Depite 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.

Introduction.- Nonspecific DNA Binding: Searching DNA and Altering DNA Properties.- DNA Search Theory.- DNA Search, Hopping vs. Sliding.- SSB DNA Search.- HN-S Proteins or DNA Sliding Search.- Processivity Clamp.- DNA Bending Proteins.- Kinetics of DNA Binding and Bending by Proteins.- Modes of DNA Interaction by Architectural Proteins.- Complex Protein-DNA Interactions.- DNA Looping by Repressor Proteins.- NF-kappaB Transcription Factor Crystallography.- Replication Complex.- DNA Recombination Complexes.- DNA Binding by Alkyltransferase Repair Proteins.- DNA Polymerase Crystallography.- Polymerase Switching in Response to DNA Damage.- Single Molecule Studies on Chromatin.- Regulation of Chromosome Conformation in Cells.- Nucleosome Positioning Across Genomes.