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 Design and Synthesis of Dynamically Controllable DNA Nanostructures written by Siddharth Agarwal and published by . This book was released on 2021 with total page 233 pages. Available in PDF, EPUB and Kindle. Book excerpt: Deoxyribonucleic acid (DNA) and Ribonucleic acid (RNA) are molecules that store and transmit genetic information and are present nearly all living organisms. The field of nucleic acid nanotechnology uses these molecules out of its biological context and employs it to build structures and then to connect their operation. Although DNA nanotechnology was originally developed to elucidate protein crystallization, recent developments in the field are testing the limits of its application towards a multitude of fields ranging from nanofabrication to computation. One of the important frontiers that remain to be addressed is the production of 'active' material that can interact with its environment and adapt to it intelligently, rivalling organelles present inside cells. This dissertation reports on the construction of responsive nucleic acid structures that can demonstrate autonomous function and capability to respond to physical and chemical inputs. As the first example, we show how the self-assembly process of monomers made out of DNA strands can be triggered into activation by specific chemical inputs, in our case RNA molecules to build tubular structures. These 'nanotubes' can be temporally controlled by simple molecular programs, mimicking the architecture used by biological cells to direct their internal scaffolds. Our molecular programs use enzymes to produce or degrade RNA molecules embedded in the DNA nanotubes. Our results indicate that RNA can be used as a fuel for assembly, and that genetic circuits and enzymes can be an integral part in the operation of active nanostructures. This activatable self-assembly technique could be used to create a programmable synthetic version of filaments whose operation may mimic the cytoskeleton. The second theme of this dissertation is the autonomous control of assembly and disassembly of nucleic acid nanotubes inside cell-sized environments. We used different designs to observe and control nucleation, polymerization and depolymerization steps in the self-assembly dynamics of encapsulated structures. The kinetics of growth and degradation of these encapsulated tubular structures were quantified using epi-fluorescence microscopy. We were also able to demonstrate the production of nucleotide assemblies with external stimuli, such as heat and light. These demonstrations can pave the way for designing and observing the functionality of responsive materials across the nanometer to micron size scales.
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 DNA Nanotechnology written by Chunhai Fan and published by Springer Nature. This book was released on 2020-09-07 with total page 406 pages. Available in PDF, EPUB and Kindle. Book excerpt: The series Topics in Current Chemistry Collections presents critical reviews from the journal Topics in Current Chemistry organized in topical volumes. The scope of coverage is all areas of chemical science including the interfaces with related disciplines such as biology, medicine and materials science. The goal of each thematic volume is to give the non-specialist reader, whether in academia or industry, a comprehensive insight into an area where new research is emerging which is of interest to a larger scientific audience. Each review within the volume critically surveys one aspect of that topic and places it within the context of the volume as a whole. The most significant developments of the last 5 to 10 years are presented using selected examples to illustrate the principles discussed. The coverage is not intended to be an exhaustive summary of the field or include large quantities of data, but should rather be conceptual, concentrating on the methodological thinking that will allow the non-specialist reader to understand the information presented. Contributions also offer an outlook on potential future developments in the field. The chapter "DNA-Programmed Chemical Synthesis of Polymers and Inorganic Nanomaterials" is available open access under a CC BY 4.0 License via link.springer.com.
Download or read book Protein Self Assembly written by Jennifer J. McManus and published by Humana. This book was released on 2020-08-08 with total page 266 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume explores experimental and computational approaches to measuring the most widely studied protein assemblies, including condensed liquid phases, aggregates, and crystals. The chapters in this book are organized into three parts: Part One looks at the techniques used to measure protein-protein interactions and equilibrium protein phases in dilute and concentrated protein solutions; Part Two describes methods to measure kinetics of aggregation and to characterize the assembled state; and Part Three details several different computational approaches that are currently used to help researchers understand protein self-assembly. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Thorough and cutting-edge, Protein Self-Assembly: Methods and Protocols is a valuable resource for researchers who are interested in learning more about this developing field.
