RNA Technologies

VolkerA.ErdmannStefanJurgaJanBarciszewski Editors

RNA and DNA Diagnostics

RNA Technologies

More information about this series athttp://www.springer.com/series/8619

Volker A. Erdmann Stefan Jurga Jan Barciszewski

Editors

RNA and DNA Diagnostics

EditorsVolker A. ErdmannFree University of BerlinInstitute of Chemistry/Biochemistry

Thielallee 63, BerlinGermany

Stefan JurgaNanobiomedical CenterAdam Mickiewicz UniversityUmultowska 85 Poznan, Poland

Jan BarciszewskiInstitute of Bioorganic Chemistry PolishAcademy of Sciences

Z. Noskowskiego 12/14 PoznanPoland

ISSN 2197-9731 ISSN 2197-9758 (electronic)RNA TechnologiesISBN 978-3-319-17304-7 ISBN 978-3-319-17305-4 (eBook)DOI 10.1007/978-3-319-17305-4

Library of Congress Control Number: 2015940998

Springer Cham Heidelberg New York Dordrecht London Springer International Publishing Switzerland 2015This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part ofthe material is concerned, specifically the rights of translation, reprinting, reuse of illustrations,recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmissionor information storage and retrieval, electronic adaptation, computer software, or by similar ordissimilar methodology now known or hereafter developed.The use of general descriptive names, registered names, trademarks, service marks, etc. in thispublication does not imply, even in the absence of a specific statement, that such names are exemptfrom 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 thisbook are believed to be true and accurate at the date of publication. Neither the publisher nor theauthors or the editors give a warranty, express or implied, with respect to the material containedherein or for any errors or omissions that may have been made.

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Preface

The cell is the fundamental unit of life, composed of a large array of biomolecules:

DNA, RNA, proteins, sugars, lipids, and small compounds which altogether define

its biochemical properties and biological functions. Each cell is able to respond to

its environment or stress and to communicate with other cells to create tissues,

organs, and whole organisms. The question is how do these cellular constituents

assemble to yield a cell with the ability to carry out different functions in response

to its surroundings, which give the property of life? A detailed understanding of the

chemistry of life, as well as the experimental tools to probe pathways and to restore

deregulated states in human pathology, will stimulate their diagnosis and treatment.

The basic units of inheritance (genes) are composed of nucleic acids. Even though

nucleic acids represent less than 5 % of the dry mass of a typical cell, nucleic acids

control for example the production of proteins that make up approximately 75 % of

the dry mass. The information encoded in the nucleic acids influences when and

how cells respond to environmental conditions through the production of proteins.

The structure, function, and reactivity of DNA and RNA are central to molecular

biology and are crucial for the understanding of the complex biological processes.

The central feature of nucleic acid technologies is the programmability of nucleic

acid structures by WatsonCrick base pairs, which are responsible for the infor-mation content of all living systems. Nucleic acids may store additional informa-

tion, like in epigenetics, for protein function. DNA and RNA, as well as their

derivatives and analogues, can be used for a variety of applications ranging from

gene regulation (RNA interference, RNA catalysis, antisense approach, etc.), the

modulation of protein function by employment of aptamers, and to molecular

diagnostics. These nucleic acid secondary and tertiary structure recognition inter-

actions are reliable, reversible, and responsive, showing low error rates.

Since the early 1970s, the use of nucleic acid sequences for specific diagnostic

applications has followed a dramatic development. Early methods for restriction

enzyme digestion, as well as reverse transcription, were followed by Southern,

Northern, and dot blotting, as well as DNA sequencing. The discovery of the

v

polymerase chain reaction (PCR) in 1985 and easy laboratory manipulation of

sufficient quantities of DNA for diagnostics, as well as the development of real-

time quantitative PCR and oligonucleotide microarrays, resulted in an explosion of

knowledge in the field of molecular and cellular biology. This advancement con-

tinues with the development of methods for direct nucleic acid target detection from

samples without in vitro amplification and enhanced transduction elements for

improved sensitivity of nucleic acid detection. The existence and success of the

field is clearly a consequence of the convenient availability of specific sequences of

nucleic acids, owing to the development of their chemical synthesis. The binding of

a probe molecule to the complementary nucleic acid target is the molecular basis

for most of the current methods in DNA- and RNA-based diagnostics. With these

tools one can detect, for example, the presence of a pathogen either by directly

probing the presence of DNA or RNA nucleic acids in the host or by first amplifying

the pathogen DNA or RNA. In the case of infectious diseases, nucleic acid-based

diagnostics detect DNA or RNA from the infecting organism, but for noninfectious

diseases, nucleic acid-based diagnostics may be used to detect a specific gene or the

expression of disease associated genes. Nucleic acid-based diagnostics have an

advantage over immunoassays in that they can detect genetic markers, such as those

for drug resistance in bacteria, beyond detecting the presence of a pathogen.

However, by infectious organisms that are able to hide in host organs, or other

areas of the body, from which the extraction of an infected sample is difficult,

nucleic acid-based diagnostics may fail to detect such a disease. Currently, nucleic

acid-based diagnostics are used to detect a wide range of conditions, including

cancer, genetic markers associated with a high risk of cancer, leishmaniosis,

tuberculosis, HIV, genetic diseases (e.g., cystic fibrosis), and a variety of infectious

diseases, including anthrax, Clostridium difficile (a common hospital acquiredbacterial infection), chlamydia, and gonorrhea. Currently, there are many new

and intelligent technologies under development for the specific detection of the

nucleic acid sequences. These include biosensors, nanopores, and next-generation

sequencing technologies. In the future, these technologies will move nucleic acid

diagnostics away from centralized laboratory facilities and into locations such as

emergency rooms, physicians offices, and even into the home. These technicaldevelopments will also provide systems for integrated information transfer from

one location to another, allowing remote diagnosis by clinicians. Thus, DNA and

RNA targeted analyses play an important role and are used in various clinical

settings. There is no doubt that the field is approaching a certain level of maturity,

but there are still many fundamental questions, which remain to be answered before

its value to molecular medicine can be fully exploited.

In this book, one can see contributions showing the state of the art in nucleic acid

diagnostics, its application, clinical practice, and the emerging technologies in the

field. They discuss future trends and expected advances in the field of molecular

medicine. The approaches presented and discussed are based on specific properties

of nucleic acids as for example electrochemical features, fluorescence of different

vi Preface

nucleic acid analogues, aptamers, microchips, single-nucleotide strategies, and

structural propensity of RNA and DNA.

Thus, in this new volume we will find most interesting contributions, which

discuss challenges in translating nucleic acid diagnostic approaches to clinical

applications.

Berlin, Germany Volker A. Erdmann

Poznan, Poland Stefan Jurga

Poznan, Poland Jan Barciszewski

Preface vii

ThiS is a FM Blank Page

Contents

Electrochemical Biosensors for miRNA Detection . . . . . . . . . . . . . . . . . 1Diego Voccia and Ilaria Palchetti

Electrochemical Detection of RNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21Christopher Pohlmann and Mathias Sprinzl

DNA and PNA Probes for DNA Detection in ElectroanalyticalSystems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47Benot Piro, Vincent Noel, and Steeve Reisberg

DNA for Non-nucleic Acid Sensing . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81Vincent Noel, Benoit Piro, and Steeve Reisberg

Aptamers in Oncotherapy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107Darija Muharemagic and Maxim V. Berezovski

Genotyping of Single Nucleotide Polymorphisms . . . . . . . . . . . . . . . . . . 123Tian Ye, Ran Tong, and Zhiqiang Gao

Environm