Peptide nucleic acids in materials science (original) (raw)
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Challenges and applications for self-assembled DNA nanostructures?
Lecture Notes in Computer Science, 2001
DNA self-assembly is a methodology for the construction of molecular scale structures. In this method, arti cially synthesized single stranded DNA self-assemble into DNA crossover molecules tiles. These DNA tiles have sticky ends that preferentially match the sticky ends of certain other DNA tiles, facilitating the further assembly into tiling lattices. We discuss key theoretical and practical challenges of DNA selfassembly, a s w ell as numerous potential applications. The self-assembly of large 2D lattices consisting of up to thousands of tiles have been recently demonstrated, and 3D DNA lattices may s o o n b e feasible to construct. We describe various novel DNA tiles with properties that facilitate self-assembly and their visualization by imaging devices such as atomic force microscope. We discuss bounds on the speed and error rates of the various types of self-assembly reactions, as well as methods that may minimize errors in self-assembly. W e brie y discuss the ongoing development of attachment chemistry from DNA lattices to various types of molecules, and consider application of DNA lattices assuming the development of such appropriate attachment chemistry from DNA lattices to these objects as a substrate for: a layout of molecular electronic circuit components, b surface chemistry, for example ultra compact annealing arrays, c molecular robotics; for manipulation of molecules using molecular motor devices. DNA self-assembly can, using only a small number of component tiles, provide arbitrarily complex assemblies. It can be used to execute computation, using tiles that specify individual steps of the computation. In this emerging new methodology for computation:-input is provided by sets of single stranded DNA that serve a s n ucleation sites for assemblies, and
Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra
Nature, 2008
DNA is renowned for its double helix structure and the base pairing that enables the recognition and highly selective binding of complementary DNA strands. These features, and the ability to create DNA strands with any desired sequence of bases, have led to the use of DNA rationally to design various nanostructures and even execute molecular computations . Of the wide range of self-assembled DNA nanostructures reported, most are one-or two-dimensional 5-9 . Examples of three-dimensional DNA structures include cubes 10 , truncated octahedra 11 , octohedra 12 and tetrahedra , which are all comprised of many different DNA strands with unique sequences. When aiming for large structures, the need to synthesize large numbers (hundreds) of unique DNA strands poses a challenging design problem 9,15 . Here, we demonstrate a simple solution to this problem: the design of basic DNA building units in such a way that many copies of identical units assemble into larger three-dimensional structures. We test this hierarchical self-assembly concept with DNA molecules that form three-point-star motifs, or tiles. By controlling the flexibility and concentration of the tiles, the one-pot assembly yields tetrahedra, dodecahedra or buckyballs that are tens of nanometres in size and comprised of four, twenty or sixty individual tiles, respectively. We expect that our assembly strategy can be adapted to allow the fabrication of a range of relatively complex three-dimensional structures.
Organic & Biomolecular Chemistry, 2006
We present a set of DNA supramolecular architectures based on the polymerization of discrete DNA tiles having the shape of parallelograms and designed to have a one-dimensional inter-tile connectivity. Tiles bind to each other with two connections, which have different thermal stabilities. We discuss how this difference in stability implies that the same monomeric tile can yield supramolecular polymers of different shapes just by changing the polymerization conditions. We show how this system reacts to external stimuli by interconverting between some of its possible states. Concurrently, we show how performing the polymerization on a surface can influence its outcome.
Self-assembled DNA Structures for Nanoconstruction
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
Templates for sequential assembly of DNA based nanostructures
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.
Functionalizing Designer DNA Crystals with a Triple-Helical Veneer
Angewandte Chemie International Edition, 2014
DNA is a very useful molecule for the programmed self-assembly of 2D and 3D nanoscale objects. [1] The design of these structures exploits Watson-Crick hybridization and strand exchange to stitch linear duplexes into finite assemblies. [2-4] The dimensions of these complexes can be increased by over five orders of magnitude through self-assembly of cohesive single-stranded segments (sticky ends). [5, 6] Methods that exploit the sequence addressability of DNA nanostructures will enable the programmable positioning of components in 2D and 3D space, offering applications such as the organization of nanoelectronics, [7] the direction of biological cascades, [8] and the structure determination of periodically positioned molecules by X-ray diffraction. [9] To this end we present a macroscopic 3D crystal based on the 3-fold rotationally symmetric tensegrity triangle [3, 6] that can be functionalized by a triplex-forming oligonucleotide on each of its helical edges.
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
Programmable assembly at the molecular scale: self-assembly of DNA lattices
Proceedings 2001 ICRA. IEEE International Conference on Robotics and Automation (Cat. No.01CH37164), 2001
DNA self-assembly is a methodology for the construction of molecular scale structures. In this method, arti cially synthesized single stranded DNA self-assemble into DNA crossover molecules tiles. These DNA tiles have sticky ends that preferentially match the sticky ends of certain other DNA tiles, facilitating the further assembly into tiling lattices. DNA self-assembly can, using only a small number of component tiles, provide arbitrarily complex assemblies. The self-assembly of large 2D lattices consisting of up to thousands of tiles have been recently demonstrated, and 3D DNA lattices may soon be feasible to construct. We describe various novel DNA tiles with properties that facilitate self-assembly and their visualization by imaging devices such as atomic force microscope. We discuss key theoretical and practical challenges of DNA self-assembly, a s w ell as numerous potential applications. We brie y discuss the ongoing development o f attachment c hemistry from DNA lattices to various types of molecules, and consider application of DNA lattices assuming the development of such appropriate attachment chemistry from DNA lattices to these objects as a substrate for: a molecular robotics; for manipulation of molecules using molecular motor devices, b layout of molecular electronic circuit components, c surface chemistry, for example ultra compact annealing arrays, We also discuss bounds on the speed and error rates of the various types of self-assembly reactions, as well as methods that may minimize errors in self-assembly.
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 .