Download or read book Emerging Applications of Nanoparticles and Architectural Nanostructures written by Abdel Salam Hamdy Makhlouf and published by William Andrew. This book was released on 2018-03-22 with total page 650 pages. Available in PDF, EPUB and Kindle. Book excerpt: Emerging Applications of Nanoparticles and Architecture Nanostructures: Current Prospects and Future Trends discusses the most important current applications of nanoparticles and architecture nanostructures in a comprehensive, detailed manner. The book covers major applications of nanoparticles and architecture nanostructures, taking into account their unusual shapes and high surface areas. In particular, coverage is given to applications in aerospace, automotive, batteries, sensors, smart textile design, energy conversion, color imaging, printing, computer chips, medical implants, pharmacy, cosmetics, and more. In addition, the book discusses the future of research in these areas. This is a valuable reference for both materials scientists, chemical and mechanical engineers working both in R&D and academia who want to learn more on how nanoparticles and nanomaterials are commercially applied. - Provides an in-depth look at the properties of nanoparticles and architecture nanostructures in terms of their applicability for industrial uses - Analyzes the most recent advances and industrial applications of different types of nanoparticles and architecture nanostructures, taking into account their unusual structures and compositions - Identifies novel nanometric particles and architectures that are of particular value for applications and the techniques required to use them effectively
Download or read book Artificially Controllable Nanodevices Constructed by DNA Origami Technology written by Yangyang Yang and published by Springer. This book was released on 2015-12-16 with total page 82 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this book, the author deals mainly with two topics: (1) single-molecule visualization of switching behaviors in the DNA nanoframe system utilizing different kinds of molecular switches through the use of high-speed atomic force microscope (AFM); (2) construction of photocontrollable DNA nanostructures in programmed patterns and direct visualization of the dynamic assembling process. Here, high-speed AFM was employed to observe the dynamic movements of single molecules. Compared to a traditional single-molecule analysis method, such as fluorescence spectroscopy or electron microscopy, high-speed AFM makes possible the real-time observation of molecule behaviors. DNA nanostructures were designed and assembled as scaffolds to incorporate interested biomolecules. The observations were carried out under robust conditions without complicated pretreatment. Moreover, the photoresponsive molecules were successfully assembled into around 100 nm-sized DNA nanostructures. The assembly/disassembly of nanostructures can be regulated reversibly by photoirradiation. This book explains how DNA origami has gradually become a useful tool for the investigation of biochemical interactions in defined nanospace. It also shows the possibility of DNA nanostructures acting as nanodevices for application in biological systems, serving as a good introduction to basic DNA nanotechnology.
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 written by Ramanathan Nagarajan and published by John Wiley & Sons. This book was released on 2019-01-07 with total page 364 pages. Available in PDF, EPUB and Kindle. Book excerpt: An introduction to the state-of-the-art of the diverse self-assembly systems Self-Assembly: From Surfactants to Nanoparticles provides an effective entry for new researchers into this exciting field while also giving the state of the art assessment of the diverse self-assembling systems for those already engaged in this research. Over the last twenty years, self-assembly has emerged as a distinct science/technology field, going well beyond the classical surfactant and block copolymer molecules, and encompassing much larger and complex molecular, biomolecular and nanoparticle systems. Within its ten chapters, each contributed by pioneers of the respective research topics, the book: Discusses the fundamental physical chemical principles that govern the formation and properties of self-assembled systems Describes important experimental techniques to characterize the properties of self-assembled systems, particularly the nature of molecular organization and structure at the nano, meso or micro scales. Provides the first exhaustive accounting of self-assembly derived from various kinds of biomolecules including peptides, DNA and proteins. Outlines methods of synthesis and functionalization of self-assembled nanoparticles and the further self-assembly of the nanoparticles into one, two or three dimensional materials. Explores numerous potential applications of self-assembled structures including nanomedicine applications of drug delivery, imaging, molecular diagnostics and theranostics, and design of materials to specification such as smart responsive materials and self-healing materials. Highlights the unifying as well as contrasting features of self-assembly, as we move from surfactant molecules to nanoparticles. Written for students and academic and industrial scientists and engineers, by pioneers of the research field, Self-Assembly: From Surfactants to Nanoparticles is a comprehensive resource on diverse self-assembly systems, that is simultaneously introductory as well as the state of the art.
Download or read book Nanomaterials in the Battle Against Pathogens and Disease Vectors written by Kaushik Pal and published by CRC Press. This book was released on 2022-02-23 with total page 325 pages. Available in PDF, EPUB and Kindle. Book excerpt: Nanomaterials in the Battle Against Pathogens and Disease Vectors presents an overview of the use of nanotechnology to mitigate pathogens of concern, and is the first book to discuss applications of nanotechnology in the fight against all three major domains of disease-causing pathogens. Bacteria, viruses, and parasites constitute the list of emerging and re-emerging pathogens of high priority. Nanotechnology has proven to be a groundbreaking success in the elimination, targeted toxicity, precise immunogenicity, diagnosis, and imaging of these major pathogens and disease vectors. This text discusses basic concepts and advanced applications for bacteria, viruses, and parasites. It describes the use of metallic and non-metallic nanoparticles and nanotoxicity, as well as presents future applications of nanotechnology in biological applications. This work is ideal for engineers and scientists across the interdisciplinary fields of materials science, biomedical engineering, biotechnology, and others concerned with mitigating the risk and effect of pathogens.
