Special Issue "Frontiers in Nucleic Acid Nanotechnology"

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

Deadline for manuscript submissions: closed (30 November 2014)

Special Issue Editor

Guest Editor
Dr. Stephen Ralph

School of Chemistry, University of Wollongong, New South Wales, 2522, Australia
Website | E-Mail
Phone: +61 2 4221 4286
Fax: +61 2 4221 4287
Interests: applications of conducting polymers and carbon nanotubes; membrane filtration; inorganic chemistry

Special Issue Information

Dear Colleagues,

Nucleic acids are arguably the most remarkable and important molecules found in nature. Their molecular structures combine design elegance with inherent purpose, enabling them to serve as the repository and means for transferring our most precious information. Over the past two decades there have been dramatic changes in the way nucleic acids are being utilized in the laboratory. Today these molecules are often viewed upon as building blocks and components of an increasingly varied range of modern materials, including 2- and 3-dimensional lattices, supramolecular polyhedra and dynamic molecular assemblies.

This Special Issue will bring together contributions from researchers at the forefront of designing and characterizing novel nucleic acid nanostructures, such as those produced using the DNA origami method. In addition, it will serve as a showcase for those interested in harnessing the unique properties of DNA and RNA for specific applications, in areas such as molecular electronics, DNA computing and nanomedicine.

Dr. Stephen Ralph
Guest Editor

Submission

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. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as 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 refereed through a 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 monthly 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 1000 CHF (Swiss Francs). English correction and/or formatting fees of 250 CHF (Swiss Francs) will be charged in certain cases for those articles accepted for publication that require extensive additional formatting and/or English corrections.


Keywords

  • DNA
  • RNA
  • nanotechnology
  • nanostructure
  • DNA computers
  • DNA tiles
  • DNA origami
  • nanomedicine
  • soft materials
  • nanoparticles

Published Papers (11 papers)

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Editorial

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Open AccessEditorial Frontiers in Nucleic Acid Nanotechnology
Nanomaterials 2015, 5(2), 750-754; doi:10.3390/nano5020750
Received: 4 May 2015 / Accepted: 7 May 2015 / Published: 8 May 2015
PDF Full-text (617 KB) | HTML Full-text | XML Full-text
Abstract This Special Issue of Nanomaterials highlights innovative work from around the world focused on harnessing the physical, chemical and topological properties of nucleic acids. [...] Full article
(This article belongs to the Special Issue Frontiers in Nucleic Acid Nanotechnology)

