Academic literature on the topic 'Nucleic acid nanostructures'

Nanoengineering exploits the interactions of materials at the nanometre scale to create functional nanostructures. It relies on the precise organization of nanomaterials to achieve unique functionality. There are no interactions more elegant than those governing nucleic acids via Watson–Crick base-pairing rules. The infinite combinations of DNA/RNA base pairs and their remarkable molecular recognition capability can give rise to interesting nanostructures that are only limited by our imagination. Over the past years, creative assembly of nucleic acids has fashioned a plethora of two-dimensional and three-dimensional nanostructures with precisely controlled size, shape and spatial functionalization. These nanostructures have been precisely patterned with molecules, proteins and gold nanoparticles for the observation of chemical reactions at the single molecule level, activation of enzymatic cascade and novel modality of photonic detection, respectively. Recently, they have also been engineered to encapsulate and release bioactive agents in a stimulus-responsive manner for therapeutic applications. The future of nucleic acid-based nanoengineering is bright and exciting. In this review, we will discuss the strategies to control the assembly of nucleic acids and highlight the recent efforts to build functional nucleic acid nanodevices for nanomedicine.

AbstractTo use nucleic acids in biomedical research and medical applications, these highly hydrophilic macromolecules have to be transported through the organism, targeted to specific cell surfaces, and have to cross cellular barriers. To this end, nanosized transfection complexes have been designed and several of them have been successfully tested. Here, the different steps of the transfection process and the particular optimization protocols are reviewed, including the physicochemical properties of such vectors (size, charge, composition), protection in serum, cellular uptake, endosomal escape, and intracellular targeting. The transfection process has been subdivided into separate steps and here special emphasis is given to peptides that have been designed to optimize these steps individually. Finally, complex devices encompassing a multitude of beneficial functionalities for transfection have been developed.

AbstractNucleic acid nanotechnology designs and develops synthetic nucleic acid strands to fabricate nanosized functional systems. Structural properties and the conformational polymorphism of nucleic acid sequences are inherent characteristics that make nucleic acid nanostructures attractive systems in biosensing. This review critically discusses recent advances in biosensing derived from molecular beacon and DNA origami structures. Molecular beacons belong to a conventional class of nucleic acid structures used in biosensing, whereas DNA origami nanostructures are fabricated by fully exploiting possibilities offered by nucleic acid nanotechnology. We present nucleic acid scaffolds divided into conventional hairpin molecular beacons and DNA origami, and discuss some relevant examples by focusing on peculiar aspects exploited in biosensing applications. We also critically evaluate analytical uses of the synthetic nucleic acid structures in biosensing to point out similarities and differences between traditional hairpin nucleic acid sequences and DNA origami. Graphical abstract

Thesis: Ph. D. in Medical Engineering and Medical Physics, Harvard-MIT Program in Health Sciences and Technology, 2016.
Cataloged from PDF version of thesis.
Includes bibliographical references (pages 137-148).
Patterning complex 3D features at the nanoscale offers potential applications for a wide range of fields from materials to medicine. While numerous methods have been developed to manipulate nanoscale materials, these methods are typically limited by their difficulty in creating arbitrary 3D patterns. Self-assembly of nucleic acids has emerged as a promising method for addressing this challenge due to the predictability and programmability of the material and its structure. While a diversity of DNA nanostructures have been designed by specifying complementarity rules between strands, creation of 3D nanostructures requires careful design of strand architecture, and patterns are often limited to a volume of 25 x 25 x 25 nm³ Here, we address the challenges in structural DNA nanotechnology by developing a modular DNA "brick" approach. These bricks are short, single-stranded oliogomers that can self-assemble in a single-pot reaction to a prescribed 3D shape. Using this modular approach, we demonstrate high efficiency in 3D design by generating 100 distinct, discrete 3D structures from a library of strands. We also created long-range ordering of channels, tunnels, and pores by growing micron-sized 3D periodic crystals made from DNA bricks. Finally, we applied this approach to control over 30,000 unique component strands to selfassemble into cuboids measuring over 100 nm in each dimension. These structures were further used to pattern highly complex cavities. Together, this work represents a simple, modular, and versatile method for 3D nanofabrication. This unique patterning capability of DNA bricks may enable development of new applications by providing a foundation for intricate and complex control of an unprecedented number of independent components.
by Luvena Le-Yun Ong.
Ph. D. in Medical Engineering and Medical Physics

