DNA Nanoarchitectures: Steps towards Biological Applications

Angewandte Chemie International Edition, 2012

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

DNA origami refers to the technique of assembling single-stranded DNA template molecules into target two- and three-dimensional shapes at the nanoscale. This is accomplished by annealing templates with hundreds of DNA strands and then binding them through the specific base-pairing of complementary bases. The inherent properties of these DNA molecules—molecular recognition, self-assembly, programmability, and structural predictability—has given rise to intriguing applications from drug delivery systems to uses in circuitry in plasmonic devices. The first book to examine this important subfield, DNA Origami brings together leading experts from all fields to explain the current state and future directions of this cutting-edge avenue of study. The book begins by providing a detailed examination of structural design and assembly systems and their applications. As DNA origami technology is growing in popularity in the disciplines of chemistry, materials science, physics, biophysics, biology, and medicine, interdisciplinary studies are classified and discussed in detail. In particular, the book focuses on DNA origami used for creating new functional materials (combining chemistry and materials science; DNA origami for single-molecule analysis and measurements (as applied in physics and biophysics); and DNA origami for biological detection, diagnosis and therapeutics (medical and biological applications). DNA Origami readers will also find: A complete guide for newcomers that brings together fundamental and developmental aspects of DNA origami technology Contributions by a leading team of experts that bring expert views from different angles of the structural developments and applications of DNA origami An emerging and impactful research topic that will be of interest in numerous multidisciplinary areas A helpful list of references provided at the end of each chapter to give avenues for further study Given the wide scope found in this groundbreaking work, DNA Origami is a perfect resource for nanotechnologists, biologists, biophysicists, chemists, materials scientists, medical scientists, and pharmaceutical researchers.

Molecules

DNA origami nanocarriers have emerged as a promising tool for many biomedical applications, such as biosensing, targeted drug delivery, and cancer immunotherapy. These highly programmable nanoarchitectures are assembled into any shape or size with nanoscale precision by folding a single-stranded DNA scaffold with short complementary oligonucleotides. The standard scaffold strand used to fold DNA origami nanocarriers is usually the M13mp18 bacteriophage’s circular single-stranded DNA genome with limited design flexibility in terms of the sequence and size of the final objects. However, with the recent progress in automated DNA origami design—allowing for increasing structural complexity—and the growing number of applications, the need for scalable methods to produce custom scaffolds has become crucial to overcome the limitations of traditional methods for scaffold production. Improved scaffold synthesis strategies will help to broaden the use of DNA origami for more biomedical applic...

Journal of The American Chemical Society, 2009

Molecular self-assembly using DNA as a structural building block has proven to be an efficient route to the construction of nanoscale objects and arrays of increasing complexity. Using the remarkable "scaffolded DNA origami" strategy, Rothemund demonstrated that a long single-stranded DNA from a viral genome (M13) can be folded into a variety of custom two-dimensional (2D) shapes using hundreds of short synthetic DNA molecules as staple strands. More recently, we generalized a strategy to build customshaped, three-dimensional (3D) objects formed as pleated layers of helices constrained to a honeycomb lattice, with precisely controlled dimensions ranging from 10 to 100 nm. Here we describe a more compact design for 3D origami, with layers of helices packed on a square lattice, that can be folded successfully into structures of designed dimensions in a one-step annealing process, despite the increased density of DNA helices. A square lattice provides a more natural framework for designing rectangular structures, the option for a more densely packed architecture, and the ability to create surfaces that are more flat than is possible with the honeycomb lattice. Thus enabling the design and construction of custom 3D shapes from helices packed on a square lattice provides a general foundational advance for increasing the versatility and scope of DNA nanotechnology.

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

Journal of Materials Science Research, 2019

The versatility of the DNA origami approach of organizing nanoparticles at the nanometer scale, together with thiol chemistry have been used. These approaches were used to design DNA origami structures and to functionalize them with gold nanoparticles after designing attachment sites on the DNA origami structures. In all two structures were designed-a cross-like structure and a nanotube but only the nanotube structure was used to form the gold nanoparticle helices. Finally, use was made of the specific affinity interaction between biotin and streptavidin to connect the DNA origami templated AuNP helices to the cross-like structure. Agarose gel electrophoresis, UVvis spectroscopy and TEM were used to characterize the structure.

The DNA origami technique has emerged as one of the most versatile bottom-up nanofabrication methods due to its ability to construct well-defined complex three-dimensional nanostructures and guide assembly of functional nanoscale objects with unprecedented precision, high yields, and controlled stoichiometry. Nonetheless, limited compatibility with biologically relevant fluids and typical solvents utilized in nanofabrication often restricts applications of DNA origami-based assemblies and devices. Here we present an approach for coating DNA origami structures with silica. By careful adjustment of experiment parameters, we achieved reproducible growth of ultrathin silica shell in solution without agglomeration or deformation of DNA origami structures. The silica-coated structures are stable in water and exhibit an increased resistivity to nuclease-mediated degradation. In addition, the coated structures preserve their structural integrity in polar organic solvents. We anticipate that our results will aid further advancement of DNA origami techniques as the nanofabrication method.

