Table Of Content

Molecular Analyses Medical Genomics and Proteomics Series Editor: Scott O. Rogers Science Publisher: Charles R. Crumly, CRC Press/Taylor & Francis Group Published Titles Molecular Analyses Edited by Scott O. Rogers For more information about this series, please visit: https://www.routledge.com/ Medical-Genomics-and-Proteomics/book-series/CRCMOLGENPRO Molecular Analyses Edited by Scott O. Rogers First edition published 2022 by CRC Press 6000 Broken Sound Parkway NW, Suite 300, Boca Raton, FL 33487-2742 and by CRC Press 4 Park Square, Milton Park, Abingdon, Oxon, OX14 4RN CRC Press is an imprint of Taylor & Francis Group, LLC © 2022 Taylor & Francis Group, LLC Reasonable efforts have been made to publish reliable data and information, but the author and publisher cannot assume responsibility for the validity of all materials or the consequences of their use. 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For works that are not available on CCC please contact [email protected] Trademark notice: Product or corporate names may be trademarks or registered trademarks and are used only for identification and explanation without intent to infringe. Library of Congress Cataloging-in-Publication Data Names: Rogers, Scott O., 1953- editor. Title: Molecular analyses / edited by Scott O. Rogers. Description: First edition. | Boca Raton : CRC Press, 2022. | Series: Medical genomics and proteomics | Includes bibliographical references and index. Identifiers: LCCN 2021056926 (print) | LCCN 2021056927 (ebook) | ISBN 9780367903718 (hardback) | ISBN 9781032161907 (paperback) | ISBN 9781003247432 (ebook) Subjects: LCSH: Nucleotide sequence. Classification: LCC QP625.N89 M65 2022 (print) | LCC QP625.N89 (ebook) | DDC 572.8/633--dc23/eng/20211209 LC record available at https://lccn.loc.gov/2021056926 LC ebook record available at https://lccn.loc.gov/2021056927 ISBN: 978-0-367-90371-8 (hbk) ISBN: 978-1-032-16190-7 (pbk) ISBN: 978-1-003-24743-2 (ebk) DOI: 10.1201/9781003247432 Typeset in Times LT Std by KnowledgeWorks Global Ltd. Contents Preface.......................................................................................................................ix List of Contributors ...................................................................................................xi Chapter 1 Nucleic Acid Extraction from Diverse Samples ...................................1 Scott O. Rogers Chapter 2 DNA Extraction from Mummified Tissues ..........................................9 Yayoi Sato Chapter 3 Commercial DNA Extraction Kits .....................................................17 Stuart C. Clarke Chapter 4 Automated Nucleic Acid Extraction ...................................................23 Juergen Loeffler, Kathrin D. Schmidt, Holger Hebart, Hermann Einsele Chapter 5 Forensic DNA Samples: Collection and Handling .............................31 Mark Benecke Chapter 6 DNA Preservation ..............................................................................53 C.William Kilpatrick Chapter 7 RNA Storage ......................................................................................71 Martin Hofmann Chapter 8 Disposable Electrochemical DNA Biosensors ...................................77 Kagan Kerman and Mehmet Ozsoz Chapter 9 Handheld Nucleic Acid Analyzer .......................................................87 James A. Higgins Chapter 10 DNA-Binding Fluorophores ...............................................................97 Mikael Kubista, Jonas Karlsson, Martin Bengtsson, Neven Zoric, Gunar Westman v vi Contents Chapter 11 Fluorescence Resonance Energy Transfer (FRET) ..........................105 Dino A. De Angelis Chapter 12 LightUp® Probes ...............................................................................115 Mikael Leijon Chapter 13 Invader® Assay .................................................................................121 Stephen Day, Andrea Mast Chapter 14 Laser-Capture Microdissection ........................................................129 Falko Fend Chapter 15 Helper-Dependent Adenoviral Vectors ............................................139 Philip Ng Chapter 16 Retroviral Vectors ............................................................................147 Erin L. Weber, Paula M. Cannon Chapter 17 Liposomal Nonviral Delivery Vehicles ............................................157 Nancy Smyth Templeton Chapter 18 Polymer-Based Nonviral Nucleic Acid Delivery and Genome Editing .........................................................................165 Janin Germer, Ernst Wagner Chapter 19 Automated DNA Sequencing ...........................................................183 Alexandre Izmailov Chapter 20 DNA Sequencing Methods ...............................................................191 Scott O. Rogers Chapter 21 Differential Sequencing by Mass Spectrometry ..............................199 Christian Jurinke, Christiane Honisch, Dirk van den Boom Chapter 22 Brief Guide