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    Quyen 2

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    Quyen 2

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    of 10

    Oksana Ableitner

    Introduction to
    Molecular Biology
    Working with DNA and RNA
    essentials
    Springer essentials
    Springer essentials provide up-to-date knowledge in a concentrated form. They
    aim to deliver the essence of what counts as “state-of-the-art” in the cur-
    rent academic discussion or in practice. With their quick, uncomplicated and
    comprehensible information, essentials provide:

    • an introduction to a current issue within your field of expertise


    • an introduction to a new topic of interest
    • an insight, in order to be able to join in the discussion on a particular topic

    Available in electronic and printed format, the books present expert knowledge
    from Springer specialist authors in a compact form. They are particularly suitable
    for use as eBooks on tablet PCs, eBook readers and smartphones. Springer essen-
    tials form modules of knowledge from the areas economics, social sciences and
    humanities, technology and natural sciences, as well as from medicine, psycho-
    logy and health professions, written by renowned Springer-authors across many
    disciplines.

    More information about this subseries at https://link.springer.com/bookseries/


    16761
    Oksana Ableitner

    Introduction
    to Molecular Biology
    Working with DNA and RNA
    Oksana Ableitner
    Graz, Austria

    ISSN 2197-6708 ISSN 2197-6716 (electronic)


    essentials
    ISSN 2731-3107 ISSN 2731-3115 (electronic)
    Springer essentials
    ISBN 978-3-658-33919-7 ISBN 978-3-658-33920-3 (eBook)
    https://doi.org/10.1007/978-3-658-33920-3

    © Springer Fachmedien Wiesbaden GmbH, part of Springer Nature 2022


    This book is a translation of the original German edition “Einführung in die Molekularbiologie” by
    Ableitner, Oksana, published by Springer Fachmedien Wiesbaden GmbH in 2018. The translation
    was done with the help of artificial intelligence (machine translation by the service DeepL.com).
    A subsequent human revision was done primarily in terms of content, so that the book will read
    stylistically differently from a conventional translation. Springer Nature works continuously to
    further the development of tools for the production of books and on the related technologies to
    support the authors.
    This work is subject to copyright. All rights are reserved by the Publisher, whether the whole
    or part of the material is concerned, specifically the rights of reprinting, reuse of illustrations,
    recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission
    or information storage and retrieval, electronic adaptation, computer software, or by similar or
    dissimilar methodology now known or hereafter developed.
    The use of general descriptive names, registered names, trademarks, service marks, etc. in this
    publication does not imply, even in the absence of a specific statement, that such names are exempt
    from the relevant protective laws and regulations and therefore free for general use.
    The publisher, the authors and the editors are safe to assume that the advice and information in this
    book are believed to be true and accurate at the date of publication. Neither the publisher nor the
    authors or the editors give a warranty, expressed or implied, with respect to the material contained
    herein or for any errors or omissions that may have been made. The publisher remains neutral with
    regard to jurisdictional claims in published maps and institutional affiliations.

    Responsible Editor: Sarah Koch


    This Springer imprint is published by the registered company Springer Fachmedien Wiesbaden
    GmbH part of Springer Nature.
    The registered company address is: Abraham-Lincoln-Str. 46, 65189 Wiesbaden, Germany
    What You Can Find in This essential

    • What DNA is and how it is constructed


    • What a nucleotide is and which types there are
    • Which differences there are between DNA and RNA
    • What a gene is and what it consists of
    • Which methods of gene detection are available
    • How genes can be made visible
    • How works gel electrophoretic separation of the DNA fragments, based on
    which properties of DNA
    • What happens to DNA in each PCR step
    • The difference between TaqMan PCR and hybridization PCR
    • An explanation of how primers are designed and how to find the specific
    sequence in a gene
    • A description of the PFGE and MLST methods
    • Why ethidium bromide is needed in the laboratory
    • How bacterial strains can be compared with each other
    • How to determine a gene sequence and thus decipher a genetic code
    • Which reagents are needed for different molecular biological methods
    • Why molecular biological methods are the methods of the future
    • What a microarray looks like
    • How to identify sources of infection
    • Which formulas one should know to be able to prepare solutions in the
    laboratory

