DNA Modification Detection Methods

DNA Modification Detection Methods

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, ...

Author: Bi-Feng Yuan

Publisher: Humana

ISBN: 107161228X

Category: Medical

Page: 194

View: 361

Understanding 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.
Categories: Medical

Selective DNA Modification Using the Cu I Catalyzed Alkyne Azide Cycloaddition

Selective DNA Modification Using the Cu I  Catalyzed Alkyne Azide Cycloaddition

DNA. Photography: An. Ultrasensitive. DNA-Detection. Method. Based. on. Photographic. Techniques. This Section was published in: D. M. Hammond, A. Manetto, J. Gierlich, V. A. Azov, P. M. E. Gramlich, G. A. Burley, M. Maul and T. Carell, ...

Author: Philipp Gramlich

Publisher: Cuvillier Verlag

ISBN: 9783736927308

Category: Science

Page: 236

View: 181

Categories: Science

Synthese nat rlicher DNA Modifikationen und deren Detektion in DNA Identifikation und Totalsynthese eines neuartigen DNA Photoschadens

Synthese nat  rlicher DNA Modifikationen und deren Detektion in DNA   Identifikation und Totalsynthese eines neuartigen DNA Photoschadens

As described before, the standard methods for the detection of 5-Me dC were either unable to detect or methylated and ... because the low abundance of the modification would require the analysis of extremely large amounts of DNA to ...

Author: Martin Münzel

Publisher: Cuvillier Verlag

ISBN: 9783736938823

Category: Science

Page: 250

View: 792

In the human body almost all cells contain the same genetic material; however, individual cells can perform vastly different functions. This is only possible, if different genes are active in different cell types. Furthermore, every cell stems from the same zygote; Hence the genetic information in cells needs to undergo reprogramming during differentiation. These processes require precise time dependent and robust control of gene expression, i.e. both stable and dynamic gene activation and silencing. The 'ATCG' DNA base sequence alone cannot control these processes. To enable the regulation of gene activity, cytosine bases in DNA can be further modified. The presence of methylated cytosines is long known to silence genes and aberrant methylation is the reason for many diseases including cancer. Thus, DNA modification is one of the most fundamental events in epigenetics. To be able to detect methylated cytosines a methodology was developed that allows the efficient discrimination of cytosine and methylcytosine in DNA. The technique relies on different reaction products of the nucleosides with O-Allylhydroxylamine. These products exhibit different base pairing properties which can be readily detected by pyrosequencing. As a further DNA modification, methylcytosine can be oxidized to hydroxymethylcytosine. By using a stable isotope dilution LC-MS approach the exact distribution of hydroxymethylcytosine in the mammalian body was determined for the first time. Especially high amounts of the nucleoside are present in the central nervous system. The hydroxymethylcytosine levels increase during brain development and are strongly reduced in cancerous tissue. It was furthermore investigated, if hydroxymethylcytosine was subject to further oxidation to formylcytosine and carboxylcytosine which - after final decarboxylation or excision by a glycosylase - would be an attractive mechanism for active DNA demethylation. This study ultimately led to the identification of formylcytosine and carboxylcytosine as constituents of mammalian DNA in our laboratory and by collaboration partners. To enable the studies, natural and isotope labeled versions of the nucleosides were synthesized using Pd(0) catalyzed carbonylative couplings. This also allowed the design and synthesis of new phosphoramidite building blocks for the incorporation of hydroxymethylcytosine, formylcytosine and carboxylcytosine into DNA. Here, a cyclic carbamate was used as a protecting group in solid phase DNA synthesis for the first time. DNA is not only subject to natural modifications, but can also be damaged by exogenous factors, of which UV light is one of the most prominent. The influence of UV light on CpG dinucleotides - the site of epigenetic modification - was investigated and new UV light induced DNA photolesions (the C(4-8)G and G(8-4)C photolesions) were identified. The photoproducts feature a bond between the exocyclic amino group of cytosine and a carbon atom on the 5 membered ring of guanine. The structures were proven by a total synthesis which featured a challenging Buchwald-Hartwig coupling as a key step. The identification of the DNA lesions shows that UV light does not only harm the genome but that it also disturbs the epigenetic information.
Categories: Science

Rapid Detection Assays for Food and Water

Rapid Detection Assays for Food and Water

There are two ways in which genetic modifications in foods can be detected : by protein based methods or DNA based methods , each has limitations but are applicable under different circumstances . 2.2 Methodology Protein - based methods ...

