer cells and conjugated them with cytochrome c to induce cancer cell apoptosis. By flow cytometry and confocal microscopy, we observed that DNA nanotubes efficiently bound to the plasma membrane as a function of the number of conjugated cholesterol moieties. The complex was taken up by the cells and localized to the endosomal compartment. Cholesterol-modified DNA nanotubes, but not unmodified ones, increased membrane permeability, caspase activation and cell death. Irreversible inhibition of caspase activity with a caspase inhibitor, however, only partially prevented cell death. Cytochrome c-conjugated DNA nanotubes were also efficiently taken up but did not increase the rate of cell death. These results demonstrate that cholesterol-modified DNA nanotubes induce cancer cell death associated with increased cell membrane permeability and are only partially dependent on caspase activity, consistent with a combined form of apoptotic and necrotic cell death. DNA nanotubes may be further developed as primary cytotoxic agents, or drug delivery vehicles, through cholesterol-mediated cellular membrane interactions and uptake. Full article

(This article belongs to the Special Issue DNA-Based Nanostructures: Emerging Trends and Applications)

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16 pages, 30561 KiB

Open AccessArticle

Morphological Manipulation of DNA Gel Microbeads with Biomolecular Stimuli

by Shu Okumura, Benediktus Nixon Hapsianto, Nicolas Lobato-Dauzier, Yuto Ohno, Seiju Benner, Yosuke Torii, Yuuka Tanabe, Kazuki Takada, Alexandre Baccouche, Marie Shinohara, Soo Hyeon Kim, Teruo Fujii and Anthony Genot

Nanomaterials 2021, 11(2), 293; https://0-doi-org.brum.beds.ac.uk/10.3390/nano11020293 - 22 Jan 2021

Cited by 6 | Viewed by 4100

Abstract

Hydrogels are essential in many fields ranging from tissue engineering and drug delivery to food sciences or cosmetics. Hydrogels that respond to specific biomolecular stimuli such as DNA, mRNA, miRNA and small molecules are highly desirable from the perspective of medical applications, however interfacing classical hydrogels with nucleic acids is still challenging. Here were demonstrate the generation of microbeads of DNA hydrogels with droplet microfluidic, and their morphological actuation with DNA strands. Using strand displacement and the specificity of DNA base pairing, we selectively dissolved gel beads, and reversibly changed their size on-the-fly with controlled swelling and shrinking. Lastly, we performed a complex computing primitive—A Winner-Takes-All competition between two populations of gel beads. Overall, these results show that strand responsive DNA gels have tantalizing potentials to enhance and expand traditional hydrogels, in particular for applications in sequencing and drug delivery. Full article

(This article belongs to the Special Issue DNA-Based Nanostructures: Emerging Trends and Applications)

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21 pages, 9888 KiB

Open AccessArticle

The Stability of a Nanoparticle Diamond Lattice Linked by DNA

by Hamed Emamy, Oleg Gang and Francis W. Starr

Nanomaterials 2019, 9(5), 661; https://0-doi-org.brum.beds.ac.uk/10.3390/nano9050661 - 26 Apr 2019

Cited by 6 | Viewed by 3635

Abstract

The functionalization of nanoparticles (NPs) with DNA has proven to be an effective strategy for self-assembly of NPs into superlattices with a broad range of lattice symmetries. By combining this strategy with the DNA origami approach, the possible lattice structures have been expanded to include the cubic diamond lattice. This symmetry is of particular interest, both due to the inherent synthesis challenges, as well as the potential valuable optical properties, including a complete band-gap. Using these lattices in functional devices requires a robust and stable lattice. Here, we use molecular simulations to investigate how NP size and DNA stiffness affect the structure, stability, and crystallite shape of NP superlattices with diamond symmetry. We use the Wulff construction method to predict the equilibrium crystallite shape of the cubic diamond lattice. We find that, due to reorientation of surface particles, it is possible to create bonds at the surface with dangling DNA links on the interior, thereby reducing surface energy. Consequently, the crystallite shape depends on the degree to which such surface reorientation is possible, which is sensitive to DNA stiffness. Further, we determine dependence of the lattice stability on NP size and DNA stiffness by evaluating relative Gibbs free energy. We find that the free energy is dominated by the entropic component. Increasing NP size or DNA stiffness increases free energy, and thus decreases the relative stability of lattices. On the other hand, increasing DNA stiffness results in a more precisely defined lattice structure. Thus, there is a trade off between structure and stability of the lattice. Our findings should assist experimental design for controlling lattice stability and crystallite shape. Full article

(This article belongs to the Special Issue DNA-Based Nanostructures: Emerging Trends and Applications)

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Review

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15 pages, 1618 KiB

Open AccessReview

Hybrid Nanoassemblies from Viruses and DNA Nanostructures

by Sofia Ojasalo, Petteri Piskunen, Boxuan Shen, Mauri A. Kostiainen and Veikko Linko

Nanomaterials 2021, 11(6), 1413; https://0-doi-org.brum.beds.ac.uk/10.3390/nano11061413 - 27 May 2021

Cited by 3 | Viewed by 4294

Abstract

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. Full article

(This article belongs to the Special Issue DNA-Based Nanostructures: Emerging Trends and Applications)

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