    v
    Preface to the 2nd Edition

    I was very pleased that my attempt to explain the basics of molecular biology
    as simply as possible were met with a grateful reader. Like any author, I always
    try to improve my book. After the first edition, I received a lot of feedback from
    students and my work colleagues, which led me to describe the processes in more
    detail at some points in the book.
    Throughout the book, I made corrections to the wording and completed it
    with more pictures. I have revised the chapter “Molecular Biological Methods”
    completely and in this context added an additional “MLST method”. It is seemed
    logical to me to complete the sequencing with the MLST method in order to show
    practical applications.
    This book is aimed at all those who are interested in genetic information. What
    material basis do our genes have? How can genes be identified? It can be high
    school or university students, but also readers who were not previously involved
    in biology or chemistry.
    Recently, more and more laboratories are switching from microbiological
    methods to molecular biological methods. My book will also be very helpful
    for those employees who had little or no molecular biology in their basic training
    to understand and master new methods.
    A new edition would never take place without feedback from my readers. I am
    grateful for their feedback, which has given me new ideas to explain terms and
    hints at mistakes. I hope that my book will make it easier for many more people
    to enter molecular biology and arouse their interest in it.

    Graz Oksana Ableitner


    October 2017

    vii
    Preface to the 1st Edition

    Many people associate the terms biochemistry and molecular biology with an
    incomprehensible and very complicated field of knowledge. I had difficulties too.
    After a failed exam in biochemistry I had a minimal amount of time to prepare
    for the repeat exam. The internet gave me far too much information; it was of
    no help in understanding the basics of biochemistry. So I developed a method for
    myself to remember the most complicated formulas and chemical equations.
    In order to understand the basics of biochemistry, one needs many images
    that serve to visualize abstract knowledge. In order to learn successfully, it was,
    therefore, also important for me to draw and write a lot.
    During my teaching activities I was able to successfully pass on my findings
    to my students.
    Every subject becomes interesting when you understand the basics in all
    details. Then you have the opportunity to build on that, and suddenly you are
    totally excited about biochemistry.
    This book is intended to be a help not only for pupils and students, but also
    for anyone interested in working in a molecular biology laboratory.
    The importance of molecular biology in our time is increasing. More and more
    molecular biology laboratories are being established to examine clinical samples
    using molecular biology methods. Analytical methods of molecular biology are
    sensitive, specific and fast. They are used in various fields.
    Some of them are listed here:

    • Determination of paternity
    • Determination of predisposition to certain diseases
    • Identification of genetically transmitted diseases
    • Identification of pathogens (e.g., bacteria or viruses)

    ix
    x Preface to the 1st Edition

    • Outbreak clarification (determination of the source of infection)


    • Identification of mutations in certain genes (cause of a disease)
    • Detection of the presence or absence of a gene

    The beginning of this book explains the basic terms needed to understand the
    molecular biological methods that follow. Finally, the most important terms are
    summarized in keywords to make it easier to repeat the subject matter. To look
    up certain terms, the glossary is at the end of the book.
    In addition to molecular biological terms, structures, and interrelationships are
    to be explained step by step in simple terms and made comprehensible through
    illustrations.
    The aim of this book is to explain the existing state of knowledge as com-
    prehensibly as possible and to get readers of different age groups excited about
    molecular biology.

    Graz Oksana Ableitner


    July 2014
    Contents

    1 Basic Concepts of Molecular Biology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1


    1.1 Nucleic Acids—Carriers of Genetic Material . . . . . . . . . . . . . . . . . . 1
    1.2 Building Blocks of Nucleic Acids . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
    1.3 Spatial Structure of Nucleic Acids . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
    1.4 Summary of the Chapter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
    2 Molecular Biological Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
    2.1 Polymerase chain reaction (PCR) – A Method for Amplifying
    DNA Fragments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
    2.1.1 PCR Reagents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
    2.1.2 Preparation and Performance of a PCR . . . . . . . . . . . . . . . . . 28
    2.2 Gel electrophoresis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
    2.3 Real-Time Polymerase Chain Reaction . . . . . . . . . . . . . . . . . . . . . . . . 37
    2.3.1 Real-time PCR with a TaqMan Probe (TaqMan PCR) . . . . 38
    2.3.2 Real-time PCR with Hybridization Probes
    (Hybridization PCR) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
    2.3.3 Comparison Between TaqMan PCR and Hybridization
    PCR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
    2.4 Sanger Sequencing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
    2.5 MLST . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
    2.6 Microarray Technology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
    2.7 PFGE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
    3 Chemical Calculation in the Laboratory . . . . . . . . . . . . . . . . . . . . . . . . . . 69
    3.1 Amount of Substance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
    3.2 Preparation of Solutions. Dilution . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70

    xi

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