Author: Stuart A. Clark

Publisher: Royal Society of Chemistry

ISBN: 0854047794

Category: Science

Page: 264

View: 683

Rapid Diagnostics Assays for Water and Food presents novel techniques used to detect harmful chemicals and microbial pathogens in foods and waters. The areas coverd include water microbiology, water chemistry, food microbology and food chemistry, which have both common and unique difficulties have to be overcome. The techniques employed range from highly efficient concentration and sample preparation methods, through cell culture to end detection. The detection methods covered include microscopy, biosensors, immunoassay, calorimeters, and molecular detection/identification.
Categories: Science

Bioanalytics

Bioanalytics

This book presents a comprehensive introduction into these analytical methods, including their physical and chemical backgrounds, as well as a discussion of the strengths and weakness of each method.

Author: Friedrich Lottspeich

Publisher: John Wiley & Sons

ISBN: 9783527694440

Category: Science

Page: 450

View: 623

Analytical methods are the essential enabling tools of the modern biosciences. This book presents a comprehensive introduction into these analytical methods, including their physical and chemical backgrounds, as well as a discussion of the strengths and weakness of each method. It covers all major techniques for the determination and experimental analysis of biological macromolecules, including proteins, carbohydrates, lipids and nucleic acids. The presentation includes frequent cross-references in order to highlight the many connections between different techniques. The book provides a bird's eye view of the entire subject and enables the reader to select the most appropriate method for any given bioanalytical challenge. This makes the book a handy resource for students and researchers in setting up and evaluating experimental research. The depth of the analysis and the comprehensive nature of the coverage mean that there is also a great deal of new material, even for experienced experimentalists. The following techniques are covered in detail: - Purification and determination of proteins - Measuring enzymatic activity - Microcalorimetry - Immunoassays, affinity chromatography and other immunological methods - Cross-linking, cleavage, and chemical modification of proteins - Light microscopy, electron microscopy and atomic force microscopy - Chromatographic and electrophoretic techniques - Protein sequence and composition analysis - Mass spectrometry methods - Measuring protein-protein interactions - Biosensors - NMR and EPR of biomolecules - Electron microscopy and X-ray structure analysis - Carbohydrate and lipid analysis - Analysis of posttranslational modifications - Isolation and determination of nucleic acids - DNA hybridization techniques - Polymerase chain reaction techniques - Protein sequence and composition analysis - DNA sequence and epigenetic modification analysis - Analysis of protein-nucleic acid interactions - Analysis of sequence data - Proteomics, metabolomics, peptidomics and toponomics - Chemical biology
Categories: Science

Capillary Electrophoresis of Nucleic Acids

Capillary Electrophoresis of Nucleic Acids

In these novel and wide-ranging volumes of Capillary Electrophoresis of Nucleic Acids, 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 ...

Author: Keith R. Mitchelson

Publisher: Humana Press

ISBN: 1617371866

Category: Science

Page: 484

View: 727

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 that permit use of this new resource for the analysis of genetic variation and for the detection of disease-causing mutations. The advent of capillary electrophoresis (CE), with its power to separate and a- lyze 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 analyses are manifold. Furthermore, the high s- sitivity of detection, and the ability to increase sample throughput with par- lel analysis, has led to the creation of a full range of analysis of DNA molecules, from modified DNA adducts and single-strand oligonucleotides through PCR-amplified DNA fragments and whole chromosomes. Capillary Elect- phoresis of Nucleic Acids focuses on analytical protocols that can be used for detection and analysis of mutations and modification, from precise DNA loci through 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.
Categories: Science

Nanotechnology in Biology and Medicine

Nanotechnology in Biology and Medicine

Using this method, multiplex detection of different DNA sequences has been demonstrated [36–38]. However, since modification of DNA target is required, methods using dye-labeled DNA are somewhat cumbersome.

Author: Tuan Vo-Dinh

Publisher: CRC Press

ISBN: 9781439893791

Category: Science

Page: 740

View: 786

The second edition of Nanotechnology in Biology and Medicine is intended to serve as an authoritative reference source for a broad audience involved in the research, teaching, learning, and practice of nanotechnology in life sciences. This technology, which is on the scale of molecules, has enabled the development of devices smaller and more efficient than anything currently available. To understand complex biological nanosystems at the cellular level, we urgently need to develop a next-generation nanotechnology tool kit. It is believed that the new advances in genetic engineering, genomics, proteomics, medicine, and biotechnology will depend on our mastering of nanotechnology in the coming decades. The integration of nanotechnology, material sciences, molecular biology, and medicine opens the possibility of detecting and manipulating atoms and molecules using nanodevices, which have the potential for a wide variety of biological research topics and medical uses at the cellular level. This book presents the most recent scientific and technological advances of nanotechnology for use in biology and medicine. Each chapter provides introductory material with an overview of the topic of interest; a description of methods, protocols, instrumentation, and applications; and a collection of published data with an extensive list of references for further details. The goal of this book is to provide a comprehensive overview of the most recent advances in instrumentation, methods, and applications in areas of nanobiotechnology, integrating interdisciplinary research and development of interest to scientists, engineers, manufacturers, teachers, and students.
Categories: Science

Environmental Health Perspectives

Environmental Health Perspectives

29-41 , 1983 New Methods for Detection of Low Levels of DNA Damage in Human Populations by William A. Haseltine , * ++ William ... This method has the advantage that low levels of DNA modifications , approximately 1 modified base per 10 ...

