Microarray technology provides a highly sensitive and precise te- nique for obtaining information from biological samples, with the added advantage that it can handle a large number of samples simultaneously that may be analyzed rapidly. Researchers are applying microarray technology to understand gene expression, mutation analysis, and the sequencing of genes. Although this technology has been experimental, and thus has been through feasibility studies, it has just recently entered into widespread use for advanced research. The purpose of DNA Arrays: Methods and Protocols is to provide instruction in designing and constructing DNA arrays, as well as hybridizing them with biological samples for analysis. An additional purpose is to p- vide the reader with a broad description of DNA-based array technology and its potential applications. This volume also covers the history of DNA arrays-from their conception to their ready off-the-shelf availability-for readers who are new to array technology as well as those who are well versed in this field. Stepwise, detailed experimental procedures are described for constructing DNA arrays, including the choice of solid support, attachment methods, and the general conditions for hybridization. With microarray technology, ordered arrays of oligonucleotides or other DNA sequences are attached or printed to the solid support using au- mated methods for array synthesis. Probe sequences are selected in such a way that they have the appropriate sequence length, site of mutation, and T .

Jac A. Nickoloff and Merl F. Hoekstra update and expand their two earlier acclaimed volumes (Vol. I: DNA Repair in Prokaryotes and Lower Eukaryotes and Vol. II: DNA Repair in Higher Eurkaryotes) with cutting-edge reviews by leading authorities of primary experimental findings about DNA repair processes in cancer biology. The reviews cover a wide range of topics from viruses and prokaryotes to higher eukaryotes, and include several new topics, among them the role of recombination in replication of damaged DNA, X-ray crystallographic analysis of DNA repair protein structures, DNA repair proteins and teleomere function, and the roles of BRCA1 and BRCA2 in DNA repair. Authoritative and up-to-date, DNA Damage and Repair, Vol. III: Advances from Phage to Humans surveys the rapidly moving research in DNA damage and repair, and explains the important functional relationships among different DNA repair pathways and the relationship between DNA repair pathways, cancer etiology, and cancer therapies.

The development of PCR, which enables extremely small amounts of DNA to be amplified, led to the rapid development of a multiplicity of a- lytical procedures to utilize this new resource for analysis of genetic variation and for the detection of disease causing mutations. The advent of capillary electrophoresis (CE), with its power to separate and analyze very small amounts of DNA, has also stimulated researchers to develop analytical procedures for the CE format. The advantages of CE in terms of speed and reproducibility of analysis are manifold. Further, the high sensitivity of detection, and the ab- ity to increase sample throughput with parallel analysis, has led to the creation of a full range of analysis of DNA molecules, from modified DNA-adducts and single-strand oligonucleotides through to PCR-amplified DNA fragments and whole chromosomes. Capillary Electrophoresis of Nucleic Acids focuses on such analytical protocols, which can be used for detection and analysis of mutations and modification, from precise DNA loci through to entire genomes of organisms. Important practical considerations for CE, such as the choice of separation media, electrophoresis conditions, and the influence of buffer additives and dyes on DNA mobility, are discussed in several key chapters and within particular applications.

Colin 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.

A comprehensive account of genomic rearrangement, focusing on the mechanisms of inversion, translocation, gene and genome duplication and gene transfer and on the patterns that result from them in comparative maps. Includes analyses of genomic sequences in organelles, prokaryotes and eukaryotes as well as comparative maps of the nuclear genomes in higher plants and animals. The book showcases a variety of algorithmic and statistical approaches to rearrangement and map data.

An outstanding panel of hands-on experts and developers of CE equipment describe in step-by-step fashion their best cutting-edge methods for the detection and analysis of DNA mutations and modifications, ranging from precise DNA loci to entire genomes of organisms. This first volume of the set, Introduction to the Capillary Electrophoresis of Nucleic Acids, covers the practical and theoretical considerations behind the use of capillary electrophoresis for the analysis of small oligonucleotides and modified nucleotides. Along with detailed instructions ensuring ready reproducibility, these protocols offer time-tested advice on instrumentation, signal detection, the capillary environment, and the integration of mass spectrometry with CE. Several chapters are devoted to the analysis of small therapeutic oligonucleotides, nucleosides, and ribonucleotides by CE. The companion volume, Practical Applications of Capillary Electrophoresis, addresses techniques for high-throughput analysis of DNA fragments using SNP detection, mutation detection, DNA sequencing methods, and DNA-ligand interactions. Comprehensive and up-to-date, the paired volumes of Capillary Electrophoresis of Nucleic Acids offer an authoritative guide with easy access to fast, versatile, reliable, and powerful technologies for all those basic and clinical investigators analyzing DNA variation today.

