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Nanomaterials
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DNA-Based Nanotechnology
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DNA-Based Nanotechnology

A special issue of Nanomaterials (ISSN 2079-4991).

Deadline for manuscript submissions: closed (30 June 2016) | Viewed by 67891

Special Issue Editor

Dr. Leonid Gurevich

E-Mail Website
Guest Editor
Department of Materials and Production, Faculty of Engineering and Science, Aalborg University, 9220 Aalborg Ø, Denmark
Interests: nanotechnology; self-assembly; DNA; AFM; drug delivery
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Unique self-assembly and recognition properties of biological molecules offer an attractive route for bottom-up construction of complex, infinitely customizable, and cost-effective nanodevices. DNA, designed by nature to store information, is arguably one of the most promising candidates for the job. From the nanotechnology prospective, DNA possess a number of attractive properties, making it a unique construction material with fantastic structuring and self-recognition properties, which also comes with a well-established enzymatic toolbox allowing to produce essentially any desired sequence with a broad range of modifications. Thus, it does not come as a surprise that a large variety of different nanostructures, including 2D and 3D DNA arrays, various DNA-nanoparticle conjugates, DNA origami, DNA robots, DNA drug-delivery system, etc., have been created during recent years.

In this Special issue, we would like to reflect the broadness of the subject and invite contributions from all walks of DNA nanotechnology, including, but not limited to, DNA origami, DNA arrays, DNA-nanoparticle conjugates, novel DNA structures, as well as applications of DNA in molecular electronics, nanophotonics, biosensing, and nanomedicine.

Assoc. Prof. Dr. 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 arrays
  • DNA origami
  • DNA-nanoparticle conjugates
  • triplex DNA
  • quadruplex DNA
  • DNA nanodevices
  • DNA biosensors, nanoplasmonics, nanophotonics, molecular electronics

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Published Papers (10 papers)

