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DNA Microarrays (Advanced Methods)
by Ulrike A NuberDNA Microarrays introduces all up-to-date microarray platforms and their various applications. It is written for scientists who are entering the field of DNA microarrays as well as those already familiar with the technology, but interested in new applications and methods.
DNA Microarrays and Related Genomics Techniques: Design, Analysis, and Interpretation of Experiments
by David B. Allison T. Mark Beasley Jode W. EdwardsConsidered highly exotic tools as recently as the late 1990s, microarrays are now ubiquitous in biological research. Traditional statistical approaches to design and analysis were not developed to handle the high-dimensional, small sample problems posed by microarrays. In just a few short years the number of statistical papers providing approaches
DNA Modification Detection Methods (Springer Protocols Handbooks)
by Bi-Feng YuanUnderstanding the functional roles of DNA modifications relies on the accurate detection, quantification, and mapping of DNA modifications. Methods for deciphering DNA modifications have substantially improved over the last several years, which greatly revolutionize the field of DNA modifications. In addition to DNA cytosine methylation (5-methylcytosine, 5mC), the best-characterized epigenetic modification, many new modifications have been discovered to present in DNA in recent years. This book provides a comprehensive overview of available techniques and methods together with detailed step-by-step protocols for experimental procedures required to successfully perform analysis on various types of DNA modifications, including 5mC, 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), 5-carboxycytosine (5caC), 5-hydroxymethyluracil (5hmU), 5-formyluracil (5fU), N6-methyladenine (6mA), β-D-glucosyl-5-hydroxymethyluracil (base J) and 8-oxo-7,8-dihydroguanine (OG). This laboratory manual is a valuable source for biochemists and molecular biologists from different fields who wish to investigate DNA modifications.
DNA Modifications: Methods and Protocols (Methods in Molecular Biology #2198)
by Alexey Ruzov Martin GeringThis book provides an overview of methods and experimental protocols that are currently used to analyze the presence and abundance of non-canonical DNA nucleotides in different biological systems. Focusing particularly on the newly discovered and less studied DNA modifications that are enzymatically produced and are likely to play specific roles in various biological processes, the volume explores chromatography- and mass spectrometry-based techniques for the detection and quantification of DNA modifications, antibody-based approaches to study their spatial distribution in different cells and tissues, and methods to analyze their genomic distribution with the help of bioinformatics tools that interrogate the corresponding datasets. Written for the highly successful Methods in Molecular Biology series, 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. Authoritative and comprehensive, DNA Modifications: Methods and Protocols serves as an ideal guide to research scientists and PhD students in this rapidly developing discipline, and, thus, will ultimately contribute to deciphering the roles of non-canonical DNA nucleotides in different biological systems.
DNA Nanoscience: From Prebiotic Origins to Emerging Nanotechnology
by Kenneth DouglasDNA Nanoscience: From Prebiotic Origins to Emerging Nanotechnology melds two tales of DNA. One is a look at the first 35 years of DNA nanotechnology to better appreciate what lies ahead in this emerging field. The other story looks back 4 billion years to the possible origins of DNA which are shrouded in mystery. The book is divided into three parts comprised of 15 chapters and two Brief Interludes. Part I includes subjects underpinning the book such as a primer on DNA, the broader discipline of nanoscience, and experimental tools used by the principals in the narrative. Part II examines the field of structural DNA nanotechnology, founded by biochemist/crystallographer Nadrian Seeman, that uses DNA as a construction material for nanoscale structures and devices, rather than as a genetic material. Part III looks at the work of physicists Noel Clark and Tommaso Bellini who found that short DNA (nanoDNA) forms liquid crystals that act as a structural gatekeeper, orchestrating a series of self-assembly processes using nanoDNA. This led to an explanation of the polymeric structure of DNA and of how life may have emerged from the prebiotic clutter.