Corepressors are newly discovered assemblies of proteins that play essential roles in eukaryotic gene regulation. Recent discoveries about corepressors have provided new insights into the molecular basis of gene regulation, and have established surprising connections between the mechanisms of action of a wide variety of transcriptional regulators. The reviews in this volume critically discuss the nature, mechanisms of action, and physiological roles of corepressors in a diverse assortment of biological systems. Both basic and clinical investigators will be able to find relevant information. The comprehensive nature of the compilation, and the breadth of the reviews, are intended to provide the reader with an excellent introduction to the newly emergent and rapidly-growing field of corepressor research. A valuable and detailed reference guide.

Since the advent of the Human Genome Project, an increasing number of disease-causing genes have been discovered and, in some cases, genetic tests developed. However, this is only the first step. The second, much larger phase is the analysis of the total sequence. What does the rest of the DNA do? The answer to this question will be determined by computer prediction, expression profiling, and comparative genome analysis. Comparative Genomics covers such topics as identifying novel genes, determining gene function, control sequences, and developmental switches. The book aims to demonstrate how different approaches taken with model organisms, such as mutation studies, expression profiling of cDNAs, in situ localization of message and comparative genome analysis (both at the gene and nucleotide level) will aid in our understanding of the results coming out of the Human Genome Project and contribute significantly to our understanding of how genes function.

The field of DNA repair is vast and advancing rapidly. Recent investigations have begun to focus on the involvement of chromatin in the repair of broken DNA. Although I have no doubt that many breakthroughs in our understanding of chromatin, chromatin regulation, and DNA repair lie in our future, presently this is a new line in inquiry. As such there are many, many unanswered questions. Indeed, most of the correct questions have probably not even been asked yet. Here I have attempted to present a review of some of the current body of knowledge that may prove relevant to understanding the role of chromatin in DNA repair. Because the volume of research, and the relevant findings, come from a staggering array of labs, systems, and ideas I have focused primarily on findings developed from the study of the budding yeast Saccharomyces cerevisiae. Unfortunately, this means that I have left out a great deal of information. It is my hope, however, that the information I do detail, particularly in Chapter 1, will give a flavor for the scope of the problem and perhaps highlight some of the interesting directions this field is taking, or may one day take. I would also point out that the primary research that is presented herein is not in any way meant to represent the comprehensive scope of research being performed. To understand DNA repair will require investigation from innumerable labs, performed by innumerable researchers, moving in unexpected directions.

A comprehensive account of genomic rearrangement, focusing on the mechanisms of inversion, translocation, gene and genome duplication and gene transfer and on the patterns that result from them in comparative maps. Includes analyses of genomic sequences in organelles, prokaryotes and eukaryotes as well as comparative maps of the nuclear genomes in higher plants and animals. The book showcases a variety of algorithmic and statistical approaches to rearrangement and map data.

Forensic DNA analysis plays a central role in the judicial system. A DNA sample can change the course of an investigation with immense consequences. Because DNA typing is recognized as the epitome of forensic science, increasing public awareness in this area is vital. Through several cases, examples and illustrations, this book explains the basic principles of forensic DNA typing, and how it integrates with law enforcement investigations and legal decisions. Written for a general readership, Understanding Forensic DNA explains both the power and the limitations of DNA analysis. This book dispels common misunderstandings regarding DNA analysis and shows how astounding match probabilities such as one-in-a-trillion are calculated, what they really mean, and why DNA alone never solves a case.