Research

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Open AccessArticle Phosphorothioate DNA Stabilized Fluorescent Gold and Silver Nanoclusters
Nanomaterials 2015, 5(2), 804-813; doi:10.3390/nano5020804
Received: 30 March 2015 / Accepted: 7 May 2015 / Published: 19 May 2015
Cited by 2 | PDF Full-text (1448 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Unmodified single-stranded DNA has recently gained popularity for the templated synthesis of fluorescent noble metal nanoclusters (NCs). Bright, stable, and biocompatible clusters have been developed primarily through optimization of DNA sequence. However, DNA backbone modifications have not yet been investigated. In this work,
[...] Read more.
Unmodified single-stranded DNA has recently gained popularity for the templated synthesis of fluorescent noble metal nanoclusters (NCs). Bright, stable, and biocompatible clusters have been developed primarily through optimization of DNA sequence. However, DNA backbone modifications have not yet been investigated. In this work, phosphorothioate (PS) DNAs are evaluated in the synthesis of Au and Ag nanoclusters, and are employed to successfully template a novel emitter using T15 DNA at neutral pH. Mechanistic studies indicate a distinct UV-dependent formation mechanism that does not occur through the previously reported thymine N3. The positions of PS substitution have been optimized. This is the first reported use of a T15 template at physiological pH for AgNCs. Full article
(This article belongs to the Special Issue Frontiers in Nucleic Acid Nanotechnology)
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Open AccessArticle Titration of DNA/Carbon Nanotube Complexes with Double-Chained Oppositely Charged Surfactants
Nanomaterials 2015, 5(2), 722-736; doi:10.3390/nano5020722
Received: 22 January 2015 / Revised: 26 March 2015 / Accepted: 10 April 2015 / Published: 30 April 2015
Cited by 2 | PDF Full-text (2011 KB) | HTML Full-text | XML Full-text
Abstract
1/1 dispersions of ss-DNA/CNT complexes in mass ratios were investigated in a mixture with didodecyldimethylammonium bromide, DDAB. Depending on the amounts of the surface-active agent and of the complexes, solutions, precipitates, or re-dissolution occur. DDAB titrates the phosphate groups on the outer surface
[...] Read more.
1/1 dispersions of ss-DNA/CNT complexes in mass ratios were investigated in a mixture with didodecyldimethylammonium bromide, DDAB. Depending on the amounts of the surface-active agent and of the complexes, solutions, precipitates, or re-dissolution occur. DDAB titrates the phosphate groups on the outer surface of the complex and controls the phase sequence in these systems. The combination of different experimental methods determined the phases that occur therein. The results are based on optical absorbance, Dynamic Light Scattering, ionic conductivity, ζ-potential, optical microscopy and AFM. From the above findings a (pseudo)-binary phase diagram is attained. The system has strong similarities with polymer-surfactant mixtures. In fact, its properties conform to cases in which interactions between rigid rod-like polyelectrolytes and oppositely charged species take place. The peculiarities of double-chained DDAB in the process imply significant differences with respect to the behavior of single chain surfactants. In fact, DDAB associates into vesicular entities, when the homologous single chain species forms small micellar aggregates. Full article
(This article belongs to the Special Issue Frontiers in Nucleic Acid Nanotechnology)
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Open AccessArticle DNA-Assisted Solubilization of Carbon Nanotubes and Construction of DNA-MWCNT Cross-Linked Hybrid Hydrogels
Nanomaterials 2015, 5(1), 270-283; doi:10.3390/nano5010270
Received: 22 December 2014 / Revised: 14 January 2015 / Accepted: 25 February 2015 / Published: 3 March 2015
Cited by 5 | PDF Full-text (1192 KB) | HTML Full-text | XML Full-text
Abstract
A simple method for preparation of DNA-carbon nanotubes hybrid hydrogel based on a two-step procedure including: (i) solubilization of multi-walled carbon nanotubes (MWCNT) in aqueous solution of DNA, and (ii) chemical cross-linking between solubilized MWCNT via adsorbed DNA and free DNA by ethylene
[...] Read more.
A simple method for preparation of DNA-carbon nanotubes hybrid hydrogel based on a two-step procedure including: (i) solubilization of multi-walled carbon nanotubes (MWCNT) in aqueous solution of DNA, and (ii) chemical cross-linking between solubilized MWCNT via adsorbed DNA and free DNA by ethylene glycol diglycidyl ether is reported. We show that there exists a critical concentration of MWCNT below which a homogeneous dispersion of MWCNT in hybrid hydrogel can be achieved, while at higher concentrations of MWCNT the aggregation of MWCNT inside hydrogel occurs. The strengthening effect of carbon nanotube in the process of hydrogel shrinking in solutions with high salt concentration was demonstrated and significant passivation of MWCNT adsorption properties towards low-molecular-weight aromatic binders due to DNA adsorption on MWCNT surface was revealed. Full article
(This article belongs to the Special Issue Frontiers in Nucleic Acid Nanotechnology)
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Open AccessArticle DNA/Ag Nanoparticles as Antibacterial Agents against Gram-Negative Bacteria
Nanomaterials 2015, 5(1), 284-297; doi:10.3390/nano5010284
Received: 4 December 2014 / Revised: 20 February 2015 / Accepted: 25 February 2015 / Published: 3 March 2015
Cited by 5 | PDF Full-text (1349 KB) | HTML Full-text | XML Full-text
Abstract
Silver (Ag) nanoparticles were produced using DNA extracted from salmon milt as templates. Particles spherical in shape with an average diameter smaller than 10 nm were obtained. The nanoparticles consisted of Ag as the core with an outermost thin layer of DNA. The
[...] Read more.
Silver (Ag) nanoparticles were produced using DNA extracted from salmon milt as templates. Particles spherical in shape with an average diameter smaller than 10 nm were obtained. The nanoparticles consisted of Ag as the core with an outermost thin layer of DNA. The DNA/Ag hybrid nanoparticles were immobilized over the surface of cotton based fabrics and their antibacterial efficiency was evaluated using E. coli as the typical Gram-negative bacteria. The antibacterial experiments were performed according to the Antibacterial Standard of Japanese Association for the Functional Evaluation of Textiles. The fabrics modified with DNA/Ag nanoparticles showed a high enough inhibitory and killing efficiency against E. coli at a concentration of Ag ≥ 10 ppm. Full article
