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2005, Nanotechnology
We report the assembly and structural characterization of a Y-shaped DNA template incorporating a central biotin moiety. We also report that this template may be used to assemble nanoscale architectures, which demonstrate the potential of this and related approaches to the fabrication of next-generation electronic devices. Of particular significance is the finding that it is possible to selectively metallize the above DNA template to obtain a three-electrode configuration. Also of particular significance is the finding that a biotin modified nanoparticle will recognize and bind selectively the central biotin moiety of the same template, once functionalized by the protein streptavidin.
Faraday Discussions, 2006
We report the assembly and structural characterization of a Y-shaped DNA template incorporating a central biotin moiety. We also report that this template may be used to assemble nanoscale architectures, which demonstrate the potential of this and related approaches to the fabrication of next-generation electronic devices. Of particular significance is the finding that it is possible to selectively metallize the above DNA template to obtain a three-electrode configuration. Also of particular significance is the finding that a biotin modified nanoparticle will recognize and bind selectively the central biotin moiety of the same template, once functionalized by the protein streptavidin.
Journal of Self-Assembly and Molecular Electronics, 2013
Recent developments in structural DNA nanotechnology have made complex and spatially exactly controlled self-assembled DNA nanoarchitectures widely accessible. The available methods enable large variety of different possible shapes combined with the possibility of using DNA structures as templates for high-resolution patterning of nano-objects, thus opening up various opportunities for diverse nanotechnological applications. These DNA motifs possess enormous possibilities to be exploited in realization of molecular scale sensors and electronic devices, and thus, could enable further miniaturization of electronics. However, there are arguably two main issues on making use of DNA-based electronics: (1) incorporation of individual DNA designs into larger extrinsic systems is rather challenging, and (2) electrical properties of DNA molecules and the utilizable DNA templates themselves, are not yet fully understood. This review focuses on the above mentioned issues and also briefly summarizes the potential applications of DNA-based electronic devices.
5th IEEE Conference on Nanotechnology, 2005., 2005
Elements of the design, synthesis, cloning, amplification, isolation and characterization of template strands of DNA applicable to the parallel construction of nanostructures via sequential assembly processes are described. Particularly, codes have been filed within bacteria which can be accessed to obtain one micron long single stranded DNA molecules which contain multiple copies of a 32nm repetitive sequence. Characterization of these template strands has been performed using Atomic Force Microscopy.
Nanotechnology, 2004
We report on the self-assembly of one-and two-dimensional DNA scaffolds, which serve as templates for the targeted deposition of ordered nanoparticles and molecular arrays. The DNA nanostructures are easy to reprogram, and we demonstrate two distinct conformations: sheets and tubes. The DNA tubes and individual DNA molecules are metallized in solution to produce ultra-thin metal wires.
2000
Summary This paper presents an overview of recent experimental progress by the Duke DNA NanoTech Group in our efforts to utilize novel DNA nanostructures for computational self-assembly as well as for templates in the fabrication of functional nano-patterned materials. We have prototyped a new DNA tile type known as the 4x4 (a cross-like structure composed of four four-arm junctions) upon
Acta Polymerica, 1998
A multistep self-assembly process is proposed for the preparation of nanometer-scale electronics. The process is based on the assembly of a DNA network that serves, in turn, as a template for the subsequent assembly of functional elements using different levels of molecular recognition ability. Inter-element connectivity and connection to the "macroscopic world" is achieved by instilling electrical functionality to the DNA network. The feasibility of this approach was demonstrated by the DNA-templated self-assembly of a 12 lm long, ca. 1 000 Å wide, conductive silver wire connecting two macroscopic electrodes.
2004
In recent years, a number of research groups have begun developing nanofabrication methods based on DNA self-assembly. Here we review our recent experimental progress to utilize novel DNA nanostructures for self-assembly as well as for templates in the fabrication of functional nano-patterned materials. We have prototyped a new DNA nanostructure known as a cross structure. This nanostructure has a 4-fold
2008
Directed, biologically-driven self-assembly has the potential to yield hybrid multicomponent architectures with applications ranging from sensors and diagnostics to nanoelectronic devices. Critical to these applications is to gain control over the precise orientation and geometry of biomolecules interacting with one-another and with surfaces. Such control has thus far been difficult to achieve in even the simplest biomolecular designs. Using a novel strategy for generation of multicomponent biological nanoarchitectures, the DNA-templated assembly of multiprotein complexes recognizing methylated DNA was achieved. The reassembly of two fragments of TEM-1 βlactamase, each one fused with a specific DNA recognition factor, into a catalytically active protein was achieved by using the cognate DNA elements of these factors. This strategy could potentially become a useful tool in studies of genomic DNA methylation in the context of cellular epigenetic processes.
