Table Of ContentMolecular 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
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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 pub-
lished. 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, pub-
lished 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 meth-
ods 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.
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