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SMC complexes : methods and protocols

Author: Anjana Badrinarayanan
Publisher: New York, NY : Humana Press, [2019] ©2019
Series: Methods in molecular biology (Clifton, N.J.), v. 2004.
Edition/Format:   eBook : Document : EnglishView all editions and formats
Summary:

The protocols explore numerous subjects such as depletion systems to assess SMC function, genetic manipulation of SMC proteins, chromosomal, biochemical, and microscopy-based assays of SMC activity,  Read more...

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Genre/Form: Electronic books
Laboratory manuals
Additional Physical Format: (OCoLC)1089003724
Material Type: Document, Internet resource
Document Type: Internet Resource, Computer File
All Authors / Contributors: Anjana Badrinarayanan
ISBN: 9781493995202 1493995200
OCLC Number: 1105930864
Description: 1 online resource (xiii, 336 pages) : illustrations (some color).
Contents: Part I: Depletion Systems to Assess SMC Function 1. Using Cell Cycle Restricted Alleles to Study the Chromatin Dynamics and Functions of the Structural Maintenance of Chromosome (SMC) Complexes In Vivo Demis Menolfi and Dana Branzei 2. Degradation of S. cerevisiae Cohesin with the Auxin-Inducible Degron System Clementine Brocas, Cecile Ducrot, and Karine Dubrana 3. Efficient Depletion of Fission Yeast Condensin by Combined Transcriptional Repression and Auxin-Induced Degradation Yasutaka Kakui and Frank Uhlmann 4. Conditional Mutation of SMC5 in Mouse Embryonic Fibroblasts Himaja Gaddipati, Marina V. Pryzhkova, and Philip W. Jordan Part II: Genetic Manipulation of SMC Function 5. High-Throughput Allelic Replacement Screening in Bacillus subtilis Marie-Laure Diebold-Durand, Frank Burmann, and Stephan Gruber 6. Identifying Functional Domains in Subunits of Structural Maintenance of Chromosome (SMC) Complexes by Transposon Mutagenesis Screen in Yeast Avi Matityahu, Michal Shwartz, and Itay Onn 7. Multicomponent Yeast Two-Hybrid System: Applications to Study Protein-Protein Interactions in SMC Complexes Jan Josef Palecek, Lucie Vondrova, Katerina Zabrady, and Jakub Otocka 8. Knocking in Multi-Functional Gene Tags into SMC Complex Subunits Using Gene Editing Paul Kalitsis, Tao Zhang, Ji Hun Kim, Christian F. Nielsen, Kathryn M. Marshall, and Damien F. Hudson Part III: Chromosomal Assays of SMC Activity 9. Chromosome Conformation Capture with Deep Sequencing to Study the Roles of the Structural Maintenance of Chromosomes Complex In Vivo Tung B.K. Le 10. Analysis of the Chromosomal Localization of Yeast SMC Complexes by Chromatin Immunoprecipitation Vasso Makrantoni, Daniel Robertson, and Adele L. Marston 11. Analysis of Cohesin Association to Newly Replicated DNA through Nascent Strand Binding Assay (NSBA) Camilla Frattini and Rodrigo Bermejo 12. Preparation of Cell Cycle Synchronized Saccharomyces cerevisiae Cells for Hi-C Stephanie A. Schalbetter and Jonathan Baxter Part IV: Biochemical Assays of SMC Activity 13. Dissecting DNA Compaction by the Bacterial Condensin MukB Rupesh Kumar, Soon Bahng, and Kenneth J. Marians 14. In Vivo and In Vitro Assay for Monitoring the Topological Loading of Bacterial Condensins on DNA Koichi Yano, Koichiro Akiyama, and Hironori Niki 15. A Protocol for Assaying the ATPase Activity of Recombinant Cohesin Holocomplexes Menelaos Voulgaris and Thomas G. Gligoris 16. In Vitro Detection of Long Noncoding RNA Generated from DNA Double-Strand Breaks Sheetal Sharma and Fabrizio d'Adda di Fagagna Part V: Microscopy-Based Assays of SMC Activity 17. Tracking Bacterial Chromosome Dynamics with Microfluidics-Based Live Cell Imaging Suchitha Raghunathan and Anjana Badrinarayanan 18. Live-Cell Fluorescence Imaging of RecN in Caulobacter crescentus under DNA Damage Afroze Chimthanawala and Anjana Badrinarayanan 19. Microinjection Techniques in Fly Embryos to Study the Function and Dynamics of SMC Complexes Catarina Carmo, Margarida Araujo, and Raquel A. Oliveira 20. Purification and Biophysical Characterization of the Mre11-Rad50-Nbs1 Complex Logan R. Myler, Michael M. Soniat, Xiaoming Zhang, Rajashree A. Deshpande, Tanya T. Paull, and Ilya J. Finkelstein Part VI: Theoretical Modeling of SMC Activity 21. Three-Dimensional Thermodynamic Simulation of Condensin as a DNA-Based Translocase Josh Lawrimore, Yunyan He, M. Gregory Forest, and Kerry Bloom 22. Molecular Dynamics Simulations of Condensin-Mediated Mitotic Chromosome Assembly Yuji Sakai, Tatsuya Hirano, and Masashi Tachikawa
Series Title: Methods in molecular biology (Clifton, N.J.), v. 2004.
Responsibility: edited by Anjana Badrinarayanan.

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