International Journal of Molecular Sciences, 2012
The exploitation of DNA for the production of nanoscale architectures presents a young yet paradigm breaking approach, which addresses many of the barriers to the self-assembly of small molecules into highly-ordered nanostructures via construct addressability. There are two major methods to construct DNA nanostructures, and in the current review we will discuss the principles and some examples of applications of both the tile-based and DNA origami methods. The tile-based approach is an older method that provides a good tool to construct small and simple structures, usually with multiply repeated domains. In contrast, the origami method, at this time, would appear to be more appropriate for the construction of bigger, more sophisticated and exactly defined structures.
Single Molecules, 2002
The use of molecular building blocks opens a new dimension for nanotechnology. Biomolecules offer a variety of possibilities for manipulation, provide a new size dimension and are especially suitable for "bottom up" approaches. Nucleic acids are of special interest due to their ability of self-organization, the achieved combinatorial information capacity and its molecular-biological processability. Here we present an approach for a molecular component systems with DNA-based ele-ments and products that is suitable for molecular nanotechnology. Oligonucleotides thereby serve as biological modifiers of nanoparticles and surfaces to form self-assembling monolayers, and genomic DNA acts as framework for the building blocks. A first application of DNA-nanoparticle complexes could be the use as a novel, highly-stable label for chip technologies, with the potential for single-molecule detection. Another field is the fabrication of novel electronic devices, based on extreme miniaturization. This paper describes the different fields of use for DNA-based molecular modules, and presents first results of the realization of this concept.
Proceedings of the National Academy of Sciences, 2008
A unique DNA scaffold was prepared for the one-step self-assembly of hierarchical nanostructures onto which multiple proteins or nanoparticles are positioned on a single template with precise relative spatial orientation. The architecture is a topologically complex ladder-shaped polycatenane in which the ''rungs'' of the ladder are used to bring together the individual rings of the mechanically interlocked structure, and the ''rails'' are available for hierarchical assembly, whose effectiveness has been demonstrated with proteins, complementary DNA, and gold nanoparticles. The ability of this template to form from linear monomers and simultaneously bind two proteins was demonstrated by chemical force microscopy, transmission electron microscopy, and confocal fluorescence microscopy. Finally, fluorescence resonance energy transfer between adjacent fluorophores confirmed the programmed spatial arrangement between two different nanomaterials. DNA templates that bring together multiple nanostructures with precise spatial control have applications in catalysis, biosensing, and nanomaterials design.
Nanomaterials
Bottom-up fabrication using DNA is a promising approach for the creation of nanoarchitectures. Accordingly, nanomaterials with specific electronic, photonic, or other functions are precisely and programmably positioned on DNA nanostructures from a disordered collection of smaller parts. These self-assembled structures offer significant potential in many domains such as sensing, drug delivery, and electronic device manufacturing. This review describes recent progress in organizing nanoscale morphologies of metals, semiconductors, and carbon nanotubes using DNA templates. We describe common substrates, DNA templates, seeding, plating, nanomaterial placement, and methods for structural and electrical characterization. Finally, our outlook for DNA-enabled bottom-up nanofabrication of materials is presented.
ChemInform, 2014
DNA's remarkable molecular recognition properties, flexibility and structural features make it one of the most promising scaffolds to design a variety of nanostructures. During the past decades, two major methods have been developed for the construction of DNA nanomaterials in a programmable way, both generating nanostructures in one, two and three dimensions: the tile-based assembly process, which provides a useful tool to construct large and simple structures, and the DNA origami method, suitable for the production of smaller, more sophisticated and well defined structures. Proteins, nanoparticles and other functional elements have been specifically positioned into designed patterns on these structures. They can also act as templates to study chemical reactions, help in the structural determination of proteins and be used as platform for genomic and drug delivery applications. In this review we examine recent progresses towards the potential use of DNA nanostructures for molecular and cellular biology.
Organic & Biomolecular Chemistry, 2005
DNA is a unique material for nanotechnology since it is possible to use base sequences to encode instructions for assembly in a predetermined fashion at the nanometre scale. Synthetic oligonucleotides are readily obtained by automated synthesis and numerous techniques have been developed for conjugating DNA with other materials. The exact spatial positioning of materials is crucial for the future development of complex nanodevices and the emerging field of DNA-nanotechnology is now exploring DNA-programmed processes for the assembly of organic compounds, biomolecules, and inorganic materials. h e m i s t r y 2 0 0 5 O r g . B i o m o l . C h e m . , 2 0 0 5 , 3 , 4 0 2 3 -4 0 3 7 4 0 2 3
2011
ChemBioChem, 2014
DNA's remarkable molecular recognition properties, flexibility and structural features make it one of the most promising scaffolds to design a variety of nanostructures. During the past decades, two major methods have been developed for the construction of DNA nanomaterials in a programmable way, both generating nanostructures in one, two and three dimensions: the tile-based assembly process, which provides a useful tool to construct large and simple structures, and the DNA origami method, suitable for the production of smaller, more sophisticated and well defined structures. Proteins, nanoparticles and other functional elements have been specifically positioned into designed patterns on these structures. They can also act as templates to study chemical reactions, help in the structural determination of proteins and be used as platform for genomic and drug delivery applications. In this review we examine recent progresses towards the potential use of DNA nanostructures for molecular and cellular biology.
