Download or read book Self Assembly with DNA From Materials Design to Chromatin written by Joshua Paul Lequieu and published by . This book was released on 2017 with total page 180 pages. Available in PDF, EPUB and Kindle. Book excerpt: The ability to engineer the self-assembly of nano-scale objects to create highly ordered materials is of considerable scientific and practical interest. This new class of materials represents a powerful approach for engineering a next generation of devices, whose mechanical, optical, and electrical properties can be precisely tuned at the molecular scale. Though significant strides towards this goal have been achieved in recent years, the complexity achieved in engineered systems is still far surpassed by that achieved by nature. Precise self-assembly is achieved by nature through proteins and nucleic acids that fold into intricate, three-dimensional, and importantly, functional structures. A promising avenue towards improved engineered systems is to draw on discoveries from biophysics in order to inspire new approaches and paradigms for self-assembly and materials design. In this work, we explore the interplay between biophysics and engineering by exploring the self-assembly of DNA. Our discussion begins at the smallest length-scales of DNA, first by understanding the hybridization of DNA, and then at how hybridization can be used in materials to direct the self-assembly of gold nanoparticles. We report the first evidence of a tunable mechanical response in these assemblies, thereby suggesting the possibility of mechanical meta-materials constructed using DNA. Our discussion then proceeds to larger length scales, where we examine the biophysical processes that control the compaction of DNA into chromatin. Using a detailed molecular model, we explore the free energies and dynamics of smallest building block of chromatin, a protein-DNA complex called the nucleosome. Our results are in quantitative agreement with existing experimental measurements, and help to explain the molecular factors that dictate the first stages of DNA compaction into chromatin. Lastly, we present a multi-scale approach that can couple information across different length scales of chromatin in order to examine the folding of large regions DNA. By drawing on both the biophysics and engineering literature, the findings presented here suggest new approaches for materials design, and offer new paradigms for synthetic systems that seek to mimic the complexity achieved by nature.
Download or read book Molecular Self Assembly written by Alex Li Dequan and published by CRC Press. This book was released on 2012-12-20 with total page 464 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the past several decades, molecular self-assembly has emerged as one of the main themes in chemistry, biology, and materials science. This book compiles and details cutting-edge research in molecular assemblies ranging from self-organized peptide nanostructures and DNA-chromophore foldamers to supramolecular systems and metal-directed assemblies
Download or read book Self assembly of Complex DNA Nanostructures and Reconfigurable DNA Devices written by Fei Zhang and published by . This book was released on 2015 with total page 332 pages. Available in PDF, EPUB and Kindle. Book excerpt: Deoxyribonucleic acid (DNA) has emerged as an excellent molecular building block for nanoconstruction in addition to its biological role of preserving genetic information. Its unique features such as predictable conformation and programmable intra- and inter-molecular Watson-Crick base pairing interactions make it a remarkable engineering material. A variety of convenient design rules and reliable assembly methods have been developed to engineer DNA nanostructures. The ability to create designer DNA architectures with accurate spatial control has allowed researchers to explore novel applications in directed material assembly, structural biology, biocatalysis, DNAcomputing, nano-robotics, disease diagnosis, and drug delivery. This dissertation focuses on developing the structural design rules for "static" DNA nano-architectures with increasing complexity. By using a modular self-assembly method, Archimedean tilings were achieved by association of different DNA motifs with designed arm lengths and inter-tile sticky end interactions. By employing DNA origami method, a new set of design rules was created to allow the scaffolds to travel in arbitrary directions in a designed geometry without local symmetry restrictions. Sophisticated wireframe structures of higher-order complexity were designed and constructed successfully. This dissertation also presents the use of "dynamic" DNA nanotechnology to construct DNA origami nanostructures with programmed reconfigurations.
