Topoisomers

Topoisomers are molecules that have the same sequence of covalently bonded atoms but differ in the three-dimensional arrangement of their atoms in space. This difference in spatial arrangement arises from the presence of different topological forms, particularly in circular DNA molecules. In essence, topoisomers are isomers that cannot be interconverted by simple bond rotation.

The most common context for topoisomers is in the study of DNA. Circular DNA molecules, such as those found in plasmids and bacterial chromosomes, can exist in different topological states. These states are determined by the number of times one strand of the DNA double helix is intertwined around the other, a property known as linking number. Changes in the linking number can occur through the breakage and rejoining of one or both DNA strands. Enzymes called topoisomerases are responsible for catalyzing these changes, allowing for the manipulation of DNA topology, which is crucial for processes like DNA replication, transcription, and recombination.

The main types of DNA topoisomers are relaxed, supercoiled, and nicked circular forms. Relaxed circular DNA has a linking number equivalent to its B-DNA form. Supercoiled DNA is more compact and has a linking number that deviates from the relaxed state, either positively or negatively. Nicked circular DNA is a circular molecule with a break in one strand, which allows it to relax and adopt a less constrained conformation, effectively eliminating supercoiling. The relative abundance and interconversion of these topoisomers are often analyzed using gel electrophoresis, where different topoisomers migrate at different rates.