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Research

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15693 KiB  
Article
Formation of Conductive DNA-Based Nanowires via Conjugation of dsDNA with Cationic Peptide
by Zeinab Esmail Nazari, Julio Gomez Herrero, Peter Fojan and Leonid Gurevich
Nanomaterials 2017, 7(6), 128; https://doi.org/10.3390/nano7060128 - 30 May 2017
Cited by 5 | Viewed by 4897
Abstract
A novel conductive DNA-based nanomaterial, DNA-peptide wire, composed of a DNA core and a peripheral peptide layer, is presented. The electrical conductivity of the wire is found to be at least three orders in magnitude higher than that of native double-stranded DNA (dsDNA). [...] Read more.
A novel conductive DNA-based nanomaterial, DNA-peptide wire, composed of a DNA core and a peripheral peptide layer, is presented. The electrical conductivity of the wire is found to be at least three orders in magnitude higher than that of native double-stranded DNA (dsDNA). High conductivity of the wires along with a better resistance to mechanical deformations caused by interactions between the substrate and electrode surface make them appealing for a wide variety of nanoelectronic and biosensor applications. Full article
(This article belongs to the Special Issue DNA-Based Nanotechnology)
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2250 KiB  
Communication
The Assembly of DNA Amphiphiles at Liquid Crystal-Aqueous Interface
by Jingsheng Zhou, Yuanchen Dong, Yiyang Zhang, Dongsheng Liu and Zhongqiang Yang
Nanomaterials 2016, 6(12), 229; https://doi.org/10.3390/nano6120229 - 1 Dec 2016
Cited by 19 | Viewed by 5359
Abstract
In this article, we synthesized a type of DNA amphiphiles (called DNA-lipids) and systematically studied its assembly behavior at the liquid crystal (LC)—aqueous interface. It turned out that the pure DNA-lipids at various concentrations cannot trigger the optical transition of liquid crystals from [...] Read more.
In this article, we synthesized a type of DNA amphiphiles (called DNA-lipids) and systematically studied its assembly behavior at the liquid crystal (LC)—aqueous interface. It turned out that the pure DNA-lipids at various concentrations cannot trigger the optical transition of liquid crystals from planar anchoring to homeotropic anchoring at the liquid crystal—aqueous interface. The co-assembly of DNA-lipid and l-dilauroyl phosphatidylcholine (l-DLPC) indicated that the DLPC assembled all over the LC-aqueous interface, and DNA-lipids prefer to couple with LC in certain areas, particularly in polarized and fluorescent image, forming micron sized net-like structures. The addition of DNA complementary to DNA-lipids forming double stranded DNA-lipids caused de-assembly of DNA-lipids from LC-aqueous interface, resulting in the disappearance of net-like structures, which can be visualized through polarized microscope. The optical changes combined with DNA unique designable property and specific interaction with wide range of target molecules, the DNA-lipids decorated LC-aqueous interface would provide a new platform for biological sensing and diagnosis. Full article
(This article belongs to the Special Issue DNA-Based Nanotechnology)
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3146 KiB  
Article
DNA Origami Reorganizes upon Interaction with Graphite: Implications for High-Resolution DNA Directed Protein Patterning
by Masudur Rahman, David Neff, Nathaniel Green and Michael L. Norton
Nanomaterials 2016, 6(11), 196; https://doi.org/10.3390/nano6110196 - 31 Oct 2016
Cited by 11 | Viewed by 7551
Abstract
Although there is a long history of the study of the interaction of DNA with carbon surfaces, limited information exists regarding the interaction of complex DNA-based nanostructures with the important material graphite, which is closely related to graphene. In view of the capacity [...] Read more.
Although there is a long history of the study of the interaction of DNA with carbon surfaces, limited information exists regarding the interaction of complex DNA-based nanostructures with the important material graphite, which is closely related to graphene. In view of the capacity of DNA to direct the assembly of proteins and optical and electronic nanoparticles, the potential for combining DNA-based materials with graphite, which is an ultra-flat, conductive carbon substrate, requires evaluation. A series of imaging studies utilizing Atomic Force Microscopy has been applied in order to provide a unified picture of this important interaction of structured DNA and graphite. For the test structure examined, we observe a rapid destabilization of the complex DNA origami structure, consistent with a strong interaction of single-stranded DNA with the carbon surface. This destabilizing interaction can be obscured by an intentional or unintentional primary intervening layer of single-stranded DNA. Because the interaction of origami with graphite is not completely dissociative, and because the frustrated, expanded structure is relatively stable over time in solution, it is demonstrated that organized structures of pairs of the model protein streptavidin can be produced on carbon surfaces using DNA origami as the directing material. Full article
(This article belongs to the Special Issue DNA-Based Nanotechnology)
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1785 KiB  
Article
Effects of G-Quadruplex Topology on Electronic Transfer Integrals
by Wenming Sun, Daniele Varsano and Rosa Di Felice
Nanomaterials 2016, 6(10), 184; https://doi.org/10.3390/nano6100184 - 15 Oct 2016
Cited by 10 | Viewed by 4831
Abstract
G-quadruplex is a quadruple helical form of nucleic acids that can appear in guanine-rich parts of the genome. The basic unit is the G-tetrad, a planar assembly of four guanines connected by eight hydrogen bonds. Its rich topology and its possible relevance as [...] Read more.
G-quadruplex is a quadruple helical form of nucleic acids that can appear in guanine-rich parts of the genome. The basic unit is the G-tetrad, a planar assembly of four guanines connected by eight hydrogen bonds. Its rich topology and its possible relevance as a drug target for a number of diseases have stimulated several structural studies. The superior stiffness and electronic π-π overlap between consecutive G-tetrads suggest exploitation for nanotechnologies. Here we inspect the intimate link between the structure and the electronic properties, with focus on charge transfer parameters. We show that the electronic couplings between stacked G-tetrads strongly depend on the three-dimensional atomic structure. Furthermore, we reveal a remarkable correlation with the topology: a topology characterized by the absence of syn-anti G-G sequences can better support electronic charge transfer. On the other hand, there is no obvious correlation of the electronic coupling with usual descriptors of the helix shape. We establish a procedure to maximize the correlation with a global helix shape descriptor. Full article