Kinetically controlled isothermal growth is fundamental to biological development, but it remains challenging to rationally design molecular systems that self-assemble isothermally into complex geometries via prescribed assembly and disassembly pathways. By exploiting the programmable chemistry of base pairing, sophisticated spatial and temporal control have both been demonstrated in DNA self-assembly, but largely as separate pursuits. This dissertation extends a new approach, called developmental self-assembly, that integrates temporal with spatial control by using a prescriptive molecular program to specify the kinetic pathways by which DNA molecules isothermally self-assemble into well-defined three-dimensional geometries.
Chemistry and Chemical Biology

This thesis presents the development of novel methodologies in the template mediated chemical synthesis of lariat and branched nucleic acids. The synthetic branched DNA and RNA may be applicable as probes in the elucidation of the splicing mechanism or as potential therapeutic agents. Furthermore, this body of work describes the novel synthesis of Ru(II) branched DNA as building blocks in the supramolecular assembly of nano-motifs. In general, insight into the utilization of nucleic acids as biological molecules and as nanomaterials is presented at the interface of chemistry and biology.
Chapter 2 delineates the regioselective template directed synthesis of Y-RNA via chemical ligation at the branch point of a 5'-phosphate to a 2'-hydroxyl. The branched molecules resemble lariats as they possess the analogous branched architecture. The oligonucleotide components are synthesized from commercially available phosphoramidite building blocks through automated solid-phase synthesis. A unique template directed method in the synthesis of DNA and RNA lariats is proposed in Chapter 3. The regioselective chemical ligation affords wild-type DNA and RNA formed through assembly of a single oligonucleotide strand. A parallel DNA:RNA hybrid association was observed in the preorganized assembly and extensively characterized. Characterization of the Y-RNA and lariat nucleic acids were carried out through techniques such as thermal denaturation analysis, polyacrylamide gel electrophoresis, enzymatic degradation with the RNA lariat debranching enzyme, alkaline treatment as well as MALDI-TOF mass spectrometry.
The second part of the thesis exploits DNA as a nanomaterial in the convergent solid-phase synthesis of Ru(II)-DNA conjugates as branched building blocks in the assembly of nanostructures. Chapter 4 describes the synthesis of Ru branched DNA, utilizing cis-[(bpy)2Ru(imidazole) 2]2+ moiety as the vertex tethered to parallel DNA covalently through flexible hexamethylene linkers. Complete physical characterization and preliminary hybridization studies are conducted. The Ru-DNA conjugates presented were found to be unstable to the protocols required for synthesis of mixed sequence derivatives. The stability and scope of synthesis of these molecules are further discussed.
As an alternative, Ru-DNA branched complexes of mixed sequences, exhibiting greater stability, were synthesized. The transition metal building blocks of Chapter 5 employ a more rigid branch point, linking two parallel DNA strands through a one methylene spacer to the cis-[Ru(bpy)2 (4,4'-bis(hydroxymethyl)-2,2'-bipyridine)][PF6]2 vertex. Physical characterization and the intrinsic luminescent properties of the transition metal complex were confirmed in both the Ru-branched DNA and hybrized forms. A comparative study of the self-assembly behavior of the Ru-DNA conjugates to that of unmetallated branched DNA was also conducted. Interestingly, results indicate a metal-mediated assembly of almost exclusive formation of one discrete Ru-DNA dimeric cyclic nanostructure, where as unmetallated DNA building blocks produced an array of products. Complete confirmation of these products is presented through PAGE and enzymatic digestions. Finally the synthesis of novel Delta and Λ Ru-branched DNA diastereomers is presented as potential building blocks in the creation of chiral metallo-supramolecular constructs.