(This article belongs to the Special Issue Frontiers in Nucleic Acid Nanotechnology)
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Open AccessArticle Polymorphic Ring-Shaped Molecular Clusters Made of Shape-Variable Building Blocks
Nanomaterials 2015, 5(1), 208-217; doi:10.3390/nano5010208
Received: 1 December 2014 / Revised: 26 January 2015 / Accepted: 3 February 2015 / Published: 16 February 2015
Cited by 1 | PDF Full-text (2596 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Self-assembling molecular building blocks able to dynamically change their shapes, is a concept that would offer a route to reconfigurable systems. Although simulation studies predict novel properties useful for applications in diverse fields, such kinds of building blocks, have not been implemented thus
[...] Read more.
Self-assembling molecular building blocks able to dynamically change their shapes, is a concept that would offer a route to reconfigurable systems. Although simulation studies predict novel properties useful for applications in diverse fields, such kinds of building blocks, have not been implemented thus far with molecules. Here, we report shape-variable building blocks fabricated by DNA self-assembly. Blocks are movable enough to undergo shape transitions along geometrical ranges. Blocks connect to each other and assemble into polymorphic ring-shaped clusters via the stacking of DNA blunt-ends. Reconfiguration of the polymorphic clusters is achieved by the surface diffusion on mica substrate in response to a monovalent salt concentration. This work could inspire novel reconfigurable self-assembling systems for applications in molecular robotics. Full article
(This article belongs to the Special Issue Frontiers in Nucleic Acid Nanotechnology)
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Open AccessCommunication The Nucleotide Capture Region of Alpha Hemolysin: Insights into Nanopore Design for DNA Sequencing from Molecular Dynamics Simulations
Nanomaterials 2015, 5(1), 144-153; doi:10.3390/nano5010144
Received: 26 November 2014 / Revised: 7 January 2015 / Accepted: 12 January 2015 / Published: 27 January 2015
Cited by 1 | PDF Full-text (3293 KB) | HTML Full-text | XML Full-text
Abstract
Nanopore technology for DNA sequencing is constantly being refined and improved. In strand sequencing a single strand of DNA is fed through a nanopore and subsequent fluctuations in the current are measured. A major hurdle is that the DNA is translocated through the
[...] Read more.
Nanopore technology for DNA sequencing is constantly being refined and improved. In strand sequencing a single strand of DNA is fed through a nanopore and subsequent fluctuations in the current are measured. A major hurdle is that the DNA is translocated through the pore at a rate that is too fast for the current measurement systems. An alternative approach is “exonuclease sequencing”, in which an exonuclease is attached to the nanopore that is able to process the strand, cleaving off one base at a time. The bases then flow through the nanopore and the current is measured. This method has the advantage of potentially solving the translocation rate problem, as the speed is controlled by the exonuclease. Here we consider the practical details of exonuclease attachment to the protein alpha hemolysin. We employ molecular dynamics simulations to determine the ideal (a) distance from alpha-hemolysin, and (b) the orientation of the monophosphate nucleotides upon release from the exonuclease such that they will enter the protein. Our results indicate an almost linear decrease in the probability of entry into the protein with increasing distance of nucleotide release. The nucleotide orientation is less significant for entry into the protein. Full article
(This article belongs to the Special Issue Frontiers in Nucleic Acid Nanotechnology)
Open AccessArticle Cellular Uptake of Tile-Assembled DNA Nanotubes
Nanomaterials 2015, 5(1), 47-60; doi:10.3390/nano5010047
Received: 2 December 2014 / Accepted: 22 December 2014 / Published: 30 December 2014
Cited by 9 | PDF Full-text (1604 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
DNA-based nanostructures have received great attention as molecular vehicles for cellular delivery of biomolecules and cancer drugs. Here, we report on the cellular uptake of tubule-like DNA tile-assembled nanostructures 27 nm in length and 8 nm in diameter that carry siRNA molecules, folic
[...] Read more.
DNA-based nanostructures have received great attention as molecular vehicles for cellular delivery of biomolecules and cancer drugs. Here, we report on the cellular uptake of tubule-like DNA tile-assembled nanostructures 27 nm in length and 8 nm in diameter that carry siRNA molecules, folic acid and fluorescent dyes. In our observations, the DNA structures are delivered to the endosome and do not reach the cytosol of the GFP-expressing HeLa cells that were used in the experiments. Consistent with this observation, no elevated silencing of the GFP gene could be detected. Furthermore, the presence of up to six molecules of folic acid on the carrier surface did not alter the uptake behavior and gene silencing. We further observed several challenges that have to be considered when performing in vitro and in vivo experiments with DNA structures: (i) DNA tile tubes consisting of 42 nt-long oligonucleotides and carrying single- or double-stranded extensions degrade within one hour in cell medium at 37 °C, while the same tubes without extensions are stable for up to eight hours. The degradation is caused mainly by the low concentration of divalent ions in the media. The lifetime in cell medium can be increased drastically by employing DNA tiles that are 84 nt long. (ii) Dyes may get cleaved from the oligonucleotides and then accumulate inside the cell close to the mitochondria, which can lead to misinterpretation of data generated by flow cytometry and fluorescence microscopy. (iii) Single-stranded DNA carrying fluorescent dyes are internalized at similar levels as the DNA tile-assembled tubes used here. Full article
(This article belongs to the Special Issue Frontiers in Nucleic Acid Nanotechnology)