Download or read book Dna Nanotechnology For Bioanalysis From Hybrid Dna Nanostructures To Functional Devices written by Giuseppe Domenico Arrabito and published by World Scientific. This book was released on 2017-09-25 with total page 216 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is intended for non-specialists and students, presenting a unique introduction to the field of DNA nanotechnology. The primary focus is on the extraordinary advantages of specificity and sensitivity obtained by integrating DNA nanostructures in bioanalytical devices.DNA Nanotechnology for Bioanalysis provides a concise and rigorous description for the fabrication of various types of functional nanostructures by optimized software-aided high-yield synthesis. Following this is the explanation of methods to decorate these nanostructures with molecules such as proteins, metal nanoparticles or bioorganic moieties covalently bonded onto DNA via self-assemblage processes. Also provided is a concise review on non-canonical DNA structures (such as G-quadruplexes) and their targeting by small molecules for applications in pharmacology. Finally, it describes the exciting applications of DNA nanostructures in life sciences and nanomedicine, including ultraspecific molecular delivery, control of cell behavior, analysis of cell lysate and DNA-based nano-tools for super-resolution sub-cellular imaging.
Download or read book Structural DNA Nanotechnology written by Nadrian C. Seeman and published by Cambridge University Press. This book was released on 2015 with total page 269 pages. Available in PDF, EPUB and Kindle. Book excerpt: Written by the founder of the field, this is a comprehensive and accessible introduction to structural DNA nanotechnology.
Download or read book Thermodynamics and Kinetics of DNA Tile based Self assembly written by Shuoxing Jiang and published by . This book was released on 2016 with total page 225 pages. Available in PDF, EPUB and Kindle. Book excerpt: Deoxyribonucleic acid (DNA) has emerged as an attractive building material for creating complex architectures at the nanometer scale that simultaneously affords versatility and modularity. Particularly, the programmability of DNA enables the assembly of basic building units into increasingly complex, arbitrary shapes or patterns. With the expanding complexity and functionality of DNA toolboxes, a quantitative understanding of DNA self-assembly in terms of thermodynamics and kinetics, will provide researchers with more subtle design guidelines that facilitate more precise spatial and temporal control. This dissertation focuses on studying the physicochemical properties of DNA tile-based self-assembly process by recapitulating representative scenarios and intermediate states with unique assembly pathways. First, DNA double-helical tiles with increasing flexibility were designed to investigate the dimerization kinetics. The higher dimerization rates of more rigid tiles result from the opposing effects of higher activation energies and higher pre-exponential factors from the Arrhenius equation, where the pre-exponential factor dominates. Next, the thermodynamics and kinetics of single tile attachment to preformed "multitile" arrays were investigated to test the fundamental assumptions of tile assembly models. The results offer experimental evidences that double crossover tile attachment is determined by the electrostatic environment and the steric hindrance at the binding site. Finally, the assembly of double crossover tiles within a rhombic DNA origami frame was employed as the model system to investigate the competition between unseeded, facet and seeded nucleation. The results revealed that preference of nucleation types can be tuned by controlling the rate-limiting nucleation step.The works presented in this dissertation will be helpful for refining the DNA tile assembly model for future designs and simulations. Moreover, the works presented here could also be helpful in understanding how individual molecules interact and more complex cooperative bindings in chemistry and biology. The future direction will focus on the characterization of tile assembly at single molecule level and the development of error-free tile assembly systems.
Download or read book DNA Origami written by Masayuki Endo and published by John Wiley & Sons. This book was released on 2022-05-10 with total page 436 pages. Available in PDF, EPUB and Kindle. Book excerpt: DNA ORIGAMI Discover the impact and multidisciplinary applications of this subfield of DNA nanotechnology 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.