When setting out to decide on the content of DNA Repair Protocols: Prokaryotic Systems, I was conscious of the need to portray the vast array of pathways and enzymatic activities that are part of the discipline of DNA repair. In addition to the classical DNA repair activities, I wanted to convey the significant interest that has been generated in recent years in the use of the proteins and repair systems as research tools, much like the use of restriction enzymes over the last few decades. Therefore, in addition to chapters deta- ing protocols for investigating specific repair activities, I have included s- eral chapters in this book on the applied use of DNA repair proteins and systems. The many years of research on bacterial DNA repair systems have allowed us to really understand the majority of DNA repair pathways in bac- rial cells. Building on this knowledge, research has lead to major advances in understanding mammalian DNA repair and uncovered its links to human d- ease, such as DNA mismatch repair and colon cancer, nucleotide excision repair and xeroderma pigmentosum, DNA helicase function in Bloom's s- drome, and so on. Such have been the advances that Science magazine iden- fied the collective DNA repair systems as its "Molecule of the Year" in 1994.

Biomedical research will be revolutionised by the current efforts to sequence the human genome and the genomes of model organisms. Of the newly sequenced genes, 50% code for proteins of unknown functions, while as little as 5% of sequences in mammalian genomes code for proteins. New, genome-wide approaches are needed to draw together the knowledge that is emerging simultaneously in a number of fields of genome research. This volume is a high-level survey of the newly emerging concepts of structural biology and functional genomics for biologists, biochemists and medical researchers interested in genome research. Topics included are chromosome and chromatin organisation, novel DNA and RNA structures, DNA flexibility, supercoiling, prediction of protein functions, strategies for large scale structural analysis, and computer modelling.

The field of eukaryotic DNA repair is enjoying a period of remarkable growth and discovery, fueled by technological advances in molecular bi- ogy, protein biochemistry, and genetics. Notable achievements include the molecular cloning of multiple genes associated with classical human repair disorders, such as xeroderma pigmentosum, Cockayne syndrome, and ataxia telangiectasia; elucidation of the core reaction of nucleotide excision repair (NER); the discovery that certain NER proteins participate not only in repair, but also in transcription; recognition of the crucial role played by mismatch repair processes in maintenance of genome stability and avoidance of cancer; the findings that the tumor suppressor protein p53 is mutated in many types of cancer, and has a key role in directing potentially malignant, genotoxin-d- aged cells towards an apoptotic fate; and the discovery and elaboration of DNA damage (and replication) checkpoints, which placed repair phenomen- ogy firmly within a cell-cycle context. Of course, much remains to be learned about DNA repair. To that end, DNA Repair Protocols: Eukaryotic Systems is about the tools and techniques that have helped propel the DNA repair field into the mainstream of biological research. DNA Repair Protocols: Eukaryotic Systems provides detailed, step-- step instructions for studying manifold aspects of the eukaryotic response to genomic injury. The majority of chapters describe methods for analyzing DNA repair processes in mammalian cells. However, many of those techniques can be applied with only minor modification to other systems, and vice versa.

The field of eukaryotic DNA repair is enjoying a period of remarkable growth and discovery, fueled by technological advances in molecular biol- ogy, protein biochemistry, and genetics. Notahle achievements include the molecular cloning of multiple genes associated with classical human repair disorders, such as xeroderma pigmentosum, Cockayne syndrome, and ataxia telangiectasia; elucidation of the core reaction of nucleotide excision repair (NER); the discovery that certain NER proteins participate not only in repair, but also in transcription; recognition of the crucial role played by mismatch repair processes in maintenance of genome stability and avoidance of cancer; the findings that the tumor suppressor protein p53 is mutated in many types of cancer, and has a key role in directing potentially malignant, genotoxin-dam- aged cells towards an apoptotic fate; and the discovery and elaboration of DNA darnage (and replication) checkpoints, which placed repair phenomenol- ogy firmly within a cell-cycle context. Of course, much remains to be learned about DNA repair. Tothat end, DNA Repair Protocols: Eukaryotic Systems is about the tools and techniques that have helped propel the DNA repair field into the mainstream of biological research. DNA Repair Protoco/s: Eukaryotic Systems provides detailed, step-by- step instructions for studying manifold aspects of the eukaryotic response to genomic injury. The majority of chapters describe methods for analyzing DNA repair processes in mammalian cells. However, many ofthose techniques can be applied with only minor modification to other systems, and vice versa.