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.

Small

The exceptional self-assembly properties of DNA, which are based on simple base-paring rules, make it a very promising construction material in the nanoworld. The development of the DNA-origami technique, which is based on the folding of long single-stranded DNA with the help of hundreds of short oligonucleotides (so-called staple strands), opened new routes to relatively simple and fast fabrication of two-and three-dimensional nanostructures of exceptional complexity. Since individual staple strands can be readily modifi ed with various functional groups, the DNA-origami structure can be used as a template for the organization of different materials, for example, proteins, metal nanoparticles, virus capsids, and carbon nanotubes, with nanometer-scale accuracy that is often not achievable with other state-of-the-art nanofabrication techniques. In other words, one can use the origami structure like a nanoscale electronic breadboard, in which a variety of (functional) components could be attached with nanometer resolution. Methods for the combination of such "nanobreadboards" with top-down fabrication approaches have been recently proposed. In addition, DNA-origami structures were used to assemble tracks for molecular walkers, [ 20 , 21 ] to follow chemical reactions on a single-molecule level, and to construct rulers for super-resolution microscopy. It is possible to fabricate DNA-origami templates with sizes up to a few micrometers. So far, origami templates have been mostly used for the assembly of objects that are round rather than elongated, for example, metal particles or proteins. However, in order to realize the full potential of DNA origami as a "nanobreadboard", methods for controlled positioning of more complex objects, such as nanowires, should

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.

Annual review of biomedical engineering, 2018

Structural DNA nanotechnology utilizes synthetic or biologic DNA as designer molecules for the self-assembly of artificial nanostructures. The field is founded upon the specific interactions between DNA molecules, known as Watson-Crick base pairing. After decades of active pursuit, DNA has demonstrated unprecedented versatility in constructing artificial nanostructures with significant complexity and programmability. The nanostructures could be either static, with well-controlled physicochemical properties, or dynamic, with the ability to reconfigure upon external stimuli. Researchers have devoted considerable effort to exploring the usability of DNA nanostructures in biomedical research. We review the basic design methods for fabricating both static and dynamic DNA nanostructures, along with their biomedical applications in fields such as biosensing, bioimaging, and drug delivery. Expected final online publication date for the Annual Review of Biomedical Engineering Volume 20 is Ju...

Nature Nanotechnology, 2009

The development of nanoscale electronic and photonic devices will require a combination of the high throughput of lithographic patterning and the high resolution and chemical precision afforded by self-assembly 1-4 . However, the incorporation of nanomaterials with dimensions of less than 10 nm into functional devices has been hindered by the disparity between their size and the 100 nm feature sizes that can be routinely generated by lithography. Biomolecules offer a bridge between the two size regimes, with sub-10 nm dimensions, synthetic flexibility and a capability for self-recognition. Here, we report the directed assembly of 5-nm gold particles into large-area, spatially ordered, two-dimensional arrays through the site-selective deposition of mesoscopic DNA origami 5 onto lithographically patterned substrates 6 and the precise binding of gold nanocrystals to each DNA structure. We show organization with registry both within an individual DNA template and between components on neighbouring DNA origami, expanding the generality of this method towards many types of patterns and sizes.

Angewandte Chemie, 2010

Nano …, 2011

Scaffolded DNA origami, a method to create self-assembled nanostructures with spatially addressable features, has recently been used to develop water-soluble molecular chips for labelfree RNA detection, platforms for deterministic protein positioning, and single molecule reaction observatories. These applications highlight the possibility of exploiting the unique properties and biocompatibility of DNA nanostructures in live, cellular systems. Herein, we assembled several DNA origami nanostructures of differing shape, size and probes, and investigated their interaction with lysate obtained from various normal and cancerous cell lines. We separated and analyzed the origami-lysate mixtures using agarose gel electrophoresis and recovered the DNA structures for functional assay and subsequent microscopic examination. Our results demonstrate that DNA origami nanostructures are stable in cell lysate and can be easily separated from lysate mixtures, in contrast to natural, single-and double-stranded DNA. Atomic force microscope (AFM) and transmission electron microscope (TEM) images show that the DNA origami structures are fully intact after separation from cell lysates and hybridize to their targets, verifying the superior structural integrity and functionality of self-assembled DNA origami nanostructures relative to conventional oligonucleotides. The stability and functionality of DNA origami structures in cell lysate validate their use for biological applications, for example, as programmable molecular rafts or disease detection platforms.