DNA Nanotechnology
by Bruno Samorì Giampaolo ZuccheriCurrently, nanotechnology is exposing the properties of DNA in unprecedented detail leading to new insights on the biological behavior and function of DNA. With the structural perfection of a self-assembling DNA nano-object, such as a DNA origami, it is clear how complex DNA is as a molecule, leading researchers to wonder how many different constructs could be designed and realized. DNA Nanotechnology: Methods and Protocols shows the procedures to follow in order to repeat methods that lead to such constructs or to the mastering of the characterization techniques used to study them. The chapters of this book are roughly divided into two parts: some cover the methods for preparing the nanostructures, from the rationale of the operations to the techniques for their handling, while other chapters deal more directly with advanced instrumental techniques that can manipulate and characterize molecules and nanostructures. Written in the highly successful Methods in Molecular BiologyTM series format, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and accessible, DNA Nanotechnology: Methods and Protocols serves as an ideal guide to scientists of all backgrounds and aims to ignite interest and spur activity in this young and rapidly growing research field. Includes cutting-edge methods and protocols Provides step-by-step detail essential for reproducible results Contains key notes and implementation advice from the experts
DNA Nanotechnology
by Chunhai FanDNA nanotechnology: From structure to function presents an overview of various facets of DNA nanotechnology, with a particular focus on their promising applications. This book is composed of three parts. Part I, Elements of DNA Nanotechnology, provides extensive basic information on DNA nanotechnology. Part II, Static and Dynamic DNA Nanotechnology, describes the design and fabrication of static and dynamic DNA nanostructures. Recent advances in DNA origami, DNA walkers and DNA nanodevices are all covered in this part. Part III, Applications of DNA Nanotechnology, introduces a variety of applications of DNA nanotechnology, including biosensing, computation, drug delivery, etc. Together these provide a comprehensive overview of this emerging area and its broad impact on biological and medical sciences. This book is intended for post-graduates, post-doctoral researchers and research scientists who are interested in expanding their knowledge of DNA nanotechnology. It provides readers an impression of the latest developments in this exciting filed.
DNA Nanotechnology for Cell Research: From Bioanalysis to Biomedicine
by Zhou NieDNA Nanotechnology for Cell Research Comprehensive coverage of DNA nanotechnology with a focus on its biomedical applications in disease diagnosis, gene therapy, and drug delivery Bringing together multidisciplinary aspects of chemical, material, and biological engineering, DNA Nanotechnology for Cell Research: From Bioanalysis to Biomedicine presents an overview of DNA nanotechnology with emphasis on a variety of different applications in cell research and engineering, covering a unique collection of DNA nanotechnology for fundamental research and engineering of living cells, mostly in cellulo and in vivo, for the first time. Broad coverage of this book ranges from pioneering concepts of DNA nanotechnology to cutting-edge reports regarding the use of DNA nanotechnology for fundamental cell science and related biomedical engineering applications in sensing, bioimaging, cell manipulation, gene therapy, and drug delivery. The text is divided into four parts. Part I surveys the progress of functional DNA nanotechnology tools for cellular recognition. Part II illustrates the use of DNA-based biochemical sensors to monitor and image intracellular molecules and processes. Part III examines the use of DNA to regulate biological functions of individual cells. Part IV elucidates the use of DNA nanotechnology for cell-targeted medical applications. Sample topics covered in DNA Nanotechnology for Cell Research include: Selections and applications of functional nucleic acid toolkits, including DNA/RNA aptamers, DNAzymes, and riboswitches, for cellular recognition, metabolite detection, and liquid biopsy. Developing intelligent DNA nanodevices implemented in living cells for amplified cell imaging, smart intracellular sensing, and in cellulo programmable biocomputing. Harnessing dynamic DNA nanotechnology for non-genetic cell membrane engineering, receptor signaling reprogramming, and cellular behavior regulation. Construction of biocompatible nucleic acid nanostructures as precisely controlled vehicles for drug delivery, immunotherapy, and tissue engineering. Providing an up-to-date tutorial style overview along with a highly valuable in-depth perspective, DNA Nanotechnology for Cell Research is an essential resource for the entire DNA-based nanotechnology community, including analytical chemists, biochemists, materials scientists, and bioengineers.
