DNA Nanotechnology

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/143775/1/cpnc1200.pd

Dissipative DNA nanotechnology

DNA nanotechnology has emerged as a powerful tool to precisely design and control molecular circuits, machines and nanostructures. A major goal in this field is to build devices with life-like properties, such as directional motion, transport, communication and adaptation. Here we provide an overview of the nascent field of dissipative DNA nanotechnology, which aims at developing life-like systems by combining programmable nucleic-acid reactions with energy-dissipating processes. We first delineate the notions, terminology and characteristic features of dissipative DNA-based systems and then we survey DNA-based circuits, devices and materials whose functions are controlled by chemical fuels. We emphasize how energy consumption enables these systems to perform work and cyclical tasks, in contrast with DNA devices that operate without dissipative processes. The ability to take advantage of chemical fuel molecules brings dissipative DNA systems closer to the active molecular devices that exist in nature

DNA nanotechnology-enabled chiral plasmonics: from static to dynamic

In this Account, we discuss a variety of static and dynamic chiral plasmonic nanostructures enabled by DNA nanotechnology. In the category of static plasmonic systems, we first show chiral plasmonic nanostructures based on spherical AuNPs, including plasmonic helices, toroids, and tetramers. To enhance the CD responses, anisotropic gold nanorods with larger extinction coefficients are utilized to create chiral plasmonic crosses and helical superstructures. Next, we highlight the inevitable evolution from static to dynamic plasmonic systems along with the fast development of this interdisciplinary field. Several dynamic plasmonic systems are reviewed according to their working mechanisms.Comment: 7 figure

Key Experimental Approaches in DNA Nanotechnology

DNA nanotechnology combines unusual DNA motifs with sticky‐ended cohesion to build polyhedral objects, topological targets, nanomechanical devices, and both crystalline and aperiodic arrays. The goal of DNA nanotechnology is control of the structure of macroscopic matter on the finest possible scale. Applications are expected to arise in the areas of X‐ray crystallography, nanoelectronics, nanorobotics, and DNA‐based computation. DNA and its close molecular relatives appear extremely well suited for these goals. This overview covers the generation of new DNA motifs, construction methods (synthesis, hybridization, phosphorylation, ligation), and a variety of methods for characterization of motifs, devices, and arrays. Finally, the use of DNA nanotechnology as a tool in biochemistry is discussed.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/143741/1/cpnc1201.pd

Programing strand displacement reaction pathways using small molecular DNA binders

DNA has been used in nature as carriers of heredity information for billions of years. The last four decades have witnessed the success of DNA nanotechnology, an interdisciplinary research area in which DNA is used as a synthetic engineering tool rather than a carrier of genetic information. The growth of DNA nanotechnology crosses the boundaries between physics, chemistry, biology and computer science and enables DNA to function as an electronic component, substrate, drug delivery vector and data storage unit. The hybridization of DNA strictly follows the by Watson-Crick rule; thus, DNA base pairs are the most reliable and predictable building block in the true nanometer range. New methods and designs for controlling DNA hybridization have always provided the most essential momentum for the development of DNA nanotechnology. When small molecules bind to the double helical structure of DNA, either through intercalation or minor groove binding, the stability and functionality of DNA may be significantly altered, which is a fundamental basis for many therapeutic and sensing applications. Herein, we reveal, for the first time, that small molecular DNA binders may also be used to program the reaction pathways of toehold-mediated DNA strand displacement, an elementary building block in DNA nanotechnology

DNA Topology Influences Molecular Machine Lifetime in Human Serum

DNA nanotechnology holds the potential for enabling new tools for biomedical engineering, including diagnosis, prognosis, and therapeutics. However, applications for DNA devices are thought to be limited by rapid enzymatic degradation in serum and blood. Here, we demonstrate that a key aspect of DNA nanotechnology—programmable molecular shape—plays a substantial role in device lifetimes. These results establish the ability to operate synthetic DNA devices in the presence of endogenous enzymes and challenge the textbook view of near instantaneous degradation

The effect of topology on the structure and free energy landscape of DNA kissing complexes

We use a recently developed coarse-grained model for DNA to study kissing complexes formed by hybridization of complementary hairpin loops. The binding of the loops is topologically constrained because their linking number must remain constant. By studying systems with linking numbers -1, 0 or 1 we show that the average number of interstrand base pairs is larger when the topology is more favourable for the right-handed wrapping of strands around each other. The thermodynamic stability of the kissing complex also decreases when the linking number changes from -1 to 0 to 1. The structures of the kissing complexes typically involve two intermolecular helices that coaxially stack with the hairpin stems at a parallel four-way junction

DNA Computing by Self-Assembly

Information and algorithms appear to be central to biological organization and processes, from the storage and reproduction of genetic information to the control of developmental processes to the sophisticated computations performed by the nervous system. Much as human technology uses electronic microprocessors to control electromechanical devices, biological organisms use biochemical circuits to control molecular and chemical events. The engineering and programming of biochemical circuits, in vivo and in vitro, would transform industries that use chemical and nanostructured materials. Although the construction of biochemical circuits has been explored theoretically since the birth of molecular biology, our practical experience with the capabilities and possible programming of biochemical algorithms is still very young

Design of Geometric Molecular Bonds

An example of a nonspecific molecular bond is the affinity of any positive charge for any negative charge (like-unlike), or of nonpolar material for itself when in aqueous solution (like-like). This contrasts specific bonds such as the affinity of the DNA base A for T, but not for C, G, or another A. Recent experimental breakthroughs in DNA nanotechnology demonstrate that a particular nonspecific like-like bond ("blunt-end DNA stacking" that occurs between the ends of any pair of DNA double-helices) can be used to create specific "macrobonds" by careful geometric arrangement of many nonspecific blunt ends, motivating the need for sets of macrobonds that are orthogonal: two macrobonds not intended to bind should have relatively low binding strength, even when misaligned. To address this need, we introduce geometric orthogonal codes that abstractly model the engineered DNA macrobonds as two-dimensional binary codewords. While motivated by completely different applications, geometric orthogonal codes share similar features to the optical orthogonal codes studied by Chung, Salehi, and Wei. The main technical difference is the importance of 2D geometry in defining codeword orthogonality.Comment: Accepted to appear in IEEE Transactions on Molecular, Biological, and Multi-Scale Communication