Rational Design of DNA Nanoarchitectures (original) (raw)
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Extending the Repertoire of Structures in DNA Nanotechnology
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.
Designed DNA molecules: principles and applications of molecular nanotechnology
DNA is now emerging as an ideal molecule for molecular nanotechnology. Biologists and biochemists have discovered DNA sequences and structures with new functional properties, which are able to prevent the expression of harmful genes or detect macromolecules at low concentrations. Physical and computational scientists can design rigid DNA structures that serve as scaffolds for the organization of matter at the molecular scale, and can build simple DNA-computing devices, diagnostic machines and DNA motors.
Handbook of Ecomaterials, 2019
Since from the past few decades DNA appeared as an excellent molecular building block for the synthesis of nanostructures because of its probable encoded and confirmation intra-and intermolecular base pairing. Various ease strategies and consistent assembly techniques have been established to manipulate DNA nanostructures to at higher complexity. The capability to develop DNA construction with precise special control has permitted scientists to discover novel applications in many ways, such as scaffolds development, sensing applications, nano devices, computational applications, nano robotics, nano electronics, biomolecular catalysis, disease diagnosis, drug delivery. The present report emphasis to brief the opportunities, challenges and future prospective on DNA nanotechnology and its advancements.
DNA-programmed assembly of nanostructures
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
Biomolecular Architecture for Nanotechnology
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.
DNA-based Molecular Nanotechnology
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.
Utilization of Computer Science for Construction and Characterization of DNA nano-Structures
2011
In the upcoming field of DNA nano-science, DNA is used as an entity for building higher order self-assembled structures rather than for storage of genetic information. The application of DNA as a building block relies, like its biological blueprinting function, on the specific pairing between bases holding pairs of DNA molecules together. However, the complexity involved in building even simple DNA architectures is usually so high that designing structures from more than a few base sequences makes the use of computer programs indispensible. Moreover, synthetic DNA nano-structures are often timeconsuming and expensive to build and their structures can be difficult to validate. Therefore, atomistic simulations, which can predict assembly efficiency and physical properties of the designed structures are of great value for both the processes of design and characterization. In this article we summarize examples of computational tools for # FFA and PV contributed equally to this work.
DNA nanotechnology: a future perspective
Nanoscale Research Letters, 2013
In addition to its genetic function, DNA is one of the most distinct and smart self-assembling nanomaterials. DNA nanotechnology exploits the predictable self-assembly of DNA oligonucleotides to design and assemble innovative and highly discrete nanostructures. Highly ordered DNA motifs are capable of providing an ultra-fine framework for the next generation of nanofabrications. The majority of these applications are based upon the complementarity of DNA base pairing: adenine with thymine, and guanine with cytosine. DNA provides an intelligent route for the creation of nanoarchitectures with programmable and predictable patterns. DNA strands twist along one helix for a number of bases before switching to the other helix by passing through a crossover junction. The association of two crossovers keeps the helices parallel and holds them tightly together, allowing the assembly of bigger structures. Because of the DNA molecule's unique and novel characteristics, it can easily be applied in a vast variety of multidisciplinary research areas like biomedicine, computer science, nano/optoelectronics, and bionanotechnology.
Constructing novel materials with DNA
Nano Today, 2007
Although the detailed structure of DNA was revealed by Watson and Crick 1,2 back in 1953, even today we continue to discover stunning and useful new structural modes for this versatile macromolecule. Taking lessons from its in vivo role and aided by technological advances, nanoengineers have begun to explore novel and creative uses for DNA including: molecular detection 3 , therapeutic regimens 4 , complex nanodevices 5 , nanomechanical actuators and motors 6-8 , directed organic synthesis 9,10 , and molecular computation 11,12 . Excellent reviews of many of these aspects of DNA can be found in this issue of Nano Today and elsewhere 10,12,13 .