DNA Nanotechnology: Methods and Protocols (Methods in Molecular Biology #1811)
by Giampaolo ZuccheriThis second edition provides new and updated methods that detail new DNA nanotechnology techniques. Chapters focus on DNA origami nanostructures for arranging matter in the nanoscale or on their manipulation with the aid of other technologies, on procedures for making nucleic acids nanostructures of different kinds, and methods to simulate complex nanostructures or to use them in biosensing. 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.Authoritative and cutting-edge, DNA Nanotechnology: Methods and Protocols, Second Edition aims to ensure successful results in the further study of this vital field.
DNA Nanotechnology: Methods and Protocols (Methods in Molecular Biology #2901)
by Giampaolo ZuccheriThis fully updated volume explores methods to create and use nanostructures for characterizing, targeting, and controlling the behavior of cells. Experts from around the globe present their procedures for designing, preparing, characterizing, and using DNA nanostructures, especially towards biological or materials science applications. Additionally, the study of fundamental aspects of nucleic acids, such as their pairing and stacking energy measured with optical tweezers, as well as the targeted delivery of lipid-encapsulated nucleic acid drugs, is also provided to complete the landscape of nanoscale nucleic acids methods. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, DNA Nanotechnology: Methods and Protocols, Third Edition serves as an ideal resource for researchers working on applications of DNA nanostructures in biotechnology and nanomedicine.
DNA Recombination
by Hideo TsubouchiHomologous recombination is important in various aspects of DNA metabolism, including damage repair, replication, telomere maintenance, and meiosis, and yeast genetics has successfully provided a framework for the mechanism of homologous recombination. Divided into four convenient sections, DNA Recombination: Methods and Protocols covers recent techniques that best utilize the advantages of the yeast system, prescribing to the belief that yeast will keep serving as a great model organism to study homologous recombination. Chapters have also been included for such exceptions as the group of genes involved in recombination that are found solely in higher eukaryotes, such as BRCA2. And looking forward, a necessary step in the direction of understanding the homologous recombination process is to isolate the machine and let it work in a test tube. Understanding the design by studying the appearance and behavior of the machinery as a single molecule will be an important milestone toward understanding the mechanism of action of the machinery. Techniques covering these topics have also been included. Written in the successful Methods in Molecular BiologyTM series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, DNA Recombination: Methods and Protocols serves as an ideal guide to scientists of all backgrounds with its well-honed methodologies and strives to bring the reader to the next level of understanding regarding this vital subject.
DNA Repair Disorders
by Kaoru Sugasawa Chikako NishigoriThis book focuses on the clinical aspects of DNA repair disorders. Nucleotide excision repair is an important pathway for humans, as it is involved in biologically fundamental functions. This work presents clinical features together with the pathogenesis of DNA repair disorders such as Xertoderma Pigmentosum (XP). Studies on animal models are included as well. Clinical feature characteristics of each clinical subtype of XP are depicted according to the genotype, giving accurate and detailed information about the clinical features in terms of gene alterations, change of protein structure, and dysfunction in some of the repair pathways. This book is unique in that it provides detailed information on clinical features from more than 100 patients with XP-A, which is characterized by very severe manifestation of skin photosensitivity and neurological dysfunction. It will give readers important knowledge for understanding the concept and molecular mechanisms of DNA repair disorders. It also describes how to treat and care for patients with XP based on vast experience in clinical practice. DNA Repair Disorders will be a useful resource not only for physicians and basic scientists who are interested in and/or take care of patients with DNA repair disorders, but also dermatologists, neurologists, and researchers in the field of radiation biology and photobiology.