(This article belongs to the Special Issue DNA-Based Nanotechnology)
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1679 KiB  
Article
Preparation, Characterization and Manipulation of Conjugates between Gold Nanoparticles and DNA
by Gennady Eidelshtein, Moran Fattal, Gavriel Avishai, Benjamin Kempinski, Clelia Giannini and Alexander Kotlyar
Nanomaterials 2016, 6(9), 167; https://doi.org/10.3390/nano6090167 - 8 Sep 2016
Cited by 4 | Viewed by 6504
Abstract
Here we described the preparation and characterization by atomic force microscopy of dumbbell-shaped conjugates between 450 bp double-stranded DNA polymer, poly(dG)-poly(dC), and 5 nm gold nanoparticles (GNPs). We have demonstrated that the size of the nanoparticles in the conjugates can be increased in [...] Read more.
Here we described the preparation and characterization by atomic force microscopy of dumbbell-shaped conjugates between 450 bp double-stranded DNA polymer, poly(dG)-poly(dC), and 5 nm gold nanoparticles (GNPs). We have demonstrated that the size of the nanoparticles in the conjugates can be increased in a controlled fashion. Application of the conjugates for measuring the electrical conductivity of DNA is discussed. Full article
(This article belongs to the Special Issue DNA-Based Nanotechnology)
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4076 KiB  
Article
Structural Changes Induced in Grapevine (Vitis vinifera L.) DNA by Femtosecond IR Laser Pulses: A Surface-Enhanced Raman Spectroscopic Study
by Nicoleta E. Dina, Cristina M. Muntean, Nicolae Leopold, Alexandra Fălămaș, Adela Halmagyi and Ana Coste
Nanomaterials 2016, 6(6), 96; https://doi.org/10.3390/nano6060096 - 25 May 2016
Cited by 11 | Viewed by 5873
Abstract
In this work, surface-enhanced Raman spectra of ten genomic DNAs extracted from leaf tissues of different grapevine (Vitis vinifera L.) varieties, respectively, are analyzed in the wavenumber range 300–1800 cm−1. Furthermore, structural changes induced in grapevine genomic nucleic acids upon [...] Read more.
In this work, surface-enhanced Raman spectra of ten genomic DNAs extracted from leaf tissues of different grapevine (Vitis vinifera L.) varieties, respectively, are analyzed in the wavenumber range 300–1800 cm−1. Furthermore, structural changes induced in grapevine genomic nucleic acids upon femtosecond (170 fs) infrared (IR) laser pulse irradiation (λ = 1100 nm) are discussed in detail for seven genomic DNAs, respectively. Surface-enhanced Raman spectroscopy (SERS) signatures, vibrational band assignments and structural characterization of genomic DNAs are reported for each case. As a general observation, the wavenumber range between 1500 and 1660 cm−1 of the spectra seems to be modified upon laser treatment. This finding could reflect changes in the base-stacking interactions in DNA. Spectral shifts are mainly attributed to purines (dA, dG) and deoxyribose. Pyrimidine residues seem to be less affected by IR femtosecond laser pulse irradiation. Furthermore, changes in the conformational properties of nucleic acid segments are observed after laser treatment. We have found that DNA isolated from Feteasca Neagra grapevine leaf tissues is the most structurally-responsive system to the femtosecond IR laser irradiation process. In addition, using unbiased computational resources by means of principal component analysis (PCA), eight different grapevine varieties were discriminated. Full article
(This article belongs to the Special Issue DNA-Based Nanotechnology)
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4652 KiB  
Article
Cationic Nanoparticles Assembled from Natural-Based Steroid Lipid for Improved Intracellular Transport of siRNA and pDNA
by Ruilong Sheng, Xiaoqing Zhuang, Zhao Wang, Amin Cao, Kaili Lin and Julian X. X. Zhu
Nanomaterials 2016, 6(4), 69; https://doi.org/10.3390/nano6040069 - 13 Apr 2016
Cited by 11 | Viewed by 6819
Abstract
Developing new functional biomaterials from biocompatible natural-based resources for gene/drug delivery has attracted increasing attention in recent years. In this work, we prepared a series of cationic nanoparticles (Diosarg-DOPE NPs) by assembly of a natural steroid diosgenin-based cationic lipid (Diosarg) with commercially-available helper [...] Read more.
Developing new functional biomaterials from biocompatible natural-based resources for gene/drug delivery has attracted increasing attention in recent years. In this work, we prepared a series of cationic nanoparticles (Diosarg-DOPE NPs) by assembly of a natural steroid diosgenin-based cationic lipid (Diosarg) with commercially-available helper lipid 1,2-dioleoyl-sn-glycero-3-phosphorethanolamine (DOPE). These cationic Diosarg-DOPE NPs were able to efficiently bind siRNA and plasmid DNA (pDNA) via electrostatic interactions to form stable, nano-sized cationic lipid nanoparticles instead of lamellar vesicles in aqueous solution. The average particle size, zeta potentials and morphologies of the siRNA and pDNA complexes of the Diosarg-DOPE NPs were examined. The in vitro cytotoxicity of NPs depends on the dose and assembly ratio of the Diosarg and DOPE. Notably, the intracellular transportation efficacy of the exogenesis siRNA and pDNA could be greatly improved by using the Diosarg-DOPE NPs as the cargoes in H1299 cell line. The results demonstrated that the self-assembled Diosarg-DOPE NPs could achieve much higher intracellular transport efficiency for siRNA or pDNA than the cationic lipid Diosarg, indicating that the synergetic effect of different functional lipid components may benefit the development of high efficiency nano-scaled gene carriers. Moreover, it could be noted that the traditional “lysosome localization” involved in the intracellular trafficking of the Diosarg and Diosarg-DOPE NPs, indicating the co-assembly of helper lipid DOPE, might not significantly affect the intracellular localization features of the cationic lipids. Full article
(This article belongs to the Special Issue DNA-Based Nanotechnology)
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Review

