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 Thermodynamics and Kinetics of DNA Origami Cross tile Array Formation written by Brett Michael Ward and published by . This book was released on 2017 with total page 65 pages. Available in PDF, EPUB and Kindle. Book excerpt: "As the cost to continue scaling photolithography to pattern smaller semiconducting devices increases exponentially, new materials and fabrication approaches are being sought to extend and enhance current capabilities. DNA nanostructures have been identified as a promising material for patterning nanoscale devices, and several studies have demonstrated the ability to program DNA nanostructures to self-assemble into large scale arrays. These DNA arrays can be designed to create the patterns necessary for fabricating semiconductor device features. However, these structures are far from ideal and contain a number of defects that limit the adoption of this approach for manufacturing. In order to create large defect-free DNA arrays, further study is needed into the fundamental mechanisms governing array formation. Toward this goal, the thermodynamics and kinetics of DNA array formation were investigated using a DNA origami cross-tile that assembles into arrays through DNA hybridization. The assembly of dimers, quadramers, and unbound arrays in solution from monomers with complementary dye and quencher labeled hybridization interfaces was monitored by observing the change in fluorescence of the solution as a function of temperature and over time under varying buffer conditions and temperatures. The melting temperature of each structure was measured and generally increased with an increasing number of active sticky-ends per monomer. Values for standard thermodynamic parameters were determined for each array design. The reaction kinetics data were fit with a second order reaction model, and the effective reaction rate increased with increasing buffer magnesium concentrations and increasing temperatures. Finally, it was determined that large, unbounded 2D DNA origami cross-tile arrays sediment out of solution in only a few hours. The findings of this study provide insight into the mechanisms of DNA array formation and establish practical ranges for key processing parameters."--Boise State University ScholarWorks.
Download or read book Thermodynamics and Kinetics of DNA Nanostructure Assembly written by Jeanette Nangreave and published by . This book was released on 2011 with total page 208 pages. Available in PDF, EPUB and Kindle. Book excerpt: The unique structural features of deoxyribonucleic acid (DNA) that are of considerable biological interest also make it a valuable engineering material. Perhaps the most useful property of DNA for molecular engineering is its ability to self-assemble into predictable, double helical secondary structures. These interactions are exploited to design a variety of DNA nanostructures, which can be organized into both discrete and periodic structures. This dissertation focuses on studying the dynamic behavior of DNA nanostructure recognition processes. The thermodynamics and kinetics of nanostructure binding are evaluated, with the intention of improving our ability to understand and control their assembly. Presented here are a series of studies toward this goal. First, multi-helical DNA nanostructures were used to investigate how the valency and arrangement of the connections between DNA nanostructures affect super-structure formation. The study revealed that both the number and the relative position of connections play a significant role in the stability of the final assembly. Next, several DNA nanostructures were designed to gain insight into how small changes to the nanostructure scaffolds, intended to vary their conformational flexibility, would affect their association equilibrium. This approach yielded quantitative information about the roles of enthalpy and entropy in the affinity of polyvalent DNA nanostructure interactions, which exhibit an intriguing compensating effect. Finally, a multi-helical DNA nanostructure was used as a model `chip' for the detection of a single stranded DNA target. The results revealed that the rate constant of hybridization is strongly dominated by a rate-limiting nucleation step.
Download or read book DNA Computing and Molecular Programming written by Yannick Rondelez and published by Springer. This book was released on 2016-08-16 with total page 204 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the 22nd International Conference on DNA Computing and Molecular Programming, DNA 22, held Munich, Germany, in September 16 The 11 full papers presented together with 10 invited and tutorial talks were carefully selected from 55 submissions Research in DNA computing and molecular programming draws together mathematics, computer science, physics, chemistry, biology, and nanotechnology to address the analysis, design, and synthesis of information-based molecular systems
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 Nanotechnology for Bioengineers written by Wujie Zhang and published by Springer Nature. This book was released on 2022-05-31 with total page 95 pages. Available in PDF, EPUB and Kindle. Book excerpt: Nanotechnology is an interdisciplinary field that is rapidly evolving and expanding. Significant advancements have been made in nanotechnology-related disciplines in the past few decades and continued growth and progression in the field are anticipated. Moreover, nanotechnology, omnipresent in innovation, has been applied to resolve critical challenges in nearly every field, especially those related to biological technologies and processes. This book, used as either a textbook for a short course or a reference book, provides state-of-the-art analysis of essential topics in nanotechnology for bioengineers studying and working in biotechnology, chemical/biochemical, pharmaceutical, biomedical, and other related fields. The book topics range from introduction to nanotechnology and nanofabrication to applications of nanotechnology in various biological fields. This book not only intends to introduce bioengineers to the amazing world of nanotechnology, but also inspires them to use nanotechnology to address some of the world's biggest challenges.
