Nucleic Acid Aptamers: Selection, Characterization, and Application

243 Pages·2016·8.73 MB·English

by  Günter Mayer (eds.)

Methods in
Molecular Biology 1380
Günter Mayer Editor
Nucleic Acid
Aptamers
Selection, Characterization,
and Application
M M B
ETHODS IN OLECULAR IOLOGY
Series Editor
John M. Walker
School of Life and Medical Sciences
University of Hertfordshire
Hatfield, Hertfordshire, AL10 9AB , UK
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Nucleic Acid Aptamers
Selection, Characterization, and Application
Edited by
Günter Mayer
University of Bonn, Bonn, Germany
Editor
Günter Mayer
University of Bonn
Bonn , G ermany
ISSN 1064-3745 ISSN 1940-6029 (electronic)
Methods in Molecular Biology
ISBN 978-1-4939-3196-5 ISBN 978-1-4939-3197-2 (eBook)
DOI 10.1007/978-1-4939-3197-2
Library of Congress Control Number: 2015956601
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Prefa ce
Aptamers are short, single chained nucleic acids that fold into a well-defi ned three-
dimensional shape, upon which a target molecule is recognized by high affi nity and specifi c-
ity. Since their very fi rst description in 1990, a plethora of aptamers have been developed,
characterized, and applied. Aptamers that recognize small molecules, proteins, and even
targets on cell surfaces have been selected and applied for different purposes. Within the last
decade, aptamers have become more and more popular, and their sophisticated biophysical
properties together with their ability to be easily modifi ed and, thus, adapted to various
regimens make them a very promising class of compounds.
This book intends to provide protocol references covering recent developments in the
aptamer fi eld. It is subdivided into three parts refl ecting the aptamer generation process,
namely the selection, characterization, and fi nally the application of aptamers.
The selection part covers methods to isolate aptamers recognizing small molecules
(Chapter 1 ) or to target molecules presented or embedded on cell surfaces (Chapters 2 and
3 ) . In Chapter 4 , the implementation of novel, noncanonical base pairs for generating new
types of aptamers is described. A protocol for Capillary Electrophoresis-based selection
schemes ( CE-SELEX ) , an emerging approach to allow the generation of aptamers for non-
tagged and non-immobilized target molecules, is given in Chapter 5 . The fi rst part of this
volume of the M ethods in Molecular Biology series is rounded out by two consecutive chap-
ters dealing with N ext Generation Sequencing for the thorough analysis of individual selec-
tion experiments (Chapters 6 and 7 ) .
The second part covers a series of analytical methods to assess biophysical properties
of aptamer–target interactions. This part contains protocols describing MicroScale
Thermophoresis (Chapter 8 ), isothermal titration calorimetry (Chapter 9 ) , and fl ow
cytometry (Chapter 1 0 ) as means to measure dissociation constants and to address speci-
fi city of aptamers in regard to cognate ligand recognition. Chapter 1 1 covers methods to
perform in vivo imaging of tissue-specifi c aptamers, whereas Chapter 1 2 provides an
approach toward generating co-crystals of aptamer–target complexes for X-ray crystallog-
raphy. With this, the second part of the volume is concluded leading into the third part,
which covers various applications of aptamers.
In this way, Chapters 1 3 – 15 provide protocols for employing aptamers as detection
modules in various assay formats, such as voltammetric assays, their simultaneous exploita-
tion as recognition elements and PCR templates (A pta-PCR ) and as capture-modules in the
so-called enzyme-capture assays. The following chapters cover protocols for cellular appli-
cations of aptamers, e.g., their compatibility with histopathology investigations (Chapter
1 6 ) and their superior properties as imaging tools in super-resolution microscopy (Chapter
17 ) . In Chapter 1 8 , a protocol for the synthesis of liposomes decorated with cell-specifi c
aptamers is described, which enables the application of aptamers as a targeting reagent for
delivery of siRNAs into distinct cells. The last chapter provides means for generating genetic
switches based on aptamer-responsive ribozymes (Chapter 1 9 ) .
v
vi Preface
I am thankful to all contributors who made this book possible. I believe that this pro-
tocol collection provides a state-of-the-art summary of recent developments in the aptamer
fi eld and will be a helpful resource for scientists in the life sciences working with aptamers
as tools to elucidate biological systems.
Bonn, Germany Günter Mayer
Contents
Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . i x
PART I SELECTION
1 Selection of Aptamers for Metabolite Sensing and Construction
of Optical Nanosensors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Yi Long , F ranziska P feiffer , Günter M ayer , T ine Daa Schrøder ,
Veli Cengiz Özalp , and Lars F olke O lsen
2 S ELEX of Cell-Specific RNA Aptamers. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Katharina Berg , Eileen M agbanua , and Ulrich Hahn
3 D eveloping Aptamers by Cell-Based SELEX . . . . . . . . . . . . . . . . . . . . . . . . . . 3 3
Silvia Catuogno , Carla L ucia E sposito , and Vittorio de Franciscis
4 DNA Aptamer Generation by Genetic Alphabet Expansion
SELEX (ExSELEX) Using an Unnatural Base Pair System. . . . . . . . . . . . . . . . 47