DNA Repair Protocols
by Pat VaughanWell-versed investigators describe in step-by-step detail a wide range of DNA repair activities, from single act-alone repair proteins to complex repair systems. These practical protocols not only detail the various repair activities found in cells, but also demonstrate the use of DNA repair proteins and systems as reagents in molecular biology and biotechnology. The techniques described here include mutation and polymorphism detection, which are useful in the search for disease genes and drug response genes, as well as for breeding and trait selection in animals and plants. Compact and highly practical, DNA Repair Protocols: Prokaryotic Systems provides expert guidance to both the DNA repair researcher studying the fundamental aspects of DNA repair and the applied researcher in human genetics and biotechnology.
DNA Repair Protocols: Mammalian Systems, 2nd Edition
by Daryl S. HendersonIn this second edition of a much praised laboratory manual devoted to eukaryotic systems, Daryl S. Henderson has refocused the book on mammalian cells, adding fourteen entirely new chapters and extensively revising many of the remaining chapters. The authors address a broad range of questions about practical mammalian DNA repair, including such arcana as "what is radioresistant DNA synthesis and how is it measured?" The techniques presented are readily reproducible and offer cutting-edge methods for cytogenetic analysis, measuring the cellular response to ionizing radiation, detecting single-strand (nicks) and double-strand DNA breaks, detecting the presence of "adducted" bases in DNA, and preparing mismatch repair (MMR) plasmid substrates. Among the highlights are excellent coverage of both base excision repair (BER) and nucleotide excision repair (NER), useful assays for identifying and quantifying UV-induced DNA lesions and DNA breakage, gene therapy, environmental mutagenesis and cancer, and gene targeting. The protocols follow the successful Methods in Molecular Biology™ series format, each offering step-by-step laboratory instructions, an introduction outlining the principles behind the technique, lists of the necessary equipment and reagents, and tips on troubleshooting and avoiding known pitfalls.<P><P> Authoritative and highly practical, DNA Repair Protocols: Mammalian Systems, Second Edition, offers investigators a wide variety of productive methods to explore and make new discoveries in the world of mammalian DNA repair.
DNA Repair and Replication: Mechanisms and Clinical Significance
by Roger J. Grand John J. ReynoldsDNA Repair and Replication brings together contributions from active researchers. The first part of this book covers most aspects of the DNA damage response, emphasizing the relationship to replication stress. The second part concentrates on the relevance of this to human disease, with particular focus on both the causes and treatments which make use of DNA Damage Repair (DDR) pathways.
DNA Repair of Cancer Stem Cells
by Stephanie M Cabarcas Lesley A Mathews Elain HurtThe existence of 'cancer stem cells' (CSCs) has been a topic of heated debate for the last few years within the field of cancer biology. Their continuous characterization in a variety of solid tumors has lead to an abundance of evidence supporting their existence. CSCs are believed to be responsible for resistance against conventional treatment regimes of chemotherapy and radiation, ultimately, leading to metastasis and patient demise. To help aid clinicians, pharmaceutical companies and academic labs investigating how to better kill these highly aggressive cells we have summarized the DNA repair mechanism(s) and their role in the maintenance and regulation of both normal and cancer stem cells. Our book represents a comprehensive investigation into the highly effective DNA repair mechanisms of CSCs and what we need to understand in order to develop more advanced therapies to eradicate them from patients. Currently, there are no other published works entirely on DNA repair and Cancer Stem Cells. In addition, our book provides a comprehensive overview of CSC isolation and characterization from a variety of solid tumor types.
DNA Replication
by Sonya Vengrova Jacob DalgaardSince the discovery of DNA structure and throughout the ensuing "DNA era", the field of DNA replication has expanded to cover a vast number of experimental systems. In DNA Replication: Methods and Protocols, expert researchers present a collection of techniques and approaches used to investigate DNA replication with an emphasis on the most recent technological developments. Beginning with several informative introductory review chapters, this extensive volume is organized for clarity while fully encouraging innovation by the mixing of methods to create new techniques. Written in the highly successful Methods in Molecular Biology(tm) series format, chapters contain brief introductions to the topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Comprehensive and cutting-edge, DNA Replication: Methods and Protocols provides an excellent tool for both established laboratories and individuals new to this exciting field of research.
