Nucleic Acid Aptamers: Selection, Characterization, and Application

ISBN-13: 9781071626948 / Angielski / Twarda / 2022

Mayer, Günter

Opis

This updated book reflects improvements in a variety of techniques used to study the aptamer field. Beginning with a section on selection procedures, the volume continues with methods to characterize aptamers’ interaction and structural properties by biophysical approaches, as well as a variety of applications that have been adapted to the aptamer compound class. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. 

Authoritative and up-to-date, Nucleic Acid Aptamers: Selection, Characterization, and Application, Second Edition serves as an ideal guide for researchers aiming to further our understanding of aptamer biology and more.

Spis treści

Part I: Selection

 

1. Automated ssDNA SELEX Using Histidine Tagged Target Proteins

            Stefan Breuers and Günter Mayer

 

2. Discovery of Aptamers against Cell Surface Markers Using Ligand-Guided Selection

            Nicole Williams, Rutika Patel, and Prabodhika Mallikaratchy

 

3. Implementation of Emulsion PCR for Amplification of Click-Modified DNA during SELEX

            Moujab Choukeife, Anna Jonczyk, and Günter Mayer

 

4. Preparation of Chemically Modified DNA Library for SELEX via Incorporation of CLB-dUTP in Primer Extension Reaction

            Magda Puchała, Marta Radzińska, Joanna Guzdek, Agnieszka Sok-Grochowska, Aleksandra Adamowicz-Skrzypkowska, Paweł Pięta, Przemysław Jurek, and Monika Czarnecka

 

5. RNA Capture-SELEX on Streptavidin Magnetic Beads

            Leon Kraus and Beatrix Suess

 

6. The Bioinformatics of Aptamers: HT-SELEX Analysis with AptaSUITE

            Jan Hoinka and Teresa M. Przytycka

 

7. Improvement of Aptamers by High-Throughput Sequencing of Doped-SELEX

            Frédéric Ducongé

 

Part II: Characterization

 

8. Analysis of Aptamer-Small Molecule Binding Interactions Using Isothermal Titration Calorimetry

            Sladjana Slavkovic and Philip E. Johnson

 

9. Determination of Aptamer Structure Using Circular Dichroism Spectroscopy

            Yannick Kerler, Stephan Sass, Carsten Hille, and Marcus M. Menger

 

10. Immobilization-Free Determination of Dissociation Constants Independent of Ligand Size Using MicroScale Thermophoresis

            Wiebke Sabrowski, Walter F.M. Stöcklein, and Marcus M. Menger

 

11. Label-Free Determination of the Kinetic Parameters of Protein-Aptamer Interaction by Surface Plasmon Resonance

            Nico Dreymann, Anja Möller, and Marcus M. Menger

 

12. Probing of Fluorogenic RNA Aptamers via Supramolecular Förster Resonance Energy Transfer with Universal Fluorescent Nucleobase Analog

            Christian Steinmetzger and Claudia Höbartner

 

13. Slow-Off-Rate-Modified Aptamer Labeling for Fluorescence Microscopy and DNA-PAINT

            Sebastian Strauss and Ralf Jungmann

 

Part III: Application

 

14. Aptamer-Field-Effect Transistors for Small-Molecule Sensing in Complex Environments

            Nako Nakatsuka

 

15. Aptasensor for Impedimetric Detection of Lysozyme

            Ece Eksin, Huseyin Senturk, and Arzum Erdem

 

16. Biophysical Analysis of Small Molecule Binding to Viral RNA Structures

            Liang-Yuan Chiu, Jesse Davila-Calderon, Zhengguo Cai, and Blanton S. Tolbert

 

17. Designing and Expressing Circular RNA Aptamers to Regulate Mammalian Cell Biology

            Jacob L. Litke and Samie R. Jaffrey

 

18. Enzyme-Linked OligoNucleotide Assay (ELONA)

            Miguel Moreno, Ana García-Sacristán, M. Elena Martín, and Víctor M. González

 

19. High-Throughput Development and Optimization of RNA-Based Fluorogenic Biosensors of Small Molecules Using Droplet-Based Microfluidics

            Claire Husser, Stéphanie Baudrey, and Michael Ryckelynck

 

20. Robotic APTamer-Enabled Electrochemical Reader (RAPTER) System for Automated Aptamer-Mediated Electrochemical Analysis

            Young Lo, Shaolin Liang, Waljit S. Dhillo, Anthony E.G. Cass, and Julian A. Tanner