2009/2010
“There is plenty of room at the bottom”. These were the famous words of Richard P. Feynman in 1959 that led to the birth of nanotechnology and nanoscience. Electronic devices based on inorganic semiconductors have been part of our daily lives for the last 60 years. Their miniaturisation has occurred gradually over the years, however, according to Moore’s law the contemporary microelectronic industry’s “top-down” manufacturing technique will soon reach its limits. Therefore, the recent development and increased knowledge of organic semiconductors has led to a tendency to explore alternative avenues with a focus on the creation of electronic devices based on organic molecules. The invention of techniques such STM (1981) and AFM (1986) have facilitated this research, allowing the imaging and manipulation of surfaces and molecules at the nanometre scale (0.1-100 nm). The next step is therefore the development of methods for the controlled fabrication of molecular assemblies and their integration into usable macroscopic systems. In this respect, the “bottom-up” approach offers considerable advantages over any other methodology (i.e. “top-down”) for the construction of nanoscale functional materials and devices. This approach generally exploits the hierarchical self-assembly of functional molecules through multiple non-covalent interactions to prepare long range ordered and defect-free assemblies barely accessible through conventional covalent synthesis. However, an intrinsic drawback of investigating such systems in solution or in a crystal is that molecular components cannot be directly addressed on a nanometric scale. As a consequence, the best engineering methodology involves modifying the surfaces of bulk materials such as metals or semiconductors by deposition of functional organic materials. The modified surfaces are then characterised using scanning probe microscopies (e.g. STM, AFM). To this end, surface-confined, supramolecularly constructed, bi-dimensional (2D) networks, featuring regular porous domains (controllable both in shape and size) are of particular significance in this research domain because their cavities can be used as receptors for the confinement of other remotely controlled functional molecules (e.g. molecular switches, luminescent chromophores). Since these complex nanostructures could ultimately find applications as optoelectronic devices, research efforts in this domain have been gathering momentum in recent years. In Chapter 1, the reader is introduced to the methods employed to construct porous networks on surfaces via supramolecular interactions. The second part of the chapter deals with recent examples of recognition, selection and immobilisation of guest molecules within the cavities of the networks, which is followed in the third part with a discussion about surface assemblies that display structural features or functionality in the third dimension. The last section of the chapter is devoted to the construction of porous networks on surfaces via the interactions of biomimetic molecules (e.g. DNA), which leads to the objectives of the present doctoral project. Inspired by the self-assembly of DNA into nanoporous arrays, it was postulated that the Watson-Crick base pairing of oligonucleotide’s nucleobases would be ideal in preparing 2D porous networks with large receptor cavities. The idea was to covalently attach complementary single stranded oligonucleotides to rigid angular and linear unit core modules respectively, and then allow the two units to self-assemble on surfaces. However, instead of using DNA oligonucleotides, the use of peptide nucleic acid (PNA) oligonucleotides was proposed since more robust architectures would be obtained due to the higher duplex stability displayed by this class of biomimetic molecules. This doctoral dissertation describes the synthetic steps taken towards achieving this goal. The design of the angular and linear units bearing complementary PNA oligomers, required for the preparation of self-assembled nanoporous arrays are described. However, prior to synthesizing these complex molecules, a simpler proof of principle was required to confirm that PNA duplexes could be formed on surfaces and also, whether the presence of chromophoric moieties (e.g. porphyrin) appended to the PNA strands had any effect on duplex formation and duplex stability. The molecule designed for this proof of principle was a self-complementary PNA dodecamer bearing a porphyrin adduct. The synthesis of the self-complementary PNA oligomer required for the preparation of the PNA-porphyrin adduct is described in the first part of Chapter 2. The main synthetic routes and protecting-group strategies used to prepare PNA monomers and oligomers are described first. This is followed by a discussion of the orthogonal protecting group strategies chosen for our project that would allow the isolation of PNA oligomers bearing protected nucleobases following resin-cleavage. This is contrary to the general norm in existing strategies wherein resin-cleavage and nucleobase deprotection is carried out in situ, however, it was required in our synthetic strategy since the terminal amino group of the PNA oligomers was required for further solution phase reactions. To this end, two protecting group strategies were proposed, a Fmoc/Mmt and Fmoc/Cbz-protecting group strategies. The solid support chosen for the Fmoc/Mmt strategy was Tentagel featuring a base-cleavable linker. Due to the failure to hydrolyse the linker during the resin-cleavage step, the Fmoc/Mmt strategy was abandoned. In the second strategy, an acid-cleavable Rink amide resin was chosen as the solid support, therefore a Fmoc/Cbz-protecting group strategy was chosen since it would allow the TFA-mediated cleavage of the oligomer from the resin, without the deprotection of the Cbz groups from the nucleobases. The preparation of the target PNA oligomer (sequence: TTAATTAATTAA) using the Fmoc/Cbz strategy is described in the next section. First, the required monomers for the oligomer synthesis were prepared using established procedures. Then, following reports of the advances in microwave assisted solid phase peptide synthesis claiming improved purity of oligomer products using short coupling times, the solid phase PNA oligomerisation was attempted using microwave irradiation. Three attempts were performed. The first, using a standard laboratory microwave, resulted in a complex mixture of products at the dodecamer stage. An improvement was observed in the results using the CEM discover SPS microwave which was specifically designed for solid phase synthesis, however, the crude dodecamer obtained was still inseparable from the by-products. Similar results were obtained with the CEM liberty microwave, which was an automated solid phase synthesis setup. Finally, utilising manual solid phase synthesis, the target PNA dodecamer was obtained. The HPLC chromatogram of crude PNA dodecamer obtained following resin cleavage displayed a single major product, which was subsequently purified. The oligomer was then deprotected by treatment with TMSI, and was analysed by mass spectrometry, which confirmed that the target dodecamer had been isolated. Section 2.2 described our efforts to prepare PNA-chromophore adducts. Following the isolation of the PNA dodecamer, attempts to covalently attach a porphyrin moiety to the resin-bound oligomer via an amide linkage failed, possibly due to steric hindrance. Subsequently, an azide linker was appended to the oligomer, and attempts to attach an acetylene functionalised porphyrin using a Cu(I)-catalysed 1,3-dipolar cycloaddition were performed. Unfortunately, this approach also did not yield the target adduct. These unsuccessful results paved the way to the development of a Cu(I)-free 1,3-dipolar cycloaddition that enabled the attachment of chromophores to the PNA oligomer. Recently published reports of Cu(I)-free 1,3-dipolar cycloaddition reactions applied on DNA oligomers offered inspiration towards this goal. The reported strategies involved the generation of a nitrile oxide species, which then reacted with either an alkene or an alkyne to form an isoxazoline or an isoxazole. Two methods of generating the nitrile oxide species were evaluated using anthracene derivatives. The first method involved the base-mediated dehydrochlorination of anthracene hydroximoyl chloride to yield the nitrile oxide, which then reacted with a dipolarophile that was introduced into the reaction mixture. The second approach to generating a nitrile oxide species involved treating an O-silylated hydroxamic acid derivative of anthracene with trifluoromethanesulfonic anhydride in the presence of a base (Carreira’s method). Following successful trapping of the nitrile oxides generated by both methods using trimethylsilyl ethylene as the dipolarophile, the reactions were applied on a resin-bound, acetylene-functionalised PNA dodecamer. Both methods yielded the target PNA-anthracene adduct. Since the nitrile oxide-acetylene 1,3-dipolar cycloaddition reaction had never been applied on porphyrins, a method had to be developed. Attempts to prepare a hydroximoyl chloride derivative of a porphyrin resulted in the decomposition of the macrocycle upon treatment with chlorinating agents (NCS, tert-BuOCl, and 1-chlorobenzotriazole), therefore, the hydroximoyl chloride method was abandoned in favour of the Carreira method. An O-silylated hydroxamic acid derivative of porphyrin was synthesized, and upon exposure to trifluoromethanesulfonic anhydride and Et3N, the nitrile oxide was generated and was trapped with a large excess (200 eq.) of trimethylsilyl ethylene yielding the target tetra-isoxazole porphyrin derivative in 62% yield, which corresponded to a yield of 89% per 1,3-dipolar cycloaddition. Optimisation of the reaction conditions using phenyl acetylene as the dipolarophile allowed similar yields to be obtained with only a 10 eq. excess of the acetylene. Having developed a protocol that was compatible with both PNA and porphyrin, the utility of the method to prepare a variety of PNA-chromophore adducts was tested. Hydroxamate derivatives of pyrene, porphyrin, phenanthroline and fluorescein chromophores were prepared. Subsequently, the corresponding nitrile oxide species were generated and were reacted with the resin-bound, acetylene-functionalised PNA dodecamer. The PNA-pyrene adduct was successfully isolated (Figure v), however, the other target PNA-chromophore products were not isolated. The porphyrin nitrile oxide derivative was insoluble in the reaction medium, thus preventing the cycloaddition reaction from proceeding. In the case of the fluorescein hydroxamate, the presence of nucleophilic functional groups in the starting material were probably reactive towards the trifluoromethanesulfonic anhydride reagent, therefore it was unlikely that the nitrile oxide species was formed, and thus the cycloaddition reaction could not proceed. Finally, the reaction with the phenanthroline derivative yielded a new product, however mass spectrometry analysis indicated that it did not correspond the target PNA-phenanthroline adduct. Further work is currently underway to re-evaluate these reactions. In parallel to the synthetic work, a preliminary study into the deposition of PNA onto mica surfaces was investigated using AFM imaging. Deposition of drops of an aqueous solution of deprotected self-complementary PNA dodecamer onto clean mica surfaces using spin coating resulted in aggregates of PNA on the surface. Following annealing of the solution, a repeated deposition of a single drop of the solution resulted in a completely different surface assembly. The surface was saturated by what was thought to be PNA duplexes. This was confirmed by the deposition of drop of a solution that was diluted ten-fold which resulted in an AFM image where bright spot were intermitted by clean mica surface. Topographical analysis of the surface indicated that the bright spots were an average in 1 nm in height, which closely corresponds to the expected height of PNA duplexes, thus confirming that PNA duplexes could be deposited onto surfaces.
XXII Ciclo
1981