In the past few years, antisense methodology has moved from in vitro studies to in vivo studies and first human trials. While the basic concept of antisense technology is simple, the methodological problems associated with its use are numerous and complex. Antisense- based methods have proven to be a field of research where careful attention to experimental protocols and appropriate controls is necessary. The Manual of Antisense Methodology emphasizes the application of antisense oligonucleotides, and is a guide for the identification of antisense and non-antisense effects in different experimental settings. The work is organized into three sections: antisense application in vitro, antisense application in vivo (animal models) and finally, clinical antisense studies. Where at all possible, the methods are described in sufficient detail to allow reproduction of a given experiment. The Manual of Antisense Methodology will be of interest to researchers in immunology, cancer research, pharmacology and internal medicine; and physicians conducting clinical studies in these fields.

Beginning with the Escherichia coli co protein, or bacterial DNA topoisomerase I, an ever-increasing number of enzymes has been identified that catalyze changes in the linkage of DNA strands. DNA topoisomerases are ubiquitous in nature and have been shown to play critical roles in most p- cesses involving DNA, including DNA replication, transcription, and rec- bination. These enzymes further constitute the cellular targets of a number of clinically important antibacterial and anticancer agents. Thus, further studies of DNA topology and DNA topoisomerases are critical to advance our und- standing of the basic biological processes required for cell cycle progression, cell division, genomic stability, and development. In addition, these studies will continue to provide critical insights into the cytofoxic action of drugs that target DNA topoisomerases. Such mechanistic studies have already played an important role in the development and clinical application of antimicrobial and chemotherapeutic agents. The two volumes of DNA Topoisomerase Protocols are designed to help new and established researchers investigate all aspects of DNA topology and the function of these enzymes. The chapters are written by prominent investigators in the field and provide detailed background information and st- by-step experimental protocols. The topics covered in Volume I; DNA Topology and Enzymes, range from detailed methods to analyze various aspects of DNA structure, from linking number, knotting/unknotting, site-specific recombi- tion, and decatenation to the overexpression and purification of bacterial and eukaryotic DNA topoisomerases from a variety of cell systems and tissues.

Damage to DNA by both exogenous and endogenous sources is increasingly regarded as highly important in the initiation and progression of cancer and in the occurance of other pathological events. DNA damage caused by reactive oxygen-derived species, also called oxidative DNA damage, is most the frequent type encountered by aerobic cells. Mechanistic studies of carcinogenesis indicate an important role of this type of damage to DNA. There is also strong evidence to support the role of oxidative DNA damage in the aging process. DNA damage is opposed in vivo by repair systems. If not repaired, DNA damage may lead to detrimental biological consequences. Therefore, the repair of DNA damage is regarded as one of the essential events in all life forms. In recent years the field of DNA repair has flourished due to new findings on DNA repair mechanisms and the molecular basis of cancer. A detailed knowledge of mechanisms of DNA damage and repair, and how individual repair enzymes function may lead to manipulation of DNA repair in cells and ultimately to an increase of the resistence of human cells to DNA-damaging agents. This volume covers the most recent devlopments in this research field and contains contributions from scientists working in the fields of biochemistry, molecular biology, enzymology, biomedical science, and radiation biology.

Sequence-specific DNA binding ligands, amongst which triple helix forming oligonucleotides are the most efficient as yet, represent promising tools in a number of fields. One of their most promising applications is as antiviral tools: they can specifically target a viral gene, even if it is integrated into the host genome, and be used to specifically inactivate the viral gene or even destroy the cells harboring this gene. However, from science fiction to science there remains a gap; and we are at the moment on the threshold of this fascinating field. Triple Helix Forming Oligonucleotides considers the different aspects of the design and improvement, current or future, of these molecules and their structural analysis, as well as their applications, with special emphasis on the attempts to obtain biological effects of these potentially important tools. What emerges is that the current state of the research is encouraging, and that these molecules are already useful in some biotechnology applications.

Cutting edge reviews by leading researchers illuminate key aspects of DNA repair in mammalian systems and its relationship to human genetic disease and cancer. Major topics include UV and X-Ray repair, repair of chemical damage, recombinational repair, mismatch repair, transcription-repair coupling, and the role of DNA repair in disease prevention. Extensive up-to-date references and rigorous peer-review of each chapter make this volume definitive and bring it to the active frontiers of research.

