Question

In molecular biology, two identical molecules with different linking number are said to be topoisomers. Describe how a circular DNA molecule can be converted from one topoisomer into another if there are no free ends?   

Answer 1

In the case of closed (circular) double stranded DNA molecules the linking number cannot change because the two ends of the DNA molecule are covalently linked (ie there are no free ends to rotate about each other in space). So these types of molecules cannot change the linking number without a chain break. Unwinding or overwinding without chain break cause torsion within the molecule and to accommodate this torsion the molecule supercoils. Supercoils are introduced into DNA when a duplex is twisted in space around its own axis. Supercoiling can occur only in closed structures because an open molecule can relax the torsion by simply unwinding.

A DNA molecule, whether open or closed that lacks supercoiling is said to be relaxed. Negative supercoils twist the DNA about its axis in the opposite direction from the clockwise turn of the right handed double helix. Negative supercoils are formed in unwound DNA. Positive supercoils are formed in DNA when a DNA molecule is over wound. Here the coiling occurs in the same direction of the intrinsic winding of the double helix. This state can be created in vitro but does not occur naturally. In fact in all prokaryotic and eukaryotic cells, DNA exists in a negatively supercoiled state. Molecules of DNA that are the same except for their linking numbers are called topological isomers. Eukaryotes and prokaryotes possess enzymes capable of converting supercoiled DNA into relaxed DNA. These enzymes are called DNA topoisomerases (DNA swivelase, nicking-closing enzyme, untwisting enzyme, DNA relaxing enzyme). Topoisomerases are a group of enzymes that converts one topological form of DNA into another. They do so by changing the linking number. Some topoisomerases remove only negative supercoils from DNA, but others remove both negative and positive supercoils. Topoisomerases are divided into two classes according to the nature of mechanisms they employ. Type I topoisomerases act by making a transient break in one strand of DNA. Type II topoisomerases function by making a transient double strand break. There are four topoisomerase enzymes in E. coli – topoisomerase I, III, IV and DNA gyrase (topoisomerase II). Topoisomerase I and III are type I enzymes. Gyrase and DNA topoisomerase IV are type II enzymes. The enzymes of the eukaryotes also follow the same principles. Most eukaryotes contain single topoisomerase I enzyme that is required both for replication fork movement and for relaxing supercoils generated by transcription.