Editorial

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Frontiers in Nucleic Acid Nanotechnology

by Stephen F. Ralph

Nanomaterials 2015, 5(2), 750-754; https://0-doi-org.brum.beds.ac.uk/10.3390/nano5020750 - 08 May 2015

Cited by 1 | Viewed by 4378

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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1448 KiB

Open AccessArticle

Phosphorothioate DNA Stabilized Fluorescent Gold and Silver Nanoclusters

by Daniel S. Weadick and Juewen Liu

Nanomaterials 2015, 5(2), 804-813; https://0-doi-org.brum.beds.ac.uk/10.3390/nano5020804 - 19 May 2015

Cited by 18 | Viewed by 7179

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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2011 KiB

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Titration of DNA/Carbon Nanotube Complexes with Double-Chained Oppositely Charged Surfactants

by Franco Tardani and Camillo La Mesa

Nanomaterials 2015, 5(2), 722-736; https://0-doi-org.brum.beds.ac.uk/10.3390/nano5020722 - 30 Apr 2015

Cited by 5 | Viewed by 5955

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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1349 KiB

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DNA/Ag Nanoparticles as Antibacterial Agents against Gram-Negative Bacteria

by Tomomi Takeshima, Yuya Tada, Norihito Sakaguchi, Fumio Watari and Bunshi Fugetsu

Nanomaterials 2015, 5(1), 284-297; https://0-doi-org.brum.beds.ac.uk/10.3390/nano5010284 - 03 Mar 2015

Cited by 33 | Viewed by 9160

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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DNA-Assisted Solubilization of Carbon Nanotubes and Construction of DNA-MWCNT Cross-Linked Hybrid Hydrogels

by Anatoly Zinchenko, Yosuke Taki, Vladimir G. Sergeyev and Shizuaki Murata

Nanomaterials 2015, 5(1), 270-283; https://0-doi-org.brum.beds.ac.uk/10.3390/nano5010270 - 03 Mar 2015

Cited by 24 | Viewed by 7046

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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2596 KiB

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Polymorphic Ring-Shaped Molecular Clusters Made of Shape-Variable Building Blocks

by Keitel Cervantes-Salguero, Shogo Hamada, Shin-ichiro M. Nomura and Satoshi Murata

Nanomaterials 2015, 5(1), 208-217; https://0-doi-org.brum.beds.ac.uk/10.3390/nano5010208 - 16 Feb 2015

Cited by 7 | Viewed by 6882

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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3293 KiB

Open AccessCommunication

The Nucleotide Capture Region of Alpha Hemolysin: Insights into Nanopore Design for DNA Sequencing from Molecular Dynamics Simulations

by Richard M. A. Manara, Susana Tomasio and Syma Khalid

Nanomaterials 2015, 5(1), 144-153; https://0-doi-org.brum.beds.ac.uk/10.3390/nano5010144 - 27 Jan 2015

Cited by 8 | Viewed by 8083

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)

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Cellular Uptake of Tile-Assembled DNA Nanotubes

by Samet Kocabey, Hanna Meinl, Iain S. MacPherson, Valentina Cassinelli, Antonio Manetto, Simon Rothenfusser, Tim Liedl and Felix S. Lichtenegger

Nanomaterials 2015, 5(1), 47-60; https://0-doi-org.brum.beds.ac.uk/10.3390/nano5010047 - 30 Dec 2014

Cited by 50 | Viewed by 9784

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)

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Review

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Hybrids of Nucleic Acids and Carbon Nanotubes for Nanobiotechnology

by Kazuo Umemura

Nanomaterials 2015, 5(1), 321-350; https://0-doi-org.brum.beds.ac.uk/10.3390/nano5010321 - 12 Mar 2015

Cited by 53 | Viewed by 7482

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)

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1633 KiB

Open AccessReview

DNA under Force: Mechanics, Electrostatics, and Hydration

by Jingqiang Li, Sithara S. Wijeratne, Xiangyun Qiu and Ching-Hwa Kiang

Nanomaterials 2015, 5(1), 246-267; https://0-doi-org.brum.beds.ac.uk/10.3390/nano5010246 - 25 Feb 2015

Cited by 21 | Viewed by 7794

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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4745 KiB

Open AccessReview

DNA-Protected Silver Clusters for Nanophotonics

by Elisabeth Gwinn, Danielle Schultz, Stacy M. Copp and Steven Swasey

Nanomaterials 2015, 5(1), 180-207; https://0-doi-org.brum.beds.ac.uk/10.3390/nano5010180 - 12 Feb 2015

Cited by 103 | Viewed by 11353

Abstract

DNA-protected silver clusters (Ag_N-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 (Ag_N-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 Ag_N-DNA. Here we review what is known about the underlying composition and structure of Ag_N-DNA, and how these relate to the optical properties of these fascinating, hybrid biomolecule-metal cluster nanomaterials. We place Ag_N-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 Ag_N-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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