Lifting the Curtain: Using Topology to Probe the Hidden Action of Enzymes

ne of the important issues in molecular biology is the three-dimensional structure (shape) of proteins and deoxyribonucleic acid (DNA) in solution in the cell and the relationship between structure and function. Ordinarily, protein and DNA structure is determined by X-ray crystallography or electron microscopy. Because of the close packing needed for crystallization and the manipulation required to prepare a specimen for electron microscopy, these methods provide little direct evidence for molecular shape in solution. Topology can shed light on this key issue. The topological approach to enzymology is an experimental protocol in which the descriptive and analytical powers of topology and geometry are employed in an indirect effort to determine the enzyme mechanism and the structure of active enzyme-DNA complexes in vitro (in a test tube). We describe how recent results in 3-dimensional topology [3, 5, 9, 10, 11] have proven to be of use in the description and quantization of the action of cellular enzymes on DNA.