3.2 Higher-order DNA structures: DNA twisting and torsional effects
As discussed earlier, the helical nature of DNA results for the most part from the properties of the bases, their interactions and the geometry of the helix itself. There is, however, another important contributor to the structure of DNA that is found within the cell. The DNA helix is actually under a torsional stress due to what is called DNA twisting, which arises when the two strands of the helix are twisted around the axis, as shown in Figure 11a.
The polynucleotide backbone is, of course, constrained by rigid bond lengths and angles and it can be twisted to only a limited extent. The torsional stress that this twisting introduces into the DNA helix acts as an internal ‘store’ of free energy which serves to drive the formation of various alternative conformational states that have higher energy requirements for their formation, including the cruciforms (Figure 11c) and Z-DNA.
As a way of visualising the energy that this twisting of the helix can introduce into the molecule, imagine twisting a rubber band a few times. What happens when you let go of one end?
The band spontaneously untwists, using the energy you put into it by twisting, and rotates a number of times about its own axis.
In its natural state within the cell, DNA does not behave like a twisted rubber band, as it does not have ‘free’ ends. The movement and conformation of the duplex DNA molecule in vivo is constrained by non-covalent interactions with proteins or, in the case of bacterial chromosomes and plasmid DNAs, direct covalent joining to form a continuous circle.
Twisting of DNA can occur in both directions, by rotation clockwise or anticlockwise around the axis of the helix. In vivo, B-DNA is negatively twisted; that is, the strands are rotated clockwise (Figure 11a).
With twisting of the DNA, parts of the helix deviate from the B form, adopting alternative conformations in an attempt to minimise the torsional strain. Such conformations, called DNA supercoils, can be either an intertwined (i.e. supercoiled) helix or a solenoidal structure, as shown in Figure 11b. In vivo, these structures are stabilised by interactions with protein components of the chromosome and we will discuss how this is achieved shortly. Depending upon the twist being introduced into the DNA chain, the supercoils can be either positive or negative.
What type of supercoiling will exist in B-DNA in vivo?
As B-DNA in vivo is negatively twisted, it will have negative supercoils.
In E. coli, the torsional stress is continually maintained by an enzyme called DNA gyrase, which introduces negative twists into the chromosome, resulting in it being negatively supercoiled. DNA gyrase belongs to a class of DNA processing enzymes called topoisomerases, which we will discuss in more detail shortly. This enzyme effectively converts the chemical energy released on hydrolysis of ATP into torsional energy in a negatively supercoiled DNA chain. As a result of DNA twisting, the Gibbs free energy content of supercoiled DNA is high. This free energy is available for various biological processes.
The opening up of the DNA helix to allow for DNA replication, repair or transcription is an energy-demanding process. Why is this so?
In order to denature duplex DNA, energy is required to overcome the base-pairing and base-stacking energies.
Negatively supercoiled DNA presents a considerably lower energy barrier for such unpairing than does non-twisted DNA, whereas positively supercoiled DNA presents a higher energy barrier. The most likely reason for the maintenance of a genome under negative supercoiling stress is that it allows the dynamic opening of the helix for transcription, replication and repair to be energetically more favourable than for non-supercoiled DNA. It is interesting to note that certain extremophile bacteria, which live at temperatures high enough to spontaneously overcome the energy barrier for denaturation of negatively supercoiled B-DNA, instead have positively supercoiled genomic DNA.