Understanding how enzymes access, transform or degrade a nucleic acid nanostructure is an essential step for the progress of functional DNA nanotechnology. Most approaches for the analysis of nucleic acids require enzymatic reactions. For instance sequencing-by-synthesis of confined DNA molecules is a most established approach for the analysis of the entire genomic information in living organisms. Little is known however about the physical factors that regulate enzymes functions in highly confined systems. In this doctoral thesis, I have investigated the activity of type II restriction enzymes (REs) on basic, two-dimensional DNA nanostructures (DNA origami, i.e. triangles and rectangles) that are formed upon the spontaneous hybridization of many single stranded (ss)DNA molecules over the 7,249-nt-long M13mp18 ssDNA phage genome that serves as scaffold for the inherent DNA self-assembly process. The primary action of REs is DNA fragmentation, and they are a primary defensive mechanism to viral infection in bacteria. Type II REs have an exquisite ability to specifically recognize dsDNA binding sites (termed restriction sites) and irreversibly cleave the inherent DNA molecules within the sites. They are in addition essential tools for DNA cloning in current bioengineering and biotechnology applications. On the other hand, the M13mp18 scaffold naturally possesses a number of restriction sites for each of several, known restriction enzymes. In addition, DNA origami are comprised of different structural motifs that are responsible for molecular confinement of the involved DNA molecules and the peculiar mechanical properties of the shape. My work primarily consists of an unprecedented investigation of the action of >10 type II restriction enzymes on two-dimensional (2D) DNA origami. For two enzymes in particular (HhaI and Hin1II) we fully mapped the site-specific action by activating one site at a time (by generating DNA origami mutants), and measuring the fragmentation pattern of the DNA scaffold by gel electrophoresis, after melting the DNA nanostructure. With such mutational analysis of 2D DNA origami we found that (a) restriction reactions can be efficiently inhibited in 2D DNA origami, while similar inhibition cannot be achieved with the corresponding unfolded dsDNA scaffold (as expected). We argue that the observed behaviour of dense nucleic acid architectures naturally emerges as a result of reduction in spatial degrees of freedom near restriction sites, which can be controlled through small changes to the degree of mechanical stress (e.g. torsion) near the sites. (b) In 2D DNA origami, the action of REs on a site can be predicted from the structure of the three 16 bp-long adjacent dsDNA segments, with the site located in the central one (16 bp is the distance between two consecutive crossovers that join the dsDNA segments). Specifically, a site can be cleaved only if (c) it is located ≥4 bp from a crossover junction, and (d) near the site, each of the adjacent dsDNA segments presents a nick in one of the two strands that form the duplex. This quantitative study reveals therefore that restriction enzyme action can be digitally controlled with the closest neighbouring 2D DNA structural pattern surrounding a restriction site. These unprecedented results also suggest how to design functional nucleic acid nanostructures, with important implications for the implementation of innovative nano-biosensor, that is briefly anticipated in the concluding section of this thesis.