Bionanoelectronics, 2012
This chapter reviews the design principles of biomolecular architecture with applications in nanotechnology and presents examples of zero-, one-, two-, and three-dimensional patterns of inorganic materials assembled on biological scaffolds. The use of nanoscale inorganic scaffolds for biomolecules is briefly discussed. Electronic nanoscale components separated by nanosized distances, which eventually lead to faster computation, require new technologies. One possible solution to the new generation of nanotechnologies involves the use of biological molecules, and in particular DNA, as scaffolds for electronic circuits. The advantages of DNA scaffolds are the self-assembly process and the specificity of AT and G-C hydrogen-bonding interactions, as well as our present ability to synthesize and amplify any desired DNA sequence. In addition, the nanostructures constructed from DNA scaffolds are physicochemically stable, which means that they can be stored and processed under environmental conditions that do not need to be especially restrictive to avoid decomposition. The processing of DNA material can be performed with atomic precision by highly specific enzymes. Because of the relevance of DNA architecture to nanotechnology, many reviews exist on this subject (see, e.g., Seeman 1998; Feldkamp and Niemeyer 2006; Jaeger and Chworos 2006; Lin et al. 2009). We only focus here on specific examples of DNA-based fabrication of inorganic nanoparticle arrays or devices with applications in nanotechnology [see also (Li et al. 2009) for a recent review]. In most cases, nanotechnology-related scaffolding relies on the possibility of attaching chemical groups at certain positions, on which properly functionalized inorganic molecules bind in a subsequent process. DNA-based nanotechnology is a bottom-up self-assembly approach that follows a different strategy compared to inorganic self-assembly: nonequilibrium processes direct the assembly in biological structures, whereas equilibrium-regulated processes are commonly employed in artificial inorganic structures.
Advanced Materials, 2004
Reported is the DNA-templated assembly of a protein-functionalized 10 nm gap electrode from suitably modified gold nanoparticles on a silicon wafer substrate. Also reported is that the above protein-functionalized electrode is recognized and bound selectively by a suitably modified gold nanoparticle that is localized in the 10 nm gap. Clearly, a range of suitably modified nanoparticles and biomolecules could similarly be localized in the above gap.
Journal of self-assembly and molecular electronics, 2018
Recent work has demonstrated that DNA, ordinarily considered a weak conductor, can be functionalized to carry electronic charge by site-specific incorporation of single silver ions inside the double helix via the non-canonical pairing of mismatched cytosines through Ag + coordination: (dC:Ag + :dC) [1,2]. Through the alteration of sequence composition and cation availability, a variety of nanowires can be synthesized with tuneable length, ion distribution, and uniformity. These wires are more thermostable than Watson-Crick DNA, can shield intercalated Ag + from aqueous solvents, and are able to form in the absence of cluster contamination. We use computational sequence design algorithms to introduce nonlinear geometry to these nanowires, with the goal of creating self-assembling DNA nanostructures that may have potential for neural architectures from electrically-functional oligonucleotide components.
American Journal of Nanotechnology, 2015
DNA nanotechnology remains an active area of research and advances have been reviewed recently. DNA nanotechnology seeks to deploy molecules at an atomic level and on a small molecule scale. Other techniques in biophysics and biochemistry do not need to address the issue of the true structure of the nucleic acids at an atomic level but, rather, at a macro-atomic level such as in genetics and in immunology, for example. Accordingly, DNA nanotechnology is perhaps uniquely dependent upon exact clarity in the secondary and tertiary structures of the nucleic acids, as well as that can ever be achieved. Challenges include expanding the use of DNA in medicine, and the construction of detectors with higher sensitivity for biological and chemical settings. Though increasingly complex architectures have been constructed, novel approaches to a greater rôle in biological computation and data storage remain important goals. Here a repertoire of structures for DNA at an atomic level is described which offers a new conjecture with which to move forward. The DNA double helix model faces many problems which have become apparent in the 62 years of research in molecular biology that have elapsed since it was formulated by Watson and Crick in 1953. Experimental evidence is set out seeking to show that the only truly side-by-side alternative, the paranemic model, accounts better for the wide range of phenomena otherwise inexplicable with the double helix model. This paranemic model can engage in a repertoire of structural options denied to the DNA double helix model. Without the requirement to postulate unwinding of the DNA strands, the nucleotide base sequence is immediately accessible to complementary DNA sequences to promote rapid detection of specific molecules in biological and medical settings. Rapid switching between Watson-Crick and Hoogsteen base pairing and four-stranded structures can allow greater complexity in the construction of molecular switches and digital programming.
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