DNA-Templated Assembly of Protein Complexes at Nanoscale

Nanotechnology, 2005

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.

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.

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.

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

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

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.

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

Nano Letters, 2005

We demonstrate the precise control of periodic spacing between individual protein molecules by programming the self-assembly of DNA tile templates. In particular, we report the application of two self-assembled periodic DNA structures, two-dimendional nanogrids, and one-dimensional nanotrack, as template for programmable self-assembly of streptavidin protein arrays with controlled density.

Chemical Research in Chinese Universities, 2020

DNA nanotechnology enables precise organization of nanoscale objects with extraordinarily structural programmability. Self-assembled DNA nanostructures possess a lot of interesting features, such as designable size and shape, and structural addressability at nanometer scale. Taking advantage of these properties, DNA n anostructures could work as templates or molds for the controllable synthesis of functional nanomaterials, such as organic macromolecules, metallic or inorganic nonmetallic nanomaterials. In this review, we summarize the recent progress in the shape-controllable synthesis of functional nanomaterials on DNA templates. The potential application fields of these nanomaterials are also discussed.

Nano Research, 2013

In order to exploit the outstanding physical properties of one-dimensional (1D) nanostructures such as carbon nanotubes and semiconducting nanowires and nanorods in future technological applications, it will be necessary to organize them on surfaces with precise control over both position and orientation. Here, we use a 1D rigid DNA motif as a model for studying directed assembly at the molecular scale to lithographically patterned nanodot anchors. By matching the inter-nanodot spacing to the length of the DNA nanostructure, we are able to achieve nearly 100% placement yield. By varying the length of single-stranded DNA linkers bound covalently to the nanodots, we are able to study the binding selectivity as a function of the strength of the binding interactions. We analyze the binding in terms of a thermodynamic model which provides insight into the bivalent nature of the binding, a scheme that has general applicability for the controlled assembly of a broad range of functional nanostructures.