Preface...
Table of Contents...
Contributing Authors...
1. Chromosome Conformation Capture in Bacteria and Archaea
Fatema-Zahra M. Rashid, Laurien Detmar, and Remus T. Dame
2. Micrococcal Nuclease Digestion Assays for the Analysis of Chromosome Structure in Archaea
Hugo Maruyama
3. Detecting DNA Methylations in the Hyperthermoacidophilic Crenarchaeon Sulfolobus acidocaldarius using SMRT-Sequencing
Christian Tellgren-Roth and Mohea Couturier
4. ProD: A Tool for Predictive Design of Tailored Promoters in Escherichia coli
Friederike Mey, Jim Clauwaert, Maarten Van Brempt, Michiel Stock, Jo Maertens, Willem Waegeman, and Marjan De Mey
5. Computational Study on the Dynamics of Mycobacterium Tuberculosis RNA Polymerase Assembly
Sneha Bheemireddy and Narayanaswamy Srinivasan
6. In Vitro Transcription Assay for Archaea Belonging to Sulfolobales
David Sybers, Daniel Charlier, and Eveline Peeters
7. Prediction of DNA-Binding Transcription Factors in Bacteria and Archaea Genomes
Leonardo Ledesma, Rafael Hernandez-Guerrero, and Ernesto Perez-Rueda
8. In Vivo Screening Method for the Identification and Characterization of Prokaryotic, Metabolite-Responsive Transcription Factors
Amber Joka Bernauw, Veerke De Kock, and Indra Bervoets
9. Application of Special Electron Microscopy Techniques to the Study of DNA-Protein Complexes in E. coli Cells
Andrey Moiseenko, Natalia Loiko, Olga S. Sokolova, and Yurii F. Krupyanskii
10. High-Speed Atomic Force Microscopy Visualization of Protein-DNA Interactions using DNA Origami Frames
Ronnie G. Willaert and Sandor Kasas
11. Separation and Characterization of Protein-DNA Complexes by EMSA and In-Gel Footprinting
Daniel Charlier and Indra Bervoets
12. Chemical Protection and Premodification Binding Interference for the Identification of Phosphate and Base-Specific Contacts in Protein-DNA Complexes
Daniel Charlier
13. Analysis of Protein-DNA Interactions using Isothermal Titration Calorimetry: Successes and Failures
San Hadzi and Jurij Lah
14. Determination of RNA Structure with In Vitro SHAPE-Experiments
Rani Baes, Daniel Charlier, and Eveline Peeters
15. Microscale Thermophoresis to Study RNA-RNA Binding Affinity
Britta Jordan, Lisa Nickel, and Ruth A. Schmitz
16. Toeprint Assays for Detecting RNA Structure and Protein-RNA Interactions
Helen Yakhnin and Paul Babitzke
Subject Index List...
