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Emerging Trend in DNA Nanotechnology
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Emerging Trend in DNA Nanotechnology

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Nanochemistry".

Deadline for manuscript submissions: closed (30 November 2019) | Viewed by 32767

Special Issue Editor

Dr. Veikko Linko

E-Mail Website
Guest Editor
Department of Bioproducts and Biosystems, Aalto University, Kemistintie 1, 02150 Espoo, Finland
Interests: DNA nanotechnology; dna origami; biohybrid materials; molecular self-assembly; nanolithography; molecular electronics; drug delivery
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

During recent years, DNA nanotechnology has taken significant leaps towards real-life applications, as programmable and fully addressable DNA nanostructures have provided a plethora of intriguing implementations—for example, in drug delivery, plasmonics, biochemistry, biology, nanofabrication, super-resolution imaging, as well as mechanical and dynamic molecular devices. Advanced design methods and software have enabled a customized and straightforward synthesis of complex DNA nanostructures for manipulating materials at nanoscale and for harnessing them in a user-defined way. I am hereby pleased to announce that scientifically valid and technically sound papers related to any aspect of DNA nanotechnology—with an emphasis on the emerging trends in the field (listed as the keywords)—will be considered for this Special Issue. Each manuscript will be handled by the editorial board and peer-reviewed by referees.

Adj. Prof. Dr. Veikko Linko
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. Molecules 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 2700 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

  • Structural DNA nanotechnology
  • Self-assembly
  • DNA origami
  • DNA simulation and modeling
  • Dynamic DNA devices
  • DNA structures at interfaces
  • DNA-based drug delivery
  • DNA-based super-resolution imaging
  • DNA-based plasmonics
  • DNA-based lithography
  • DNA templates for molecular components
  • DNA–protein hybrids

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Published Papers (6 papers)

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Editorial

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4 pages, 176 KiB  
Editorial
At the Dawn of Applied DNA Nanotechnology
by Veikko Linko
Molecules 2020, 25(3), 639; https://doi.org/10.3390/molecules25030639 - 3 Feb 2020
Cited by 5 | Viewed by 4457
Abstract
Deoxyribonucleic acid (DNA) serves not only as a genetic information carrier but also as an excellent material for programmable nanoscale assembly [...] Full article
(This article belongs to the Special Issue Emerging Trend in DNA Nanotechnology)

Research

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10 pages, 2826 KiB  
Article
DNA Origami “Quick” Refolding inside of a Micron-Sized Compartment
by Taiki Watanabe, Yusuke Sato, Hayato Otaka, Ibuki Kawamata, Satoshi Murata and Shin-Ichiro M. Nomura
Molecules 2020, 25(1), 8; https://doi.org/10.3390/molecules25010008 - 18 Dec 2019
Cited by 5 | Viewed by 4203
Abstract
Investigations into the refolding of DNA origami leads to the creation of reconstructable nanostructures and deepens our understanding of the sustainability of life. Here, we report the refolding of the DNA origami structure inside a micron-sized compartment. In our experiments, conventional DNA origami [...] Read more.
Investigations into the refolding of DNA origami leads to the creation of reconstructable nanostructures and deepens our understanding of the sustainability of life. Here, we report the refolding of the DNA origami structure inside a micron-sized compartment. In our experiments, conventional DNA origami and truss-type DNA origami were annealed and purified to remove the excess staples in a test tube. The DNA origami was then encapsulated inside of a micron-sized compartment of water-in-oil droplets, composed of neutral surfactants. The re-annealing process was then performed to initiate refolding in the compartment. The resulting 100-nm-sized DNA nanostructures were observed using atomic force microscopy (AFM), and the qualities of their structures were evaluated based on their shape. We found that the refolding of the DNA origami structure was favored inside the droplets compared with refolding in bulk solution. The refolded structures were able to fold even under “quick” one-minute annealing conditions. In addition, the smaller droplets (average diameter: 1.2 µm) appeared to be more advantageous for the refolding of the origamis than larger droplets. These results are expected to contribute to understanding the principles of life phenomena based on multimolecular polymer self-assembly in a micron-sized compartment, and for the production and maintenance of artificially designed molecules. Full article
(This article belongs to the Special Issue Emerging Trend in DNA Nanotechnology)
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Graphical abstract

12 pages, 2835 KiB  
Article
Effect of Staple Age on DNA Origami Nanostructure Assembly and Stability
by Charlotte Kielar, Yang Xin, Xiaodan Xu, Siqi Zhu, Nelli Gorin, Guido Grundmeier, Christin Möser, David M. Smith and Adrian Keller
Molecules 2019, 24(14), 2577; https://doi.org/10.3390/molecules24142577 - 16 Jul 2019
Cited by 20 | Viewed by 5291
Abstract
DNA origami nanostructures are widely employed in various areas of fundamental and applied research. Due to the tremendous success of the DNA origami technique in the academic field, considerable efforts currently aim at the translation of this technology from a laboratory setting to [...] Read more.
DNA origami nanostructures are widely employed in various areas of fundamental and applied research. Due to the tremendous success of the DNA origami technique in the academic field, considerable efforts currently aim at the translation of this technology from a laboratory setting to real-world applications, such as nanoelectronics, drug delivery, and biosensing. While many of these real-world applications rely on an intact DNA origami shape, they often also subject the DNA origami nanostructures to rather harsh and potentially damaging environmental and processing conditions. Furthermore, in the context of DNA origami mass production, the long-term storage of DNA origami nanostructures or their pre-assembled components also becomes an issue of high relevance, especially regarding the possible negative effects on DNA origami structural integrity. Thus, we investigated the effect of staple age on the self-assembly and stability of DNA origami nanostructures using atomic force microscopy. Different harsh processing conditions were simulated by applying different sample preparation protocols. Our results show that staple solutions may be stored at −20 °C for several years without impeding DNA origami self-assembly. Depending on DNA origami shape and superstructure, however, staple age may have negative effects on DNA origami stability under harsh treatment conditions. Mass spectrometry analysis of the aged staple mixtures revealed no signs of staple fragmentation. We, therefore, attribute the increased DNA origami sensitivity toward environmental conditions to an accumulation of damaged nucleobases, which undergo weaker base-pairing interactions and thus lead to reduced duplex stability. Full article
(This article belongs to the Special Issue Emerging Trend in DNA Nanotechnology)
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Graphical abstract