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 DNA Computing and Molecular Programming written by David Soloveichik and published by Springer. This book was released on 2013-09-19 with total page 217 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the 19th International Conference on DNA Computing and Molecular Programming, DNA 19, held in Tempe, AZ, USA, in September 2013. The 14 full papers presented were carefully selected from 29 submissions. The papers are organized in many disciplines (including mathematics, computer science, physics, chemistry, material science and biology) to address the analysis, design, and synthesis of information-based molecular systems.
Download or read book Structural and Thermodynamic Anaylsis of Self assembled DNA Cross tiles written by Lauren Hakker and published by . This book was released on 2012 with total page 27 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book DNA Computing and Molecular Programming written by David Soloveichik and published by Springer. This book was released on 2013-08-21 with total page 210 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the 19th International Conference on DNA Computing and Molecular Programming, DNA 19, held in Tempe, AZ, USA, in September 2013. The 14 full papers presented were carefully selected from 29 submissions. The papers are organized in many disciplines (including mathematics, computer science, physics, chemistry, material science and biology) to address the analysis, design, and synthesis of information-based molecular systems.
Download or read book A Computational Model for the Isothermal Assembly of Tiled DNA Nanostructures written by Benjamin Craig Steele and published by . This book was released on 2014 with total page 54 pages. Available in PDF, EPUB and Kindle. Book excerpt: Complex DNA nanostructures have proven difficult to assemble from starting materials. Inefficient nanostructure assembly constitutes a barrier to the widespread use of DNA nanotechnology and is difficult to investigate experimentally due to the complicated nature of the assembly. This work introduces a type of tile assembly model, the isothermal tile assembly model (iTAM). The iTAM seeks to capture the behavior of assembling DNA tile nanostructures to identify design factors and reaction conditions which improve assembly yields. Simulations using the iTAM model explain the experimental observation that only a narrow range of temperatures permit optimal isothermal assembly of tile-based DNA nanostructures. This narrow temperature range reflects a balance between the stabilization of non-designed interactions at low temperatures and the destabilization of the overall designed structure at high temperature. Simulations based on the iTAM are effective at estimating the temperature of optimal assembly unique to 25 two-dimensional tile designs, with an mean error of estimation of 4.6 degrees C. Results from the iTAM indicate that optimal assembly temperatures are determined largely by the strength of tile-tile domain interactions. For a given tile design, tile concentration and the length of time represent convenient axes of control over tile assembly. Kinetic trapping that blocks complete assembly of a tile design is likely to be overcome by increasing the both temperature and tile concentration in the assembly reaction. Such a change also substantially decreases the computationally predicted time required for complete assembly.
Download or read book DNA Computing and Molecular Programming written by Robert Brijder and published by Springer. This book was released on 2017-08-22 with total page 278 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the 23th International Conference on DNA Computing and Molecular Programming, DNA 23, held Austin, TX, USA, in September 2017. The 16 full papers presented were carefully selected from 23 submissions. Research in DNA computing aims to draw together mathematics, computerscience, physics, chemistry, biology, and nanotechnology to address the analysis, design, and synthesis of information-based molecular systems. The papers address all areas related to biomolecular computing such as: algorithms and models for computation with biomolecular systems; computational processes in vitro and in vivo; molecular motors and molecular robotics; studies of fault-tolerance and error correction; software tools for analysis, simulation, and design; synthetic biology and in vitro evolution; applications in engineering, physics, chemistry, biology, and medicine.