Download or read book Structural DNA Nanotechnology Design and Self assembly of 2D and 3D Crystalline Lattices written by Tong Wang and published by . This book was released on 2007 with total page 388 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Control and Optimization of Self assembly Systems written by Yu Gao and published by . This book was released on 2017 with total page 136 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Self Assembly by Instruction written by and published by . This book was released on 2012 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: In the field of nanoscience, if you can control how nanoparticles self-assemble in particular structures -- joining each other, for example, as molecules can form, atom-by-atom -- you can design new materials that have unique properties that industry needs. Nature already uses the DNA genetic code to instruct the building of specific proteins and whole organisms in both plants and people. Taking a cue from nature, scientists at BNL devised a way of using strands of synthetic DNA attached to the surface of nanoparticles to instruct them to self-assemble into specific nanoscale structures, clusters, and three-dimensional organizations. Novel materials designed and fabricated this way promise use in photovoltaics, energy storage, catalysis, cell-targeted systems for more effective medical treatments, and biomolecular sensing for environmental monitoring and medical applications. To find out more about the rapid evolution of this nanoassembly method and its applications, join Physicist Oleg Gang of the Center for Functional Nanomaterials (CFN) as he gives the 474th Brookhaven Lecture, titled "Self-Assembly by Instruction: Designing Nanoscale Systems Using DNA-Based Approaches." Gang, who has led this work at the CFN, will explain the rapid evolution of this nanoassembly method, and discuss its present and future applications in highly specific biosensors, optically active nano-materials, and new ways to fabricate complex architectures in a rational manner via self-assembly. Gang and his colleagues used the CFN and the National Synchrotron Light Source (NSLS) facilities to perform their groundbreaking research. At the CFN, the scientists used electron microscopes and optical methods to visualize the clusters that they fabricated. At the NSLS, they applied x-rays to study a particles-assembly process in solution, DNA's natural environment. Gang earned a Ph. D. in soft matter physics from Bar-Ilan University in 2000, and he was a Rothschild Fellow at Harvard University from 1999 to 2002. After joining BNL as a Goldhaber Fellow in 2002, he became an assistant scientist at the CFN in 2004. He became the CFN's leader for Soft and Biological Nanomaterials Theme Group in 2006, and earned the title of scientist in 2009. Gang has received numerous honors and recognitions, including the 2010 Gordon Battelle Prize for Scientific Discovery.
Download or read book Design and Self assembly of DNA Nano architectures for Bio therapeutic and Bio technological Applications written by Rufaro Charidza-Wylie Tafadzwa and published by . This book was released on 2015 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Rational Design of DNA as a Nanoscale Material written by Junhao Shawn Tan and published by . This book was released on 2013 with total page 152 pages. Available in PDF, EPUB and Kindle. Book excerpt: One of the fundamental challenges of nanoscience and nanotechnology today is to organize nanoparticles, now increasingly recognized as 'artificial atoms', into higher-ordered structures analogous to molecules, polymers, and crystals. Inorganic nanoparticles in particular have garnered significant interest for their unique size- and morphology-dependent properties in the nanoscale, much unlike bulk materials which typically possess constant physical properties. Furthermore, the collective properties of nanoparticle assemblies in well-defined spatial configurations and crystal lattices can result in a dramatically different electromagnetic coupling profile among nanoparticles as compared to those of materials in the bulk phase, isolated nanoparticles, and disordered nanoparticle assemblies. The potential for a new generation of designer materials and devices created from nanoparticle "atoms" spurred on developments in the nanoparticle assembly that included the rapid rise of DNA-based nanoparticle assembly. DNA has long been investigated as genetic material but has quickly emerged in the past decade as excellent "generic" polymer that can be potentially engineered to organize complex, functional systems through self-assembly. Aside from its high monodispersity and outstanding stability, DNA possess the unique advantage of programmability via Watson-Crick basepairing. In the last decade alone, DNA-based nanoparticle "molecules", "polymers" and "crystals" have been successfully demonstrated in a variety of formats, configurations and with different materials. In spite of the recent suc- cesses, there is still a tremendous lack of understanding on the nanoscale interactions that govern the assembly process, thus limiting the customizability, complexity, and utility of the final assembled product. The works discussed in this dissertation not only seek to challenge existing notions of DNA-based assembly but also to provide new insights into DNA-based nanoparticle assembly that could pave the way towards a blueprint for rational design of complex nanoparticle assemblies. In the following chapters, we explore how nanoparticles capped with linear DNA strands assemble into tunable crystals in various formats by rational control over DNA length, DNA sequence and ionic environment. In addition, we present how branched DNA can also be rationally designed to direct the assembly of nanoparticle molecules.
