Williams M.C. Biophysics of DNA-Protein Interactions: From Single Molecules to Biological Systems

Springer Science+Business Media, 2011,
Pages: 349Depite the rapid expansion of the field of biophysics, there are very few books that comprehensively treat specific topics in this area. Recently, the field of single molecule biophysics has developed very quickly, and a few books specifically treating single molecule methods are beginning to appear. However, the promise of single molecule biophysics is to contribute to the understanding of specific fields of biology using new methods. This book would focus on the specific topic of the biophysics of DNA-protein interactions, and would include the use of new approaches, including both bulk methods as well as single molecule methods. This would make the book attractive to anyone working in the general area of DNA-protein interactions, which is of course a much wider market than just single molecule biophysicists or even biophysicists.The subject of the book will be the biophysics of DNA-protein interactions, and will include new methods and results that describe the physical mechanism by which proteins interact with DNA. For example, there has been much recent work on the mechanism by which proteins search for specific binding sites on DNA. A few chapters will be devoted to experiments and theory that shed light on this important problem. We will also cover proteins that alter DNA properties to facilitate interactions important for transcription or replication. Another section of the book will cover the biophysical mechanism by which motor proteins interact with DNA. Finally, we will cover larger protein-DNA complexes, such as replication forks, recombination complexes, DNA repair interactions, and their chromatin context.Contents
Binding DNA and Changing its Shape
Introduction to Biophysics of DNA-Protein Interactions: From Single Molecules to Biological Systems
Single-Molecule Imaging of LacI Diffusing Along Nonspecific DNA
How Proteins Slide on DNA
Role of DNA Conformations in Gene Regulation
Recognition of Nucleic Acids by Transcription Factor NF-κB
Dynamics and Mechanism of DNA-Bending Proteins in Binding Site Recognition
Studies of Sequence-Nonspecific HMGB DNA-Binding Proteins
DNA Interactions with Single-Stranded DNA Binding Proteins and Retroviral Nucleic Acid Chaperones by Force Spectroscopy
Complex Protein-DNA Interactions
DNA Looping in Prophage Lambda: New Insight from Single-Molecule Microscopy
Dynamics of Protein-ssDNA Interactions in the Bacteriophage T4 Homologous Recombination System
Polymerase Switching in Response to DNA Damage
Topological Probes of a Cooperative, Nonspecific Protein-DNA Complex
How to Think Like a Single Molecule: Obtaining Quantitative Measurements on Single DNA Molecules and Chromatin Fibers
Long-Range Chromatin Interactions in Cells