in a remarkable experiment a cell of eoli was liced releasing its chromosome for electron microscopy what spewed out of this single cell was a strand of DNA 1,500 times longer than eoli itself how could this enormous molecule fit into a single cell inside a bacterial cell the DNA is much more tidy the DNA is compacted into a structure called a nucleoid a nucleoid consists of DNA arranged in tightly wound loops with the boundaries of the loop domains defined by histonelike anchoring proteins the DNA in the loops is super coiled that is the double helix of DNA coils upon itself creating a tighter more compact structure if one of the strands of a double helix is cut the DNA loses its super coils as the tension dissipates however the other domains remain supercoiled because they are constrained at their bases by the anchoring proteins which prevent rotation to understand super coiling consider a completely relaxed circular piece of DNA an unstressed DNA molecule naturally forms a helix with about 10 base pairs per turn now consider cutting a strand unwinding a turn and then resealing the DNA the DNA is now underwound and has one too few helical turns the DNA will naturally attempt to return to the same number of turns as before but considering the DNA has been resealed in this underwound form it must now create a super coil in the opposite direction in order to relieve the stress negative super coils such as this one relieve the torsional strain of underwound DNA while positive super coils relieve The Strain from overwound DNA this circular double stranded DNA has five negative super coils if the super coils were removed the DNA would be revealed to be underwound by about five turns the tortional stress in the underwound DNA is relieved by rewinding and at the same time creating negative super coils how does DNA achieve a supercoiled state a bacterial cell produc produces enzymes that can twist DNA into Super coils and relieve super coils enzymes that change DNA supercoiling are called topoisomerases because they change the topology of DNA type one topoisomerases cleave only one strand of a double helix while type 2 enzymes cleave both strands type one enzymes are generally used to relieve or unwind super coils while type 2 enzymes use energy to add super coils Topo isomerase 1 binds to DNA and opens up the two strands loosening the double helix this loss of a turn in the double helix allows the DNA to convert from five Super coils to four Topo isomerase 1 Cleaves one strand of a double helix holds on to both ends and passes the other intact strand through the brake after which it relates the strand the topoisomerase comes off the DNA leaving the circular molecule with four super coils instead of five an example of a type 2 Topo isomerase is DNA gyas whose function is to introduce negative super coils in double stranded DNA rather than to remove them the active gyas complex is a tetramer composed of two gy a and two gy B proteins first g b grabs one section of the double stranded DNA then G A introduces a double strand break in the DNA and becomes coal attached to the brakes as it holds the two ends apart adding a negative super coil to DNA requires energy which is gained through ATP hydris gy a which is an ATP Ace uses the energy of ATP hydrolysis to pass the intact double stranded section through the double strand break gy B then rejoins the cleave DNA and opens at the other end to release the newly sealed strand the DNA molecule now contains one negative super coil to maintain proper DNA super coiling levels a cell must delicately balance the activities of the two types of tobo isomerases the nucleoids of bacteria and most ARA as well as the nuclear DNA of ukar are kept negatively supercoiled because the DNA is underwound the two strands of negatively supercoiled DNA are easier to separate than positively supercoiled DNA which is important for transcription enzymes like RNA polymerase that must separate strands of DNA to make RNA some archal species living in acid at high temperature have a challenge of keeping their DNA from denaturing that is separating into singl stranded DNA to solve this problem their DNA is overwhel resulting in positive super coils it is proposed that the extra turns in the DNA tighten the coil which would require more energy in the form of heat to separate the strands