Download or read book Self assembly of Three dimensional Nucleic Acid Nanostructures written by Luvena Le-Yun Ong and published by . This book was released on 2016 with total page 149 pages. Available in PDF, EPUB and Kindle. Book excerpt: Patterning complex 3D features at the nanoscale offers potential applications for a wide range of fields from materials to medicine. While numerous methods have been developed to manipulate nanoscale materials, these methods are typically limited by their difficulty in creating arbitrary 3D patterns. Self-assembly of nucleic acids has emerged as a promising method for addressing this challenge due to the predictability and programmability of the material and its structure. While a diversity of DNA nanostructures have been designed by specifying complementarity rules between strands, creation of 3D nanostructures requires careful design of strand architecture, and patterns are often limited to a volume of 25 x 25 x 25 nm3 Here, we address the challenges in structural DNA nanotechnology by developing a modular DNA "brick" approach. These bricks are short, single-stranded oliogomers that can self-assemble in a single-pot reaction to a prescribed 3D shape. Using this modular approach, we demonstrate high efficiency in 3D design by generating 100 distinct, discrete 3D structures from a library of strands. We also created long-range ordering of channels, tunnels, and pores by growing micron-sized 3D periodic crystals made from DNA bricks. Finally, we applied this approach to control over 30,000 unique component strands to selfassemble into cuboids measuring over 100 nm in each dimension. These structures were further used to pattern highly complex cavities. Together, this work represents a simple, modular, and versatile method for 3D nanofabrication. This unique patterning capability of DNA bricks may enable development of new applications by providing a foundation for intricate and complex control of an unprecedented number of independent components.
Download or read book Design and Synthesis of Dynamically Assembling DNA Nanostructures written by John Paul Sadowski and published by . This book was released on 2014 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Kinetically controlled isothermal growth is fundamental to biological development, but it remains challenging to rationally design molecular systems that self-assemble isothermally into complex geometries via prescribed assembly and disassembly pathways. By exploiting the programmable chemistry of base pairing, sophisticated spatial and temporal control have both been demonstrated in DNA self-assembly, but largely as separate pursuits. This dissertation extends a new approach, called developmental self-assembly, that integrates temporal with spatial control by using a prescriptive molecular program to specify the kinetic pathways by which DNA molecules isothermally self-assemble into well-defined three-dimensional geometries.
Download or read book DNA Macromolecule Conjugates written by Karina Carneiro and published by . This book was released on 2013 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: "The remarkable molecular recognition specificity of DNA, combined with its structural and biological properties, makes it useful as a programmable and addressable building block for materials science. The materials constructed from nucleic acids have expanded the role of DNA and RNA beyond biology, into a useful component of advanced synthetic materials. The study of DNA self-assembly is rapidly evolving and will most likely find new and unforeseen applications ranging from medicine and biology to nanoelectronics and nano-optics. The error-free and predictable self-assembly of DNA over many length scales is necessary for their use as components of nanodevices and in nanomedicine. The work within this thesis describes an investigation of the self-assembly properties of DNA-macromolecule conjugates with a goal towards predictable long-range order. Conceptually, the work presented in this thesis can be divided into three parts. (1) The first part describes methods to introduce the long-range order achieved by block copolymer assemblies into DNA strands. We present the synthesis of DNA amphiphiles and their hierarchical assembly into nanofibers and ordered networks. (2) In the second part, we use a monodisperse 3D DNA nanoconstruct to direct alkyl chain aggregation below their critical micelle concentration (CMC) through DNA's base pairing ability. (3) The last part describes the hierarchical placement of DNA amphiphiles and of their assemblies along DNA nanotubes. The work described herein offers insight into the synthesis and self-assembly properties of DNA-macromolecule conjugates, and into their hierarchical self-assembly with DNA nanostructures. " --
