Polymerase Switching in Response to DNA Damage

Abstract

Protein–DNA interactions are required for all the major functionsof DNA: ­transcription and regulation, replication and repair, eventhe packaging of DNA into chromosomes. Not only are protein–DNAinteractions crucial for all these cellular activities, but theyare also, in our view, among the most fascinating macromolecular­interactions because of their dynamics. In this chapter, we focuson DNA sliding by proteins, particularly diffusive sliding. Suchsliding is typically part of the search for a target on the DNA itselfor for another protein bound to the DNA. Of particular interest hereare the proteins known as DNA sliding clamps that can remain boundto the DNA while diffusing vast distances along the double helixof DNA. We do not yet know the detailed mechanisms of protein slidingon DNA, but we aim to familiarize the reader with what is known observationallyand to provide some discussion of potential mechanisms.