Michiko Kimoto , Ken-ichiro Matsunaga , and I chiro Hirao
5 C apillary Electrophoresis for the Selection of DNA Aptamers
Recognizing Activated Protein C . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Nasim S hahidi Hamedani and J ens M üller
6 Preparation of SELEX Samples for Next-Generation Sequencing. . . . . . . . . . . 7 7
Fabian T olle and Günter M ayer
7 Next-Generation Analysis of Deep Sequencing Data: Bringing Light
into the Black Box of SELEX Experiments . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 5
Michael Blank
PART II CHARACTERIZATION
8 Aptamer Binding Studies Using MicroScale Thermophoresis. . . . . . . . . . . . . . 9 9
Dennis B reitsprecher , Nina S chlinck , D avid W itte , S tefan Duhr ,
Philipp B aaske , and Thomas Schubert
9 L abel-Free Determination of the Dissociation Constant of Small
Molecule-Aptamer Interaction by Isothermal Titration Calorimetry . . . . . . . . 1 13
Marc V ogel and B eatrix S uess
10 A pplications of Aptamers in Flow and Imaging Cytometry . . . . . . . . . . . . . . . 1 27
Isis C . Nascimento , Arthur A. N ery , V inicius B assaneze , José E . Krieger ,
and Henning U lrich
11 In Vitro and In Vivo Imaging of Fluorescent Aptamers. . . . . . . . . . . . . . . . . . 1 35
Ioanna Théodorou , N am Nguyen Q uang , Karine Gombert , B enoit Thézé ,
Benoit L elandais , and Frédéric Ducongé
12 Crystallographic Pursuit of a Protein-RNA Aptamer Complex. . . . . . . . . . . . . 1 51
John J . G. T esmer
vii
viii Contents
PART III APPLICATION
13 Voltammetric Aptasensor Based on Magnetic Beads Assay
for Detection of Human Activated Protein C . . . . . . . . . . . . . . . . . . . . . . . . . 163
Arzum E rdem , Gulsah C ongur , and Ece Eksin
14 A pta-PCR. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171
Alessandro Pinto , P edro N adal P olo , M iriam Jauest Rubio,
Marketa Svobodova , Teresa M airal L erga , and Ciara K . O’Sullivan
15 Aptamer-Based Enzyme Capture Assay for Measurement
of Plasma Thrombin Levels. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179
Jens Müller , Tobias B echer , Günter M ayer , and Bernd Pötzsch
16 Application of Aptamers in Histopathology. . . . . . . . . . . . . . . . . . . . . . . . . . . 191
Sarah Shigdar , Li L v , Lifen W ang , and Wei D uan
1 7 Aptamer Stainings for Super-resolution Microscopy. . . . . . . . . . . . . . . . . . . . . 1 97
Maria A ngela Gomes de Castro , B urkhard Rammner , and Felipe O pazo
18 S ynthesis and Characterization of Aptamer-Targeted SNALPs
for the Delivery of siRNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 11
Samantha E. W ilner and Matthew L evy
19 S creening of Genetic Switches Based on the Twister Ribozyme Motif . . . . . . . 2 25
Michele Felletti , Benedikt K lauser , and Jörg S . Hartig
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 41
Contributors
PHILIPP BAASKE • NanoTemper Technologies GmbH , M unich, Germany
VINÍCIUS BASSANEZE • Laboratory of Genetics and Molecular Cardiology/LIM 13,
Heart Institute (InCor), University of São Paulo Medical School , S ão Paulo, Brazil
TOBIAS B ECHER • Institute for Experimental Haematology and Transfusion Medicine ,
University of Bonn Medical Centre , Bonn, Germany
KATHARINA B ERG • Chemistry Department, Institute for Biochemistry
and Molecular Biology, MIN-Faculty, H amburg University , H amburg, Germany
MICHAEL BLANK • AptaIT GmbH , Munich, G ermany
DENNIS B REITSPRECHER • NanoTemper Technologies GmbH , Munich, Germany
SILVIA C ATUOGNO • Istituto per l’Endocrinologia e l’Oncologia Sperimentale del CNR
“G. Salvatore” , N aples , I taly
GULSAH CONGUR • Faculty of Pharmacy, Analytical Chemistry Department,
Ege University , Bornov, Izmir , T urkey
WEI D UAN • School of Medicine, Deakin University , W aurn Ponds, V IC , A ustralia
FRÉDÉRIC D UCONGÉ • CEA, I2BM, Molecular Imaging Research Center (MIRCen) ,
Fontenay-aux-Roses, France ; I NSERM U1023, P aris, France; Université Paris Sud ,
Paris , F rance
STEFAN DUHR • NanoTemper Technologies GmbH , Munich, G ermany
ECE E KSIN • Faculty of Pharmacy, Analytical Chemistry Department, Ege University ,
Bornov , I zmir , T urkey
ARZUM ERDEM • Faculty of Pharmacy, Analytical Chemistry Department, Ege University ,
Bornov , I zmir , T urkey
CARLA LUCIA ESPOSITO • Istituto per l’Endocrinologia e l’Oncologia Sperimentale del CNR
“G. Salvatore” , Naples, Italy
MICHELE F ELLETTI • Department of Chemistry and Konstanz Research School Chemical
Biology , U niversity of Konstanz , Konstanz, G ermany
VITTORIO D E FRANCISCIS • Istituto per l’Endocrinologia e l’Oncologia Sperimentale del
CNR “G. Salvatore” , Naples, I taly
KARINE GOMBERT • INSERM U1023, Paris , France ; U niversité Paris Sud, P aris, France;
CEA, I2BM, Service Hospitalier Frédéric Joliot (SHFJ) Paris, France
MARIA A NGELA GOMES DE CASTRO • Department of Neuro- and Sensory Physiology,
Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain ,
University of Göttingen Medical Center , G öttingen, Germany
ULRICH HAHN • Chemistry Department, Institute for Biochemistry and Molecular Biology,
MIN-Faculty , H amburg University , Hamburg, G ermany
NASIM S HAHIDI H AMEDANI • Institute for Experimental Haematology and Transfusion
Medicine, U niversity of Bonn Medical Centre , B onn , G ermany
JÖRG S. H ARTIG • Department of Chemistry and Konstanz Research School Chemical
Biology , U niversity of Konstanz , Konstanz, G ermany
ix