13 In Situ Detection of MicroRNA Expression with RNAscope Probes. ......... 197
Viravuth P. Yin
14 Padlock Probes to Detect Single Nucleotide Polymorphisms. ................ 209
Tomasz Krzywkowski and Mats Nilsson
15 Quantifying Gene Expression in Living Cells with Ratiometric
Bimolecular Beacons.................................................... 231
Yantao Yang, Mingming Chen, Christopher J. Krueger, Andrew Tsourkas,
and Antony K. Chen
16 Optimizing Molecular Beacons for Intracellular Analysis of RNA............. 243
Mingming Chen, Yantao Yang, Christopher J. Krueger,
and Antony K. Chen
17 Live Imaging of Nuclear RNPs in Mammalian Complex Tissue
with ECHO-liveFISH................................................... 259
Dan Ohtan Wang
18 In Vivo Visualization and Function Probing of Transport mRNPs
Using Injected FIT Probes. .............................................. 273
Jasmine Chamiolo, Imre Gaspar, Anne Ephrussi, and Oliver Seitz
19 Visualizing RNA in Live Bacterial Cells Using Fluorophore-
and Quencher-Binding Aptamers......................................... 289
Murat Sunbul, Ankita Arora, and Andres Jaschke€
20 Method for Imaging Live-Cell RNA Using an RNA Aptamer
and a Fluorescent Probe................................................. 305
Shin-ichi Sato, Kenji Yatsuzuka, Yousuke Katsuda, and Motonari Uesugi
21 RNA Live Imaging in the Model MicroorganismUstilago maydis............. 319
Sabrina Zander, Kira Muntjes, and Michael Feldbr€ ugge€
22 Real-Time Fluorescence Imaging of Single-Molecule Endogenous
Noncoding RNA in Living Cells.......................................... 337
Hideaki Yoshimura and Takeaki Ozawa
23 Live Imaging of mRNA Synthesis inDrosophila............................. 349
Hernan G. Garcia and Thomas Gregor
24 Imaging Newly Transcribed RNA in Cells by Using a Clickable
Azide-Modified UTP Analog............................................. 359
Anupam A. Sawant, Sanjeev Galande, and Seergazhi G. Srivatsan
25 Detection of the First Round of Translation: The TRICK Assay.............. 373
Franka Voigt, Jan Eglinger, and Jeffrey A. Chao
26 Imaging Translation Dynamics of Single mRNA
Molecules in Live Cells.................................................. 385
Suzan Ruijtenberg, Tim A. Hoek, Xiaowei Yan,
and Marvin E. Tanenbaum
27 Systematic Detection of Poly(A)+RNA-Interacting Proteins
and Their Differential Binding............................................ 405
Miha Milek and Markus Landthaler
viii Contents