DNA Replication
by Jacob Z. Dalgaard Sonya VengrovaSince the discovery of DNA structure and throughout the ensuing "DNA era", the field of DNA replication has expanded to cover a vast number of experimental systems. In DNA Replication: Methods and Protocols, expert researchers present a collection of techniques and approaches used to investigate DNA replication with an emphasis on the most recent technological developments. Beginning with several informative introductory review chapters, this extensive volume is organized for clarity while fully encouraging innovation by the mixing of methods to create new techniques. Written in the highly successful Methods in Molecular BiologyTM series format, chapters contain brief introductions to the topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Comprehensive and cutting-edge, DNA Replication: Methods and Protocols provides an excellent tool for both established laboratories and individuals new to this exciting field of research.
DNA Replication - Damage from Environmental Carcinogens
by Huidong ZhangThis book reviews the main concepts concerning DNA damage due to environmental carcinogens, the effects of DNA damage on DNA replication using a single DNA polymerase or DNA replisome, and the effects of carcinogens on various cell activities. It also introduces the detailed protocols for bypassing DNA damage. As we know, various environmental carcinogens are produced as a result of industry, agriculture, chemical engineering and vehicle exhaust in our daily life. It has been reported that the environmental carcinogens can be connected to tumors and cancer, directly threatening human health. In this regard, DNA replication is highly susceptible to damage. This book provides graduate students and researchers with an overview of the effects of environmental carcinogens on DNA replication and biological activities in cells. It offers important information for research in the areas of biochemistry, cell biology, medicine, toxicology and public health.
DNA Replication Control in Microbial Cell Factories
by Monika Glinkowska Lidia Boss Grzegorz WegrzynThis work describes the current knowledge of biochemical mechanisms regulating initiation of DNA replication in Escherichia coli, which focuses on the control of activity of the DnaA protein. Examples of direct linkages between DNA replication and other cellular processes are provided. In addition, similarities of the mechanisms of regulation of DNA replication operating in prokaryotic and eukaryotic cells are identified, and implications for understanding more complex processes, like carcinogenesis are suggested. Studies of recent years provided evidence that regulation of DNA replication in bacteria is more complex than previously anticipated. Multiple layers of control seem to ensure coordination of this process with the increase of cellular mass and the division cycle. Metabolic processes and membrane composition may serve as points where integration of genome replication with growth conditions occurs. It is also likely that coupling of DNA synthesis with cellular metabolism may involve interactions of replication proteins with other macromolecular complexes, responsible for various cellular processes. Thus, the exact set of factors participating in triggering the replication initiation may differ depending on growth conditions. Therefore, understanding the regulation of DNA duplication requires placing this process in the context of the current knowledge on bacterial metabolism, as well as cellular and chromosomal structure. Moreover, in both Escherichia coli and eukaryotic cells, replication initiator proteins were shown to play other roles in addition to driving the assembly of replication complexes, which constitutes another, yet not sufficiently understood, layer of coordinating DNA replication with the cell cycle.