Download or read book Automation in Proteomics and Genomics written by Gil Alterovitz and published by John Wiley & Sons. This book was released on 2009-03-16 with total page 340 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the last decade DNA sequencing costs have decreased over a magnitude, largely because of increasing throughput by incremental advances in tools, technologies and process improvements. Further cost reductions in this and in related proteomics technologies are expected as a result of the development of new high-throughput techniques and the computational machinery needed to analyze data generated. Automation in Proteomics & Genomics: An Engineering Case-Based Approach describes the automation technology currently in the areas of analysis, design, and integration, as well as providing basic biology concepts behind proteomics and genomics. The book also discusses the current technological limitations that can be viewed as an emerging market rather than a research bottleneck. Topics covered include: molecular biology fundamentals: from ‘blueprint’ (DNA) to ‘task list’ (RNA) to ‘molecular machine’ (protein); proteomics methods and technologies; modelling protein networks and interactions analysis via automation: DNA sequencing; microarrays and other parallelization technologies; protein characterization and identification; protein interaction and gene regulatory networks design via automation: DNA synthesis; RNA by design; building protein libraries; synthetic networks integration: multiple modalities; computational and experimental methods; trends in automation for genomics and proteomics new enabling technologies and future applications Automation in Proteomics & Genomics: An Engineering Case-Based Approach is an essential guide to the current capabilities and challenges of high-throughput analysis of genes and proteins for bioinformaticians, engineers, chemists, and biologists interested in developing a cross-discipline problem-solving based approach to systems biology.
Download or read book Robust Self assembly written by Ho-Lin Chen and published by . This book was released on 2007 with total page 290 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Thermodynamics and Biological Applications of DNA Nanostructures written by Wei, Xixi and published by . This book was released on 2014 with total page 237 pages. Available in PDF, EPUB and Kindle. Book excerpt: DNA nanotechnology is one of the most flourishing interdisciplinary research fields. Through the features of programmability and predictability, DNA nanostructures can be designed to self-assemble into a variety of periodic or aperiodic patterns of different shapes and length scales, and more importantly, they can be used as scaffolds for organizing other nanoparticles, proteins and chemical groups. By leveraging these molecules, DNA nanostructures can be used to direct the organization of complex bio-inspired materials that may serve as smart drug delivery systems and in vitro or in vivo bio-molecular computing and diagnostic devices. In this dissertation I describe a systematic study of the thermodynamic properties of complex DNA nanostructures, including 2D and 3D DNA origami, in order to understand their assembly, stability and functionality and inform future design endeavors. It is conceivable that a more thorough understanding of DNA self-assembly can be used to guide the structural design process and optimize the conditions for assembly, manipulation, and functionalization, thus benefiting both upstream design and downstream applications. As a biocompatible nanoscale motif, the successful integration, stabilization and separation of DNA nanostructures from cells/cell lysate suggests its potential to serve as a diagnostic platform at the cellular level. Here, DNA origami was used to capture and identify multiple T cell receptor mRNA species from single cells within a mixed cell population. This demonstrates the potential of DNA nanostructure as an ideal nano scale tool for biological applications.
Download or read book DNA Computing written by Junghuei Chen and published by Springer Science & Business Media. This book was released on 2004-02-18 with total page 236 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the thoroughly refereed post-proceedings of the 9th International Workshop on DNA Based Computers, DNA9, held in Madison, Wisconsin, USA in June 2003. The 22 revised full papers presented were carefully selected during two rounds of reviewing and improvement from initially 60 submissions. The papers are organized in topical sections on new experiments and tools, theory, computer simulation and sequence design, self-assembly and autonomous molecular computation, experimental solutions, and new computing models.
Download or read book RNA Nanotechnology written by Bin Wang and published by CRC Press. This book was released on 2014-04-02 with total page 468 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the past few decades there has been incredible growth in "bionano"-related research, which has been accompanied by numerous publications in this field. Although various compilations address topics related to deoxyribonucleic acid (DNA) and protein, there are few books that focus on determining the structure of ribonucleic acid (RNA) and using RNA as building blocks to construct nanoarchitectures for biomedical and healthcare applications. RNA Nanotechnology is a comprehensive volume that details both the traditional approaches and the latest developments in the field of RNA-related technology. This book targets a wide audience: a broad introduction provides a solid academic background for students, researchers, and scientists who are unfamiliar with the subject, while the in-depth descriptions and discussions are useful for advanced professionals. The book opens with reviews on the basic aspects of RNA biology, computational approaches for predicting RNA structures, and traditional and emerging experimental approaches for probing RNA structures. This section is followed by explorations of the latest research and discoveries in RNA nanotechnology, including the design and construction of RNA-based nanostructures. The final segment of the book includes descriptions and discussions of the potential biological and therapeutic applications of small RNA molecules, such as small/short interfering RNAs (siRNAs), microRNAs (miRNAs), RNA aptamers, and ribozymes.
