Single-molecule reviews

The discovery of the double-helical structure of DNA ushered in a new era of molecular biology. Among the many experimental approaches to study protein-DNA interactions, single-molecule techniques are frequently chosen for their unique capability of following transient and heterogeneous molecular events in an asynchronous population, which allows the user to delineate the time-dependent behavior of individual molecules or complexes in exquisite detail. With these tools, researchers are able to obtain mechanistic insights that are often hidden from ensemble measurements yet crucial for informing protein function. There are two major branches of single-molecule methodology, fluorescence-based visualization and force-based manipulation. The former is used to describe the compositional and conformational dynamics of molecular assemblies, while the latter is harnessed to elucidate the mechanical nature of biomolecular interactions and the operation of molecular machines. As such, these two approaches provide complementary information on molecular mechanisms. These platforms, often referred to as single-molecule correlative force and fluorescence microscopy, are ideally suited for studying protein-DNA interactions as they facilitate investigations on how DNA structure regulates protein behavior and, conversely, how protein activities affect the physical state and metabolism of DNA.