to Conducting Biological Database Searches ...............209 John Gray Contents vii Chapter 23 Accessing Genomic Databases.........................................................225 Robert J. Trumbly Chapter 24 Phylogenetics, Comparative Genomics, and Phylogenomics ..................................................................................237 Scott O. Rogers Chapter 25 DNannotator: Annotation Software Tool Kit for Regional Genomic Sequences .........................................................................251 Chunyu Liu Chapter 26 ESTAnnotator: A Tool for High-Throughput EST Annotation .......261 Agnes Hotz-Wagenblatt and Thomas Hankeln Chapter 27 The Basics of Omics.........................................................................269 Scott O. Rogers Chapter 28 Ribotyping ........................................................................................283 Tim J. Inglis Chapter 29 Forensic DNA Typing: Y Chromosome ...........................................289 Lluís Quintana-Murci Chapter 30 Forensic Identification: An Overview on Molecular Diagnostic Technology .....................................................................297 Adrian Linacre, Yvonne E. Cruickshank Chapter 31 Denaturing Gradient Gel Electrophoresis (DGGE) .........................305 Luciana Cresta de Barros Dolinsky Chapter 32 Heteroduplex Analysis (HA) ............................................................311 Philip L. Beales Chapter 33 NEBcutter: A Program to Cleave DNA with Restriction Enzymes.........................................................................321 Janos Posfai, R. J. Roberts, Tamas Vincze viii Contents Chapter 34 Differential Display (DD) Analysis ..................................................329 Farid E. Ahmed Chapter 35 Protein Truncation Test (PTT) .........................................................337 Sadanand Gite, Mark Lim, Kenneth Rothschild Index ......................................................................................................................351 Preface In 2005, the Encyclopedia of Medical Genomics and Proteomics (MGP) was published. It consisted of two large volumes of analytical methods and equipment that were applicable to medical and other studies of genomics and proteomics. While it was a comprehensive collection at the time, many variations, improvements, and new technological developments have occurred during the past 17 years. Also, the alphabetical arrangements of the chapters made searching by topic somewhat cum- bersome. Finally, the Encyclopedia was originally available in print version only. All of these factors necessitated an extensive revision in content, format, and organiza- tion, with the new title, Series in MGP. Currently, at least one dozen volumes are planned, including those in methods of fluorescence in situ hybridization (FISH), analyses for cancer detection, bacterial pathogens, and others. This is the inaugural volume in the Series in MGP, entitled Molecular Analyses. The volume and the series are roughly based on the Encyclopedia of MGP, published in 2005. However, there has been significant updating and reorganization of the chapters. This volume is divided into five sections including 35 chapters. The first section includes chapters on the extraction and preservation of nucleic acids. This is followed by sections on the detection of nucleic acids, delivery of nucleic acids using both viral and nonviral delivery systems, methods of nucleic acid sequencing and analyses, and a variety of other methods for analyzing nucleic acids as well as proteins. Some of the original chapters have been included because they are still relevant, while others are included because they contain information of historical interest. That is, they show some of the historical developmental stages of methods and analyses currently being employed. Many of these may be important to the development of new technological directions. Additionally, several chapters have been updated to include new developments in specific areas. Several new chapters also have been added that describe some of the latest methods and analyses used in molecular research. Additional volumes are currently in active development. Scott Orland Rogers is a professor emeritus of molecular biology and evolution at Bowling Green State University, Bowling Green, Ohio. He received his PhD in plant molecular biology from the University of Washington, Seattle. He was an assistant professor and associate professor at the State University of New York College of Environmental Science and Forestry before moving to BGSU. He has taught courses in biology, botany, cell physiology, molecular biology, molecular genetics, bioinfor- matics, and molecular evolution. Research in his lab includes studies of microbes and nucleic acids preserved in ice, life in extreme environments, group I introns, molecular microbial phylogenetics, microbial metagenomics/metatranscriptomics, ancient DNA, and plant development. ix