Review

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Open AccessReview Hybrids of Nucleic Acids and Carbon Nanotubes for Nanobiotechnology
Nanomaterials 2015, 5(1), 321-350; doi:10.3390/nano5010321
Received: 22 January 2015 / Revised: 25 February 2015 / Accepted: 5 March 2015 / Published: 12 March 2015
Cited by 14 | PDF Full-text (1794 KB) | HTML Full-text | XML Full-text
Abstract
Recent progress in the combination of nucleic acids and carbon nanotubes (CNTs) has been briefly reviewed here. Since discovering the hybridization phenomenon of DNA molecules and CNTs in 2003, a large amount of fundamental and applied research has been carried out. Among thousands
[...] Read more.
Recent progress in the combination of nucleic acids and carbon nanotubes (CNTs) has been briefly reviewed here. Since discovering the hybridization phenomenon of DNA molecules and CNTs in 2003, a large amount of fundamental and applied research has been carried out. Among thousands of papers published since 2003, approximately 240 papers focused on biological applications were selected and categorized based on the types of nucleic acids used, but not the types of CNTs. This survey revealed that the hybridization phenomenon is strongly affected by various factors, such as DNA sequences, and for this reason, fundamental studies on the hybridization phenomenon are important. Additionally, many research groups have proposed numerous practical applications, such as nanobiosensors. The goal of this review is to provide perspective on biological applications using hybrids of nucleic acids and CNTs. Full article
(This article belongs to the Special Issue Frontiers in Nucleic Acid Nanotechnology)
Open AccessReview DNA under Force: Mechanics, Electrostatics, and Hydration
Nanomaterials 2015, 5(1), 246-267; doi:10.3390/nano5010246
Received: 9 December 2014 / Revised: 16 January 2015 / Accepted: 12 February 2015 / Published: 25 February 2015
Cited by 2 | PDF Full-text (1633 KB) | HTML Full-text | XML Full-text
Abstract
Quantifying the basic intra- and inter-molecular forces of DNA has helped us to better understand and further predict the behavior of DNA. Single molecule technique elucidates the mechanics of DNA under applied external forces, sometimes under extreme forces. On the other hand, ensemble
[...] Read more.
Quantifying the basic intra- and inter-molecular forces of DNA has helped us to better understand and further predict the behavior of DNA. Single molecule technique elucidates the mechanics of DNA under applied external forces, sometimes under extreme forces. On the other hand, ensemble studies of DNA molecular force allow us to extend our understanding of DNA molecules under other forces such as electrostatic and hydration forces. Using a variety of techniques, we can have a comprehensive understanding of DNA molecular forces, which is crucial in unraveling the complex DNA functions in living cells as well as in designing a system that utilizes the unique properties of DNA in nanotechnology. Full article
(This article belongs to the Special Issue Frontiers in Nucleic Acid Nanotechnology)
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Open AccessReview DNA-Protected Silver Clusters for Nanophotonics
Nanomaterials 2015, 5(1), 180-207; doi:10.3390/nano5010180
Received: 16 December 2014 / Accepted: 5 February 2015 / Published: 12 February 2015
Cited by 15 | PDF Full-text (4745 KB) | HTML Full-text | XML Full-text
Abstract
DNA-protected silver clusters (AgN-DNA) possess unique fluorescence properties that depend on the specific DNA template that stabilizes the cluster. They exhibit peak emission wavelengths that range across the visible and near-IR spectrum. This wide color palette, combined with low toxicity, high
[...] Read more.
DNA-protected silver clusters (AgN-DNA) possess unique fluorescence properties that depend on the specific DNA template that stabilizes the cluster. They exhibit peak emission wavelengths that range across the visible and near-IR spectrum. This wide color palette, combined with low toxicity, high fluorescence quantum yields of some clusters, low synthesis costs, small cluster sizes and compatibility with DNA are enabling many applications that employ AgN-DNA. Here we review what is known about the underlying composition and structure of AgN-DNA, and how these relate to the optical properties of these fascinating, hybrid biomolecule-metal cluster nanomaterials. We place AgN-DNA in the general context of ligand-stabilized metal clusters and compare their properties to those of other noble metal clusters stabilized by small molecule ligands. The methods used to isolate pure AgN-DNA for analysis of composition and for studies of solution and single-emitter optical properties are discussed. We give a brief overview of structurally sensitive chiroptical studies, both theoretical and experimental, and review experiments on bringing silver clusters of distinct size and color into nanoscale DNA assemblies. Progress towards using DNA scaffolds to assemble multi-cluster arrays is also reviewed. Full article
(This article belongs to the Special Issue Frontiers in Nucleic Acid Nanotechnology)
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