Main description:

This volume provides readers with a broad collection of theoretical, computational, and experimental methods to quantitatively study the properties of phase-separate biomolecular condensates in diverse systems. The chapters in this book cover topics such as theoretical and computational methods; methods for in vitro characterization of biomolecular condensates; and techniques that enable in-cell characterization of biomolecular condensates. Written in the highly successful Methods in Molecular Biology series format, chapters include introduction to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and expert tips on troubleshooting and avoiding known pitfalls.

Comprehensive and thorough, Phase-Separated Biomolecular Condensates: Methods and Protocols is a valuable resource that helps researchers learn and use established methods to study both biophysical properties and biological functions of biomolecular condensates.

Contents:

Preface...Table of Contents...Contributing Authors...
1. Calculating Binodals and Interfacial Tension of Phase-Separated Condensates from Molecular Simulations, with Finite-Size CorrectionsKonstantinos Mazarakos, Sanbo Qin, and Huan-Xiang Zhou
2. Field-Theoretic Simulation Method to Study the Liquid-Liquid Phase Separation of PolymersSaeed Najafi, James McCarty, Kris T. Delaney, Glenn H. Fredrickson, and Joan-Emma Shea
3. Numerical Techniques for Applications of Analytical Theories to Sequence-Dependent Phase Separations of Intrinsically Disordered ProteinsYi-Hsuan Lin, Jonas Wessen, Tanmoy Pal, Suman Das, and Hue Sun Chan
4. An Introduction to the Stickers-and-Spacers Framework as Applied to Biomolecular CondensatesGarrett M. Ginell and Alex S. Holehouse
5. Multi-Scale Modeling of Protein-RNA Condensation In and Out of EquilibriumRabia Laghmach, Isha Malhotra, and Davit A. Potoyan
6. Fluorescence Lifetime Imaging Microscopy of Biomolecular CondensatesMy Diem Quan. Shih-Chu Leff Liao, Josephine C. Ferreon, and Allan Chris M. Ferreon
7. Single-Molecule Fluorescence Methods to Study Protein-RNA Interactions Underlying Biomolecular CondensatesLaura R. Ganser, Yingda Ge, and Sua Myong
8. Fluorescence Correlation Spectroscopy and Phase SeparationJuan Jeremias Incicco, Debjit Roy, Melissa D. Stuchell-Brereton, and Andrea Soranno
9. Measurement of Protein and Nucleic Acid Diffusion Coefficients within Biomolecular Condensates Using In-Droplet Fluorescence Correlation SpectroscopyIbraheem Alshareedah and Priya R. Banerjee
10. Single-Molecule Imaging of the Phase Separation-Modulated DNA Compaction to Study Transcriptional RepressionLinyu Zuo, Luhua Lai, and Zhi Qi
11. Phase Separation-Based Biochemical Assays for Biomolecular InteractionsGaofeng Pei, Min Zhou, Weifan Xu, Jing Wang, and Pilong Li
12. Determining Thermodynamic and Material Properties of Biomolecular Condensates by Confocal Microscopy and Optical TweezersArchishman Ghosh, Divya Kota, and Huan-Xiang Zhou
13. A High-Throughput Method to Profile Protein Liquid-Liquid Phase SeparationYichen Li, Jinge Gu, Cong Liu, and Dan Li
14. Phase Separation of Rubisco by the Folded SSUL Domains of CcmM in Beta-Carboxysome BiogenesisHuping Wang and Manajit Hayer-Hartl
15. Cryo-Electron Tomography of Reconstituted Biomolecular CondensateFergus Tollervey, Xiaojie Zhang, Mainak Bose, Jenny Sachweh, Jeffrey B. Woodruff, Titus M. Franzmann, and Julia Mahamid
16. Sedimentation Assays to Assess the Impact of Post-Translational Modifications on Phase Separation of RNA-Binding Proteins In Vitro and In CellsLara A. Gruijs da Silva and Dorothee Dormann
17. Synthetic Organelles for Multiple mRNA Selective Genetic Code Expansion in EukaryotesChristopher D. Reinkemeier and Edward A. Lemke
18. Single Molecule Tracking of RNA Polymerase In and Out of Condensates in Live Bacterial Cells Baljyot Singh Parmar and Stephanie C. Weber
19. An Optogenetic Toolkit for the Control of Phase Separation in Living CellsChaelim Kim and Yongdae Shin
20. Assessing the Phase Separation Propensity of Proteins in Living Cells Through Optodroplet Formation Anne Rademacher, Fabian Erdel, Robin Weinmann, and Karsten Rippe
21. Mass Balance Imaging: A Phase Portrait Analysis for Characterizing Growth Kinetics of Biomolecular Condensates Jan Giesler, Victoria Tianjing Yan, Stephan Grill, and Arjun Narayanan
22. Characterizing Properties of Biomolecular Condensates Below the Diffraction Limit In VivoGanesh Pandey, Alisha Budhathoki, and Jan-Hendrik Spille
Subject Index List...