Download or read book Interfacing DNA Nanotechnology with Biological Systems written by Justin Conway and published by . This book was released on 2015 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: "Deoxyribonucleic acid (DNA) has evolved in nature to store and transfer the genetic information of all life on earth. The fidelity of information processing relies on the precise pairing through non-covalent interactions of a molecular code consisting of four unique nucleobases. By using this programmability DNA can be taken of a biological context and used as building material for the programmable assembly of nanostructures. The routine automated synthesis of DNA has allowed researchers to explore many different DNA architecture designs and applications leading to the creation of the diverse field now termed DNA nanotechnology. DNA nanotechnology has generated many examples of scaffolds, cages, and networks able to precisely position molecules for applications in therapeutics, diagnostics, light harvesting devices, nanopatterning and even molecular computing. The objective of this thesis is to expand the interface between DNA nanotechnology and biological systems. In this way, DNA nanostructures can be used as modular platforms for the design of cellular probes and drug delivery vehicles. We focus our efforts on examining DNA and lipid bilayer interactions as well as increasing DNA nanostructure serum stability.Chapter 1 of this thesis discusses the origins and evolution of the field of DNA nanotechnology and focuses on specific examples within all three major divisions of this field. Chapter 2 describes our work investigating spherically supported bilayers as a platform to land and reversibly assemble DNA cages. This work examines the dynamic addressability of the cages on bilayers, their diffusion properties and depth of anchored cages, and the bilayer templated assembly of DNA structures. Chapter 3 investigates the selective deposition of DNA tile networks on saturated and unsaturated supported lipid bilayers using three structurally different hydrophobic anchors. It is shown that correct network assembly only occurs with compatible packing between the DNA-anchor and the lipid alkyl chains. The variation of the anchor and bilayer chemistry generates switchable network morphologies and filamentous materials. Chapter 4 describes our research towards improving the serum stability of DNA nanostructures, using a combination of folding topology and small synthetic end modifications to the DNA. This work uses a DNA triangular prism cage formed from three DNA strands. It is shown that the folded architecture of these cages and small chemical modifications on the DNA ends significantly stabilize the single stranded DNA and the final cages from fetal bovine serum degradation. We also show how this cage can be fully ligated to create a closed structure with the highest observed serum stability. These projects intend to demonstrate new ways in which DNA nanotechnology can be applied to biological systems for both medicinal and material based applications." --
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 Dynamic DNA Origami Assemblies for Signal Transmission written by Andres Serrano Paladines and published by . This book was released on 2021 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Scaffolded DNA origami has emerged as a prevalent technique for the design and construction of nanostructures of specific size, geometry, and function. Specifically, this technology enables programming nanostructure functionality by defining structural, mechanical and dynamic properties. Recent advancements have focused on integrating individual dynamic nanostructures to create reconfigurable supramolecular systems. Subsequently, these functional systems can be triggered by biological or environmental inputs to undergo conformational changes capable of reconfiguring other materials, providing measurable readouts, or influencing biological processes. This work aims to expand on dynamic functions by developing a reconfigurable assembly where local conformational changes can be physically communicated to other parts of the assembly through cascaded motion. We have designed a dynamic DNA nanostructure that can be assembled into arrays that can reach length scales ~10-100 times larger than the individual structure. We have demonstrated proof-of-concept for propagating conformational changes across nanodevices. DNA strands specific to one end of the array initiate motion for the "trigger" structure at that end, which in turn propagates motion to a neighboring structure, and so on in a sequential manner. This propagated motion is designed to transmit a signal across large distances. Creating programmable hierarchical assemblies capable of driving directional motion or signal has become a key goal in DNA nanotechnology. These systems could lead to customizable molecular transport systems, programmable circuits, and the catalysis of biochemical reactions