Projeto de Pós-Graduação/Dissertação apresentado à Universidade Fernando Pessoa como parte dos requisitos para obtenção do grau de Mestre em Ciências Farmacêuticas
Os produtos biofarmacêuticos englobam os produtos à base de proteínas terapêuticas, de ácidos nucleicos e os que são usados em terapia celular. Com o crescimento exponencial que se tem verificado nos últimos anos para a biotecnologia farmacêutica, o uso clínico destes produtos tem vindo a aumentar. Contudo, tendo em conta as características físico-químicas das moléculas, têm surgido algumas limitações relativas à administração de produtos biofarmacêuticos. Com efeito, a investigação tem-se focado nos estudos relativos ao desenvolvimento de novos sistemas para veicular estes produtos. Neste contexto, e tendo em conta as vantagens que apresentam, as nanopartículas lipídicas têm sido apresentadas como promissoras. Na primeira parte deste trabalho é efectuada uma revisão bibliográfica relativa aos diferentes produtos biofarmacêuticos, às suas características e limitações de administração. Na segunda parte, é apresentada uma revisão relativa ao estado da arte do uso de nanopartículas lipídicas para promover a administração de produtos biofarmacêuticos. Biopharmaceutical products include therapeutic proteins, nucleic acids and cell-based products. Within the exponential growth of pharmaceutical biotechnology the clinical use of these products has been increasing. Nevertheless, according to the physical and chemical nature of the molecules, some limitations have appeared, limiting the use of biopharmaceutical products. In this way, the number of studies related with the development of new solutions for using biopharmaceutical products has been growing. Accordingly, due to its advantages, lipid nanoparticles have been presented as promising candidates. The first part of this work provides a bibliographic overview of the different biopharmaceutical products, and their characteristics and limitations for therapeutic use. In the second part, is presented a review of the state-of-the-art of using lipid nanoparticles systems to improve the therapeutic efficacy of biopharmaceutical products.