Evaluating the Statistical Significance of Multiple Distinct Local Alignments; S.F. Altscul. Hidden Markov Models for Human Genes: Periodic Patterns in Exon Sequence; S. Brunak. Identification of Muscle-Specific Transcriptional Regulatory Regions; J.W. Fickett. A Systematic Analysis of Gene Functions by the Metabolic Pathway Database; M. Kanehisa. Polymer Dynamics of DNA, Chromatin and Chromosomes; J. Langowski. Is Whole Human Genome Sequencing Feasible?; E.W. Myers. Sequence patterns Diagnostic of Structure and Function; T.F. Smith. Recognizing Functional Domains in Biological Sequences; G.D. Stormo. Stochastic Modelling in Molecular Genetics; P. Tautu. The Integrated Genomic Database (IGD): Enhancing the Productivity of Gene Mapping Projects; S.P. Bryant. Error Analysis of Genetic Linkage Data; R. Cottingham. Managing Accelerating Data Growth in the Genome Database; K.H. Fasman. Advances in Statistical Methods for Linkage Analysis; D.E. Weeks. Exploring Heterogeneous Molecular Biology Databases in the Context of the Object-Protocol Model; V.M. Markowitz. Comprehensive Genome Information Systems; O. Ritter. Visualizing the Genome; D.B. Searls. Data Management for Ligand-Based Drug Design; K. Aberer. 7 Additional Articles. Index.

Bacterial Genomes provides an in-depth review of the latest research on the structure and stability of microbial genomes, and the techniques used to analyze and "fingerprint" them. Maps of a variety of microorganisms are featured, along with articles describing their construction and relevant features. Extensive tables summarizing the different types of techniques available to analyze the genomes of these microorganisms are also presented. Among those who will find this text most useful are genome researchers, microbiologists, molecular biologists, bacteriologists, infectious disease researchers, and molecular evolutionary biologists. Researchers and students working in the field of molecular evolution in general will also be interested in this book since microbes are such popular model systems.

Environmental DNA (eDNA) refers to DNA that can be extracted from environmental samples (such as soil, water, feces, or air) without the prior isolation of any target organism. The analysis of environmental DNA has the potential of providing high-throughput information on taxa and functional genes in a given environment, and is easily amenable to the study of both aquatic and terrestrial ecosystems. It can provide an understanding of past or present biological communities as well as their trophic relationships, and can thus offer useful insights into ecosystem functioning. There is now a rapidly-growing interest amongst biologists in applying analysis of environmental DNA to their own research. However, good practices and protocols dealing with environmental DNA are currently widely dispersed across numerous papers, with many of them presenting only preliminary results and using a diversity of methods. In this context, the principal objective of this practical handbook is to provide biologists (both students and researchers) with the scientific background necessary to assist with the understanding and implementation of best practices and analyses based on environmental DNA.

nd During June 13 -June 23 1996, the 2 EL. B. A. Foundation course on Genome, a NATO Advanced Study Institute, was held at Marcian Marina, Isle of Elba, Italy, - sponsored by the North Atlantic Treaty Organization and the EL. B. A. Fundation. The subject of the course was "Genome Structure and Function" with participants selected worldwire from 15 afferent countries. The purpose of the course and of the resulting book is the study of DNA structure (from the primary to the quintemary) and gene expression in the control of cell function and cell cycle progression; the topics were presented by top experts, covering both structural (cbwn to the atomic resolution) and functional (cbwn to gene level) aspects. The topics were presented by top experts and scientists active in the field, with the goal to give an insight into modm problems of genome study and recent ochievements in related fielm of molecular and cell biology, genetic engineering, biochemistry and biophysics, oncology and biotechnology. This resulting book is intenred to give a broad perspecti ve of the current stand of these fields. The major emphasis is towarm a reep unrerstanang of DNA structure and function in intetphase and metaphase chromosomes, originating by the parallel biophysical (namely NMR X-Ray and neutron scattering, spectropolarimetry, image analysis, calorimetry) and biochemical study conwcted on a wire range of cell systems placing the emphasis on either the higher orrer DNA structure or gene structure and function.

Discusses the problem of structural-functional organization of eukaryotic cell nuclei with special emphasis on the genome spatial organization and functioning. The opening chapters describe the nuclear matrix and the fate of its components in the course of mitosis. In the next eight chapters the organization of chromosomal DNA into large loops and