Download or read book Molecular scale Simulations of Dynamic DNA Nanostructures written by Ze Shi and published by . This book was released on 2018 with total page 139 pages. Available in PDF, EPUB and Kindle. Book excerpt: Structural DNA nanotechnology, the assembly of rigid 3D structures of complex yet precise geometries, has recently been used to design dynamic, mechanically-compliant nanostructures with tunable equilibrium conformations and conformational distributions. Introduction of additional stimuli-responsive behavior in such dynamic nanostructures should further widen the possible applications of DNA nanotechnology. The overarching goal of this dissertation is to explore the potential of coarse-grained molecular modeling and simulations as a design tool for predicting the mechanical properties, the free energy landscape, and stimuli-responsive responsive behavior of dynamic DNA nanostructures. In the first part of this dissertation, coarse-grained molecular dynamics simulations are used to provide insights into the conformational dynamics of a set of mechanically compliant DNA nanostructures, namely, DNA origami hinges. An approach is also proposed for rapidly predicting equilibrium hinge angles from individual force-deformation behaviors of their single- and double-stranded DNA components. In the second part, molecular basis for the mechanism of salt-actuation of such DNA hinges is provided by computing their free energy landscape with respect to the hinge angle using a novel methodology. A simple analytical statistical-mechanical model is also introduced to model the actuation response curves obtained experimentally. This work provides some of the first molecular-scale insights into the conformational dynamics and ion-activated actuation of mechanically compliant DNA nanostructures, which should help guide the design and optimization of new nanodevices.
Download or read book Programmable Biomolecular Integration and Dynamic Behavior of DNA based Systems for Development of Biomedical Nano devices written by Jaeseung Hahn and published by . This book was released on 2019 with total page 157 pages. Available in PDF, EPUB and Kindle. Book excerpt: Departing from the traditional role as a carrier of genetic information, DNA has emerged as an engineering material for construction of nano-devices. The advances in the field of DNA nanotechnology have enabled design and synthesis of DNA nanostructures of arbitrary shapes and manipulation of the nanostructures' conformations in a programmable way. DNA-based systems offer potential applications in medicine by manipulating the biological components and processes that occur at the nanometer scale. To accelerate the translation of DNA-based systems for medical applications, we identified some of the challenges that are hindering our ability to construct biomedical nano-devices and addressed these challenges through advances in both structural and dynamic DNA nanotechnology. First, we tested the stability of DNA nanostructures in biological environments to highlight the necessity of and path towards protection strategies for prolonged integrity of biomedical nano-devices. Then, we constructed a platform for robust 3D molecular integration using DNA origami technique and implemented the platform for a nanofactory capable of production of therapeutic RNA to overcome the challenges in RNA delivery. Moreover, we established a mechanism to drive DNA devices by changing temperature with prolonged dynamic behavior that was previously challenging to accomplish without special modification of DNA and/or equipment not readily available in a typical lab setting. Together, the progress made in this thesis bring us another step closer to realization of medical applications of DNA nanotechnology by focusing on the challenges in both structural and dynamic aspects of the technology.
Download or read book Self assembling Biomaterials written by Helena S. Azevedo and published by Woodhead Publishing. This book was released on 2018-04-17 with total page 614 pages. Available in PDF, EPUB and Kindle. Book excerpt: Self-assembling biomaterials: molecular design, characterization and application in biology and medicine provides a comprehensive coverage on an emerging area of biomaterials science, spanning from conceptual designs to advanced characterization tools and applications of self-assembling biomaterials, and compiling the recent developments in the field. Molecular self-assembly, the autonomous organization of molecules, is ubiquitous in living organisms and intrinsic to biological structures and function. Not surprisingly, the exciting field of engineering artificial self-assembling biomaterials often finds inspiration in Biology. More important, materials that self-assemble speak the language of life and can be designed to seamlessly integrate with the biological environment, offering unique engineering opportunities in bionanotechnology. The book is divided in five parts, comprising design of molecular building blocks for self-assembly; exclusive features of self-assembling biomaterials; specific methods and techniques to predict, investigate and characterize self-assembly and formed assemblies; different approaches for controlling self-assembly across multiple length scales and the nano/micro/macroscopic properties of biomaterials; diverse range of applications in biomedicine, including drug delivery, theranostics, cell culture and tissue regeneration. Written by researchers working in self-assembling biomaterials, it addresses a specific need within the Biomaterials scientific community. - Explores both theoretical and practical aspects of self-assembly in biomaterials - Includes a dedicated section on characterization techniques, specific for self-assembling biomaterials - Examines the use of dynamic self-assembling biomaterials
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.