Le travail de recherche de cette thèse consiste en le développement de nouveaux matériaux hybrides organiques-inorganiques pour des applications en nanotechnologie, nanomédicine et diagnostic. Dans ce contexte, des cristaux poreux de zéolite-L ont été utilisé comme nano-vecteur pour faire de la transfection d’ADN et d’ANP, en combinaison avec le relargage de molécules hôtes placées dans les pores. Des nanoparticules de silice mesoporeuses multifonctionnelles ont été utilisées pour traiter le glioblastome, en combinant la thérapie génique avec l’administration durable d’un principe actif. Des nano-coquilles hybrides biodégradables ont été encore développés pour encapsuler des protéines et les relâcher dans les cellules vivantes. Dans le domaine de la détection d’acides nucléiques, des fibres optiques à cristal photonique, fonctionnalisées avec des sondes d’ANP, ont été exploitées comme plateformes optiques pour faire de la détection ultra-sensible d’oligonucléotides ou d’ADN génomique. Enfin, la squelette de l’ANP a été modifié à créer des sondes fluorescentes pour reconnaître et détecter la présence des séquences cibles spécifiques
The research work presented throughout this thesis focuses on the development of novel organic-inorganichybrid materials for applications in nanotechnology, nanomedicine and diagnostics. In such a context, porous zeolite-L crystals have been used as nanocarriers to deliver either DNA or PNA in live cells, in combination with the release of guest molecules placed into the pores. Multifunctional mesoporous silica nanoparticles have been designed to treat glioblastoma, combining gene therapy with the sustained delivery of a chemotherapy agent. Biodegradable hybrid nano-shells have been furthermore created to encapsulate proteins and release them in living cells upon degradation of the outer structure in reductive environment. In the field of nucleic acid detection, photonic crystal fibers, functionalized with specific PNA probes, have been exploited as optical sensing devices to perform ultra-sensitive detection of DNA oligonucleotides or genomic DNA. Eventually, the PNA backbone has served as scaffold to synthesize fluorescent switching probes able to recognize and to detect the presence of specific target sequences

This Handbook consolidates some of the major scientific and technological achievements in different aspects of the field of nanoscience and technology. It consists of theoretical papers, many of which are linked with current and future nanodevices, molecular-based materials and junctions (including Josephson nanocontacts). Self-organization of nanoparticles, atomic chains, and nanostructures at surfaces are further described in detail. Topics include: a unified view of nanoelectronic devices; electronic and transport properties of doped silicon nanowires; quasi-ballistic electron transport in atomic wires; thermal transport of small systems; patterns and pathways in nanoparticle self-organization; nanotribology; and the electronic structure of epitaxial graphene. The volume also explores quantum-theoretical approaches to proteins and nucleic acids; magnetoresistive phenomena in nanoscale magnetic contacts; novel superconducting states in nanoscale superconductors; left-handed metamaterials; correlated electron transport in molecular junctions; spin currents in semiconductor nanostructures; and disorder-induced electron localization in molecular-based materials.