DNA Replication, Recombination, and Repair
by Fumio Hanaoka Kaoru SugasawaThis book is a comprehensive review of the detailed molecular mechanisms of and functional crosstalk among the replication, recombination, and repair of DNA (collectively called the "3Rs") and the related processes, with special consciousness of their biological and clinical consequences. The 3Rs are fundamental molecular mechanisms for organisms to maintain and sometimes intentionally alter genetic information. DNA replication, recombination, and repair, individually, have been important subjects of molecular biology since its emergence, but we have recently become aware that the 3Rs are actually much more intimately related to one another than we used to realize. Furthermore, the 3R research fields have been growing even more interdisciplinary, with better understanding of molecular mechanisms underlying other important processes, such as chromosome structures and functions, cell cycle and checkpoints, transcriptional and epigenetic regulation, and so on. This book comprises 7 parts and 21 chapters: Part 1 (Chapters 1-3), DNA Replication; Part 2 (Chapters 4-6), DNA Recombination; Part 3 (Chapters 7-9), DNA Repair; Part 4 (Chapters 10-13), Genome Instability and Mutagenesis; Part 5 (Chapters 14-15), Chromosome Dynamics and Functions; Part 6 (Chapters 16-18), Cell Cycle and Checkpoints; Part 7 (Chapters 19-21), Interplay with Transcription and Epigenetic Regulation. This volume should attract the great interest of graduate students, postdoctoral fellows, and senior scientists in broad research fields of basic molecular biology, not only the core 3Rs, but also the various related fields (chromosome, cell cycle, transcription, epigenetics, and similar areas). Additionally, researchers in neurological sciences, developmental biology, immunology, evolutionary biology, and many other fields will find this book valuable.
DNA Sequencing
by Dr Luke AlpheyThe technique of DNA Sequencing lies at the heart of modern molecular biology. Since current methods were first introduced, sequence databases have grown exponentially, and are now an indispensable research tool. This up-to-date, practical guide is unique in covering all aspects of the methodology of DNA sequencing, as well as sequence analysis. It describes the basic methods (both manual and automated) and the more advanced techniques (for example, those based on PCR) before moving on to key applications. The final section focuses on the analysis of sequence data; it details the software available, and explains how the Internet can be used for accessing software and major databases.By explaining the options available and their merits, DNA Sequencing allows newcomers to the field to decide which method is the most suitable for their application. For experienced sequencers the book is a useful reference source for details of the less common techniques and as a means of updating knowledge.
DNA Sequencing Protocols
by Alison J.M. Hill Colin A GrahamColin Graham and a team of leading investigators and expert clinical scientists update the acclaimed first edition with a collection of powerful, up-to-date PCR-based methods for DNA sequencing, many suitable for human genome sequencing and mutation detection in human disease. This second edition offers new material on automated DNA sequencers, capillary DNA sequencers, heterozygote mutation detection, web-based sequencing databases and genome sequencing sites, and the human genome project. State-of-the-art and highly practical, DNA Sequencing Protocols, 2nd Edn. constitutes an essential laboratory handbook for geneticists and molecular biologists, offering concise, easy-to-follow methods that will work and impact today's genome sequencing projects.
DNA Sequencing Protocols
by Annette M. Griffin Hugh G. GriffinDNA Sequencing Protocols provides you with the knowledge to become a sequencing expert. An all-star cast of investigators covers virtually all aspects, including developments in cycle sequencing, sequencing PCR products, sequencing lambda and cosmids, multiplex sequencing, direct blotting electrophoresis, sequencing of chemiluminescence, and automated sequencing.
DNA Systems Under Internal and External Forcing: An Exploration Using Coarse-Grained Modelling (Springer Theses)
by Megan Clare EngelThe interactions of DNA with force are central to manifold fields of inquiry, including the de novo design of DNA nanostructures, the use of DNA to probe the principles of biological self-assembly, and the operation of cellular nanomachines. This work presents a survey of three distinct ways coarse-grained simulations can help characterize these interactions. A non-equilibrium energy landscape reconstruction technique is validated for use with the oxDNA model and a practical framework to guide future applications is established. A novel method for calculating entropic forces in DNA molecules is outlined and contrasted with existing, flawed approaches. Finally, a joint experimental-simulation study of large DNA origami nanostructures under force sheds light on design principles and, through vivid illustrations, their unfolding process. This text provides an accessible and exciting launching point for any student interested in the computational study of DNA mechanics and force interactions.