3.2 Higher-order DNA structures: DNA twisting and torsional effects (continued)
Torsional energy can be taken up by alternative DNA conformations
The energy introduced into DNA by twisting has great potential as a regulatory mechanism, since the free energy can be stored in a variety of different high-energy conformations along the chain.
This fluidity of DNA structure can be demonstrated by considering an experiment with a circular eubacterial plasmid DNA molecule that has three naturally occurring negative supercoils introduced by DNA gyrase. What would you predict would happen if a short DNA fragment of sequence 5′-(GC)n-3′ is introduced into such a plasmid? (Hint: look back to Section 3.1 to remind yourself of the particular structural propensity of this sequence.)
Remembering that this particular sequence of alternating purine and pyrimidine bases allows the DNA helix to adopt a Z-form helical structure, you would predict that the increased free energy introduced into the plasmid by DNA gyrase, instead of driving the formation of supercoils, could result in the formation of Z-DNA helix in the stretch of DNA carrying the GC-rich insert.
Transitions from B-DNA to alternative structures such as Z-DNA are, of course, energy-consuming because they require the unwinding of the helix, followed by rewinding in the opposite direction. The formation of a single 12 bp turn of Z-DNA requires an energy input equivalent to that required to form two negative supercoils. Whilst the formation of such Z-DNA regions in vivo is still uncertain, there are many examples of short DNA sequences, containing alternating purines and pyrimidines, that could form such structures. For example, the human genome contains over 45 000 stretches of (CA)n.
Another DNA sequence that can form a novel conformation can occur at what are termed inverted repeats, stretches of DNA sequences that have internal complementarity. These sequences can fold up on themselves in the shape of a cross, forming a structure known as a cruciform (Figure 11c). Formation of a cruciform structure requires unpairing of the existing B-DNA helix, followed by re-pairing into two hairpins, one in each strand, and can serve to release local torsional stresses induced by twisting. Thus the free energy required for twisting is used to drive the unpairing and unstacking of the existing B-DNA, allowing the cruciform structure to be produced.