Download or read book Reprogramming and Manipulating DNA Assembly Using Simple Self assembly Principles written by Nicole Avakyan and published by . This book was released on 2019 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: "Supramolecular chemistry is the "chemistry of molecular information". Information stored in the structural features of molecules is recognized and processed at the supramolecular level and drives the ever more complex organization of matter - from the formation of simple host-guest complexes, to the assembly of viral capsids and the emergence of life itself. The work presented in this thesis uses basic principles governing intermolecular interactions to manipulate the assembly of DNA, a molecule that exemplifies the concept of information storage in its structure. In Chapter 2, simple molecular recognition principles are applied to expand the DNA base-pairing alphabet. A small molecule, cyanuric acid, with three thymine-like faces, is determined to reprogram the assembly of poly(adenine) strands into micron-long fibers with a unique internal structure. Adenine residues and cyanuric acid molecules are shown to associate into hexameric rosettes that bring about the formation of poly(adenine) triplexes and subsequent polymerization into nanofibers. Fundamentally, this finding demonstrates that a small molecule can induce nucleic acid assembly, giving rise to a new type of structure from inexpensive, readily available materials. Further examination of the mechanisms involved in nanofiber formation in Chapter 3 uncovers that the supramolecular polymerization of poly(adenine) strands proceeds through a cooperative mechanism. A new methodology to analyse thermal hysteresis profiles provides a quantitative understanding of the kinetics and thermodynamics of the assembly process. In addition, key parameters influencing assembly are identified and can be tuned to modify nanofiber properties in potential nanomaterials applications. While hydrogen bonding and [pi]-stacking interactions dominate the co-assembly of poly(adenine) and cyanuric acid described in Chapters 2 and 3, a different combination of intermolecular interactions is used to manipulate the long-range assembly of DNA nanostructures into ordered networks in Chapter 4. Blunt-ended DNA tiles, or tiles lacking complementary single-stranded portions at the duplex ends, with and without a cholesterol anchoring moiety, are interfaced with lipid bilayers, a soft support with composition-dependent properties. The balance of pi-stacking interactions between DNA duplex ends, cholesterol-mediated nanostructure anchoring, electrostatic DNA binding to the bilayer surface, and the fluid nature of the lipid bilayer enable the formation of dynamic materials with long-range order and tunable morphology on a cell membrane-like support. In turn, these lattices represent a tool for organizing materials such as nanoparticles or proteins at a biological interface, with potential applications in cellular recognition, development of model systems for study of membrane proteins or plasmonics. Altogether, this thesis demonstrates that information encoded in molecular building blocks and the interplay between intermolecular interactions can be used to manipulate the assembly and long-range organization of DNA to achieve new structures and higher complexity. " --
Download or read book Hierarchical and Synergistic Assembly of Amphiphilic DNA Nanostructures written by Pongphak Chidchob and published by . This book was released on 2018 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: "DNA assembly offers a powerful molecular tool to create arbitrary structures with excellent size and shape control through selective assembly, sequence programmability and well-defined, rigid structure of DNA. As designer scaffolds, DNA materials have a tremendous potential for precise organization of molecules into any pattern. In most DNA-based constructions, Watson-Crick base-pairing serves as the only instruction rule. However, their efficiency can reach a limit when the design complexity increases. As a unique approach, supramolecular DNA assembly has emerged from the deliberate blend between the toolbox of supramolecular chemistry and DNA programmability to address this complexity-efficiency issue and to generate new structures and functions. The aim of this thesis is to integrate hydrophobic interactions as orthogonal instruction rules in the design and assembly of amphiphilic DNA nanostructures, through the use of small molecule- and polymer-DNA conjugates. Firstly, polymer-DNA conjugates are anisotropically organized on DNA cages. The polymer association modes are directed by their decoration geometry on DNA cages. A library of well-defined, hierarchical amphiphilic DNA nanostructures can be generated by polymer's sequence regulation. Secondly, to demonstrate the versatility of DNA cages in the structure-function design, multiple cholesterol units are site-specifically organized on DNA cubes to allow their binding to lipid vesicles. The membrane interactions of these nanostructures are dependent on the decoration geometry as well as structural flexibility. Finally, to further improve the stability of hydrophobic interactions, three chemical approaches are developed to crosslink the hydrophobic micellar cores of amphiphilic DNA nanostructures. Overall, the work presented herein demonstrate that there is a synergy between DNA base-pairing and hydrophobic interactions that lead to new or even unprecedented structural and functional modes of amphiphilic DNA nanostructures. The opportunity from this work could not only contribute to a better fundamental understanding of self-assembly, but also provide guidelines to rationally design target structures, which could facilitate the development of advanced materials for applications in materials science and biomedicine." --
