Single-molecule micromanipulation studies of DNA and architectural proteins

Architectural proteins play a key role in the folding, organization and compaction of genomic DNA in all organisms. By bending, bridging or wrapping DNA, these proteins ensure that its effective volume is reduced sufficiently to fit inside the cell or a dedicated cellular organelle, the nucleus (in bacteria/archaea and in eukaryotes respectively). In addition, the properties of many of these proteins permit them to play specific roles as architectural cofactors in a large variety of DNA transactions. However, as architectural proteins often bind DNA with low sequence specificity and affinity, it is hard to investigate their interaction using biochemical ensemble techniques. Single-molecule micromanipulation approaches that probe the properties of DNA-binding proteins by pulling on individual protein–DNA complexes have, in this respect, proved to be a very powerful alternative. Besides revealing architectural properties, these approaches can also reveal unique parameters not accessible to biochemical approaches, such as the binding kinetics and unbinding forces of individual proteins.