Author:

Publisher:

ISBN: MINN:30000010711830

Category: Electronic journals

Page: 160

View: 914

Categories: Electronic journals

Testing and Analysis of GMO containing Foods and Feed

Testing and Analysis of GMO containing Foods and Feed

... See Certified reference materials (CRMs) Croplife international detection methods database, 281–282 Crushing, ... 92–93 Enzyme-linked Immunosorbent Assay (ELISA), 92–96 tests for genetic modification crops, 96–100 EPSPS gene, ...

Author: Salah E. O. Mahgoub

Publisher: CRC Press

ISBN: 9781351713856

Category: Health & Fitness

Page: 288

View: 927

An increasing number of genetically modified organisms (GMOs) continues to be produced every day. In response to the concerns raised by the development of GMOs and their incorporation in foods and feed, guidelines and regulations to govern and control the use of GMOs and their products have been enacted. These regulations necessitated the design of methods to detect and analyse the presence of GMOs or their products in agriculture produce, food and feed production chains. Design of techniques and instruments that would detect, identify, and quantify GM ingredients in food and feed will help inspection authorities to relay reliable information to consumers who might be concerned about the presence of GM ingredients. Information generated by detection of GMOs in food and feed would be helpful for setting regulations that govern the use of GM components as well as for labeling purposes. Qualitative detection methods of GM-DNA sequences in foods and feeds have evolved fast during the past few years. There is continuous need for the development of more advanced multi-detection systems and for periodic updates of the databases related to these systems. Testing and Analysis of GMO-containing Foods and Feed presents updates and comprehensive views on the various methods and techniques in use today for the detection, identification and quantification of GMOs in foods and feed. The eleven book chapters cover recent developments on sample preparation techniques, immunoassays methods and the PCR technique used in GMO analysis, the use of biosensors in relation to GMO analysis, the application of nucleic acid microarrays for the detection of GMOs, validation and standardization methods for GMO testing, in addition to the type of reference material and reference methods used in GMO testing and analysis. Some of the ISO standards designed for identifying and detecting the presence of GM material in foods are also presented in the book.
Categories: Health & Fitness

Advanced Technologies for Meat Processing

Advanced Technologies for Meat Processing

the kind of change and its sequence context, the design of a routine detection method can be anything from straightforward to ... Not all DNA modifications yield proteomic changes and in these cases, protein testing will not be able to ...

Author: Fidel Toldrá

Publisher: CRC Press

ISBN: 9781498754606

Category: Technology & Engineering

Page: 721

View: 460

As with the first edition, the main goal of Advanced Technologies for Meat Processing is to provide the reader with recent developments in new advanced technologies for the full meat- processing chain. This book is written by distinguished international contributors with recognized expertise and excellent reputations, and brings together all the advances in a wide and varied number of technologies that are applied in different stages of meat processing. This second edition contains 21 chapters, combining updated and revised versions of several chapters with entirely new chapters that deal with new online monitoring techniques like hyperspectral imaging and Raman spectroscopy, the use of nanotechnology for sensor devices or new packaging materials and the application of omics technologies like nutrigenomics and proteomics for meat quality and nutrition. The book starts with the control and traceability of genetically modified farm animals, followed by four chapters reporting the use of online non-destructive monitoring techniques like hyperspectral imaging and Raman spectroscopy, real-time PCR for pathogens detection, and nanotechnology-based sensors. Then, five chapters describe different advanced technologies for meat decontamination, such as irradiation, hydrostatic and hydrodynamic pressure processing, other non-thermal technologies, and the reduction in contaminants generation. Nutrigenomics in animal nutrition and production is the object of a chapter that is followed by five chapters dealing with nutritional-related issues like bioactive peptides, functional meats, fat and salt reduction, processing of nitrite-free products, and the use of proteomics for the improved processing of dry-cured meats. The last four chapters are reporting the latest developments in bacteriocins against meat-borne pathogens, the functionality of bacterial starters, modified atmosphere packaging and the use of new nanotechnology-based materials for intelligent and edible packaging.
Categories: Technology & Engineering