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2413 KiB  
Review
Probe Microscopic Studies of DNA Molecules on Carbon Nanotubes
by Kazuo Umemura, Katsuki Izumi and Shusuke Oura
Nanomaterials 2016, 6(10), 180; https://doi.org/10.3390/nano6100180 - 8 Oct 2016
Cited by 14 | Viewed by 6565
Abstract
Hybrids of DNA and carbon nanotubes (CNTs) are promising nanobioconjugates for nanobiosensors, carriers for drug delivery, and other biological applications. In this review, nanoscopic characterization of DNA-CNT hybrids, in particular, characterization by scanning probe microscopy (SPM), is summarized. In many studies, topographical imaging [...] Read more.
Hybrids of DNA and carbon nanotubes (CNTs) are promising nanobioconjugates for nanobiosensors, carriers for drug delivery, and other biological applications. In this review, nanoscopic characterization of DNA-CNT hybrids, in particular, characterization by scanning probe microscopy (SPM), is summarized. In many studies, topographical imaging by atomic force microscopy has been performed. However, some researchers have demonstrated advanced SPM operations in order to maximize its unique and valuable functions. Such sophisticated approaches are attractive and will have a significant impact on future studies of DNA-CNT hybrids. Full article
(This article belongs to the Special Issue DNA-Based Nanotechnology)
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3893 KiB  
Review
Metallic Nanostructures Based on DNA Nanoshapes
by Boxuan Shen, Kosti Tapio, Veikko Linko, Mauri A. Kostiainen and Jari Jussi Toppari
Nanomaterials 2016, 6(8), 146; https://doi.org/10.3390/nano6080146 - 10 Aug 2016
Cited by 18 | Viewed by 8799
Abstract
Metallic nanostructures have inspired extensive research over several decades, particularly within the field of nanoelectronics and increasingly in plasmonics. Due to the limitations of conventional lithography methods, the development of bottom-up fabricated metallic nanostructures has become more and more in demand. The remarkable [...] Read more.
Metallic nanostructures have inspired extensive research over several decades, particularly within the field of nanoelectronics and increasingly in plasmonics. Due to the limitations of conventional lithography methods, the development of bottom-up fabricated metallic nanostructures has become more and more in demand. The remarkable development of DNA-based nanostructures has provided many successful methods and realizations for these needs, such as chemical DNA metallization via seeding or ionization, as well as DNA-guided lithography and casting of metallic nanoparticles by DNA molds. These methods offer high resolution, versatility and throughput and could enable the fabrication of arbitrarily-shaped structures with a 10-nm feature size, thus bringing novel applications into view. In this review, we cover the evolution of DNA-based metallic nanostructures, starting from the metallized double-stranded DNA for electronics and progress to sophisticated plasmonic structures based on DNA origami objects. Full article
(This article belongs to the Special Issue DNA-Based Nanotechnology)
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2132 KiB  
Review
DNA-Based Enzyme Reactors and Systems
by Veikko Linko, Sami Nummelin, Laura Aarnos, Kosti Tapio, J. Jussi Toppari and Mauri A. Kostiainen
Nanomaterials 2016, 6(8), 139; https://doi.org/10.3390/nano6080139 - 27 Jul 2016
Cited by 63 | Viewed by 9413
Abstract
During recent years, the possibility to create custom biocompatible nanoshapes using DNA as a building material has rapidly emerged. Further, these rationally designed DNA structures could be exploited in positioning pivotal molecules, such as enzymes, with nanometer-level precision. This feature could be used [...] Read more.
During recent years, the possibility to create custom biocompatible nanoshapes using DNA as a building material has rapidly emerged. Further, these rationally designed DNA structures could be exploited in positioning pivotal molecules, such as enzymes, with nanometer-level precision. This feature could be used in the fabrication of artificial biochemical machinery that is able to mimic the complex reactions found in living cells. Currently, DNA-enzyme hybrids can be used to control (multi-enzyme) cascade reactions and to regulate the enzyme functions and the reaction pathways. Moreover, sophisticated DNA structures can be utilized in encapsulating active enzymes and delivering the molecular cargo into cells. In this review, we focus on the latest enzyme systems based on novel DNA nanostructures: enzyme reactors, regulatory devices and carriers that can find uses in various biotechnological and nanomedical applications. Full article
(This article belongs to the Special Issue DNA-Based Nanotechnology)
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