Nucleic Acid Aptamers: Selection, Characterization, and Application: 2016 (Methods in Molecular Biology)

This volume provides protocol references covering recent developments in the aptamer field. Within the last decade, aptamers have become more and more popular, and their sophisticated biophysical properties together with their ability to be easily modified and, thus, adapted to various regimens makes them a very promising class of compounds. Divided into three sections, the book covers selection, a series of analytical methods to assess biophysical properties of aptamer-target interactions, as well as various applications of aptamers. 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, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Practical and easy to follow, Nucleic Acid Aptamers: Selection, Characterization, and Application provides a state-of-the-art summary of recent developments in the aptamer field and will be a helpful resource for scientists in the life sciences working with aptamers as tools to elucidate biological systems. Part I: Selection   1. Selection of Aptamers for Metabolite Sensing and Construction of Optical Nanosensors             Yi Long, Franziska Pfeiffer, Gnter Mayer, Tine Daa Schrder, Veli Cengiz zalp, and Lars Folke Olsen   2. SELEX of Cell-Specific RNA Aptamers             Katharina Berg, Eileen Magbanua, and Ulrich Hahn   3. Developing Aptamers by Cell-Based SELEX             Silvia Catuogno, Carla Lucia Esposito, and Vittorio de Franciscis   4. DNA Aptamer Generation by Genetic Alphabet Expansion SELEX (ExSELEX) Using an Unnatural Base Pair System             Michiko Kimoto, Ken-Ichiro Matsunaga, and Ichiro Hirao   5. Capillary Electrophoresis for the Selection of DNA Aptamers Recognizing Activated Protein C             Nasim Shahidi Hamedani and Jens Mller   6. Preparation of SELEX Samples for Next-Generation Sequencing             Fabian Tolle and Gnter Mayer   7. Next Generation Analysis of Deep Sequencing Data: Bringing Light into the Black Box of SELEX Experiments             Michael Blank   Part II: Characterization   8. Aptamer Binding Studies Using MicroScale Thermophoresis             Dennis Breitsprecher, Nina Schlinck, David Witte, Stefan Duhr, Philipp Baaske, and Thomas Schubert   9. Label-Free Determination of the Dissociation Constant of Small Molecule-Aptamer Interaction by Isothermal Titration Calorimetry             Marc Vogel and Beatrix Suess   10. Applications of Aptamers in Flow and Imaging Cytometry             Isis C. Nascimento, Arthur A. Nery, Vinicius Bassaneze, Jos E. Krieger, and Henning Ulrich   11. In Vitro and In Vivo Imaging of Fluorescent Aptamers             Ioanna Thodorou, Nam Nguyen Quang, Karine Gombert, Benoit Thz, Benoit Lelandais, and Frdric Ducong   12. Crystallographic Pursuit of a Protein-RNA Aptamer Complex             John J.G. Tesmer   Part III: Application   13. Voltammetric Aptasensor Based on Magnetic Beads Assay for Detection of Human Activated Protein C             Arzum Erdem, Gulsah Congur, and Ece Eksin   14. Apta-PCR             Alessandro Pinto, Pedro Nadal Polo, Marketa Svobodova, Teresa Mairal Lerga, and Ciara K. O'Sullivan   15. Aptamer-Based Enzyme-Capture-Assay for Measurement of Plasma Thrombin Levels             Jens Mller, Tobias Becher, Gnter Mayer, and Bernd Ptzsch   16. Application of Aptamers in Histopathology             Sarah Shigdar, Li Lv, Lifen Wang, and Wei Duan   17. Aptamer Stainings for Super-Resolution Microscopy             Maria Angela Gomes de Castro, Burkhard Rammner, and Felipe Opazo   18. Synthesis and Characterization of Aptamer Targeted SNALPs for the Delivery of siRNA             Samantha E. Wilner and Matthew Levy   19. Screening of Genetic Switches Based on the Twister Ribozyme Motif             Michele Felletti, Benedikt Klauser, and Jrg S. Hartig