10 pages, 1953 KiB  
Article
Amorphous Carbon Generation as a Photocatalytic Reaction on DNA-Assembled Gold and Silver Nanostructures
by Christian Heck, Yuya Kanehira, Janina Kneipp and Ilko Bald
Molecules 2019, 24(12), 2324; https://doi.org/10.3390/molecules24122324 - 24 Jun 2019
Cited by 21 | Viewed by 5432
Abstract
Background signals from in situ-formed amorphous carbon, despite not being fully understood, are known to be a common issue in few-molecule surface-enhanced Raman scattering (SERS). Here, discrete gold and silver nanoparticle aggregates assembled by DNA origami were used to study the conditions for [...] Read more.
Background signals from in situ-formed amorphous carbon, despite not being fully understood, are known to be a common issue in few-molecule surface-enhanced Raman scattering (SERS). Here, discrete gold and silver nanoparticle aggregates assembled by DNA origami were used to study the conditions for the formation of amorphous carbon during SERS measurements. Gold and silver dimers were exposed to laser light of varied power densities and wavelengths. Amorphous carbon prevalently formed on silver aggregates and at high power densities. Time-resolved measurements enabled us to follow the formation of amorphous carbon. Silver nanolenses consisting of three differently-sized silver nanoparticles were used to follow the generation of amorphous carbon at the single-nanostructure level. This allowed observation of the many sharp peaks that constitute the broad amorphous carbon signal found in ensemble measurements. In conclusion, we highlight strategies to prevent amorphous carbon formation, especially for DNA-assembled SERS substrates. Full article
(This article belongs to the Special Issue Emerging Trend in DNA Nanotechnology)
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Review

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11 pages, 1061 KiB  
Review
The Business of DNA Nanotechnology: Commercialization of Origami and Other Technologies
by Katherine E. Dunn
Molecules 2020, 25(2), 377; https://doi.org/10.3390/molecules25020377 - 16 Jan 2020
Cited by 13 | Viewed by 6182
Abstract
It is often argued that DNA nanotechnology has a multitude of possible applications. However, despite great advances in the understanding of the fundamental principles of the field, to date, there has been comparatively little commercial activity. Analysis of patent applications and company case [...] Read more.
It is often argued that DNA nanotechnology has a multitude of possible applications. However, despite great advances in the understanding of the fundamental principles of the field, to date, there has been comparatively little commercial activity. Analysis of patent applications and company case studies suggests that this is now starting to change. The number of patent application filings is increasing, and new companies are being formed to exploit technologies based on nanoscale structures and devices made from DNA. There are parallels between the commercial developments in this field and those observed in other areas of innovation. Further commercialization is expected and new players will emerge. Full article
(This article belongs to the Special Issue Emerging Trend in DNA Nanotechnology)
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24 pages, 18392 KiB  
Review
Manipulating Enzymes Properties with DNA Nanostructures
by Andreas Jaekel, Pierre Stegemann and Barbara Saccà
Molecules 2019, 24(20), 3694; https://doi.org/10.3390/molecules24203694 - 14 Oct 2019
Cited by 28 | Viewed by 6224
Abstract
Nucleic acids and proteins are two major classes of biopolymers in living systems. Whereas nucleic acids are characterized by robust molecular recognition properties, essential for the reliable storage and transmission of the genetic information, the variability of structures displayed by proteins and their [...] Read more.
Nucleic acids and proteins are two major classes of biopolymers in living systems. Whereas nucleic acids are characterized by robust molecular recognition properties, essential for the reliable storage and transmission of the genetic information, the variability of structures displayed by proteins and their adaptability to the environment make them ideal functional materials. One of the major goals of DNA nanotechnology—and indeed its initial motivation—is to bridge these two worlds in a rational fashion. Combining the predictable base-pairing rule of DNA with chemical conjugation strategies and modern protein engineering methods has enabled the realization of complex DNA-protein architectures with programmable structural features and intriguing functionalities. In this review, we will focus on a special class of biohybrid structures, characterized by one or many enzyme molecules linked to a DNA scaffold with nanometer-scale precision. After an initial survey of the most important methods for coupling DNA oligomers to proteins, we will report the strategies adopted until now for organizing these conjugates in a predictable spatial arrangement. The major focus of this review will be on the consequences of such manipulations on the binding and kinetic properties of single enzymes and enzyme complexes: an interesting aspect of artificial DNA-enzyme hybrids, often reported in the literature, however, not yet entirely understood and whose full comprehension may open the way to new opportunities in protein science. Full article
(This article belongs to the Special Issue Emerging Trend in DNA Nanotechnology)
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