Targeted delivery and controlled release of oligonucleotide therapeutics in vivo are essential aspects of an ideal delivery vehicle. Here we demonstrate the synthesis and in vitro/intracellular characterization of silver nanoparticle (SNP) photolabile nucleic acid conjugates, with the aim of developing a nanoparticulate platform for inducible gene silencing. Due to unique size related properties, nanostructures are being increasingly utilized for intracellular diagnostics and delivery applications. While most nanoscale delivery platforms are polymeric in composition, studies of metallic nanoparticles have highlighted their suitability for delivery of therapeutic agents such as antisense oligonucleotides [1]. The potential benefits of noble metal nanoparticles in delivery applications include tunable size and shape, ease of bulk synthesis and functionalization via ‘wet chemistry’ techniques, and enhanced stability of tethered DNA [2]. Silver is one of the best surface-enhancing substrates available for nanostructure synthesis [3]. SNP composites afford external control over surface-tethered drug release via external triggers.

Tuberculosis (TB) is one of the most widely spread diseases. In 2006, 9.2 million new TB cases were reported with 1.7 million victims [1]. To diagnose TB, Mycobacterium tuberculosis (MTB) is identified in clinical samples. The challenge of TB diagnostics is high-performance screening conducted by nontrained personnel. Currently, nucleic acid testing with target-amplification strategy such as polymerase chain reaction (PCR) is available for detection of TB. However, this entails cumbersome procedures run by skilled operators with expensive instrumentation and reagents. To overcome these challenges, this paper presents a nanotip sensor to diagnose TB rapidly without target-amplification. The proposed methodology uses a nanostructured tip as a biosensor to detect target analytes. The novelty of this approach is in the superior concentration and detection mechanisms of nucleic acids on the terminal end of a nanotip using an alternating current (AC) electric field, specific chemical binding, and capillary action. Confirmatory identification of MTB is achieved by detecting MTB strains on a nanostructured tip through DNA hybridization. In this paper, the working principle is presented with the demonstration of amplification-free detection of MTB genomic DNA using the nanotip sensor. The performance of the tip sensor is characterized.

A critical challenge in the field of medicine is to develop a low cost sensor competent of detecting specific bacterial pathogens via a precise deoxyribonucleic acid (DNA) sequence. In order to identify such biological agents in a patient’s blood or other bodily fluids at the onset of infection, detection of specific pathogen genomic DNA is considered a reliable approach. Current techniques involving multiplex DNA/RNA detection arrays or immunoassays [1] require cumbersome sample preparation, aggressive nucleic acid amplification protocols and must be operated by trained personnel. To overcome the aforementioned obstacles, a time-dependent dielectrophoretic force driven sensor consisting of nanostructured tip is being developed.

The Japan Atomic Energy Agency (JAEA) has been conducting research and development on the thermo-chemical iodine–sulfur (IS) process, which is one of the most attractive water-splitting hydrogen production methods using the nuclear heat of a high-temperature gas-cooled reactor (HTGR). In researching this IS process, a silicon carbide (SiC) heat exchanger with good corrosion resistance was used in a corrosive situation in boiling sulfuric acid. With the aim of enhancing heat transfer in the SiC heat exchanger, a nanostructured surface made of carbon nanotubes (CNTs) was produced on a SiC substrate by surface decomposition. Two types of SiC, one produced by pressureless sintering (PLS-SiC) and one by chemical vapor deposition (CVD-SiC), were used as substrates. CNTs formed by the surface decomposition of SiC can vary depending on the crystal structure of the substrates. Additionally, in order to investigate surface wettability, nanostructured surfaces on the CVD-SiC with hydrophilicity and hydrophobicity were produced. The effects of heat transfer enhancement by the nanostructured surfaces were evaluated by a convective heat transfer test using de-ionized water. The nanostructured surface on the CVD-SiC with hydrophilicity was the only surface that showed any heat transfer enhancement. However, this enhancement was much smaller than those previously reported. The experiment showed that the small size of the nanopores influenced the heat transfer enhancement and that the wettability of the nanostructured surface was related to heat transfer enhancement.