SupercoiledDNA: Structure
Authors: Bowater Richard P 
Published: July 2015

AbstractSupercoiling is introduced into DNA molecules when the double helix is twisted around its own axis in three‐dimensional space. Experimental techniques that are sensitive to molecular shape can be used to analyse the topological states of DNA, but the approaches used most successfully are high‐speed centrifugation, high‐resolution microscopy and gel electrophoresis. Generally, DNA molecules are negatively supercoiled inside cells, although the level of supercoiling is not equal throughout the genome and many supercoils may be constrained by bound proteins. Supercoiling increases the free energy of DNA and influences DNA metabolism by promoting or hindering specific enzymatic processes. DNA topoisomerases are the main enzymes that regulate DNA topology and several different types of enzymes are present in all cells.Key ConceptsDouble‐stranded DNA helices can wind in three‐dimensional space to form further helices of higher order, formingsupercoiledDNA.Since the early 1960s, the importance of DNA supercoiling to cellular processes has been apparent, with its most obvious consequence being that it aids compaction of large DNA molecules into the relatively small volume of cells.The extent of supercoiling in a DNA molecule is influenced by environmental conditions, such as ionic strength and temperature; since supercoiling of DNA influences the biological pathways in which it is involved, the level of DNA supercoiling inside cells is tightly regulated.Supercoiling provides a significant amount of free energy to DNA molecules and, inside cells, this can be used to drive structural transitions and other metabolic processes that would normally be thermodynamically unfavourable, such as opening of the DNA helix during replication and transcription.Mathematical and modelling studies have provided insight for quantitative analyses of DNA supercoiling, leading to definitions fortwist, which describes how the individual strands of DNA coil around its axis, andwrithe, which describes how the helix axis coils in three‐dimensional space.DNA inside cells contains supercoils of two types: interwound supercoiling occurs when circular DNA winds around its own axis and toroidal supercoiling occurs when the DNA helix forms a series of spirals around an imaginary ring.Any technique that is sensitive to molecular shape will be useful for experimental analysis of supercoiled DNA, but the large size of the molecules means few techniques have been used successfully; those that have been widely used include high‐speed centrifugation, high‐resolution microscopy (e.g. electron microscopy (EM) and scanning‐force microscopy) and agarose gel electrophoresis.A wide variety of proteins that bind to DNA alter the local geometry of its helix and influence DNA topology; an important characterised example of this effect is the winding of DNA around the eukaryotic histone octamer to form the nucleosome.A fundamental feature of closed domains of DNA, such as a circular molecule, is that the two strands of DNA are topologically linked and strand separation can be achieved only by breakage of one of the strands; the main enzymes that regulate DNA topology are DNA topoisomerases and they usually act to remove or introduce negative supercoils or they may remove both positive and negative supercoils.Cellular processes that move macromolecular assemblies along DNA may generate localised DNA supercoiling since as the large protein complex moves along the DNA, its rotation around the DNA may be inhibited.