| dc.description |
There exist naturally occurring enzymes (topoisomerases and recombinases), which, in order to mediate the vital life processes of replication, transcription, and recombination, manipulate cellular DNA in topologically interesting and non-trivial ways [24, 30]. These enzyme actions include promoting the coiling up (supercoiling) of DNA molecules, passing one strand of DNA through another via a transient enzyme-bridged break in one of the strands (a move performed by topoisomerase), and breaking a pair of strands and recombining them to different ends (a move performed by recombinase). An interesting development for topology has been the emergence of a new experimental protocol, the topological approach to enzymology [30], which directly exploits knot theory in an effort to understand enzyme action. In this protocol, one reacts artificial circular DNA substrate with purified enzyme in vitro (in the laboratory); the enzyme acts on the circular DNA, causing changes in both the euclidean geometry (supercoiling) of the molecules and in the topology (knotting and linking) of the molecules. These enzyme-caused changes are experimental observables, using gel electrophoresis to fractionate the reaction products, and rec A enhanced electron microscopy [15] to visualize directly and to determine unambiguously the DNA knots and links which result as products of an enzyme reaction. This experimental technique calls for the building of knot-theoretic models for enzyme action, in which one wishes mathematically to extract information about enzyme mechanism from the observed changes in the DNA molecules. |
