HENRY M. SOBELL
B- to Z- STRUCTURAL PHASE TRANSITION
Although B- and A- DNA are right handed double-helical structures, DNA molecules containing the alternating poly d (G-C): poly d (G-C) sequence can, under certain conditions, assume a left-handed double helical conformation (i.e., in the presence of high salt and/or negative superhelicity). This structure, called Z-DNA, contains the dinucleotide (G-C) as the asymmetric unit, held together by Watson-Crick base pairs. Being a left-handed double helical structure, Z-DNA contains sugar-phosphate backbone conformations radically different from either B- or A- DNA.
What is the nature of the B to Z junction, and how does this structural phase transition take place?
The transition arises as the result of a bifurcation that takes place during the formation of the dislocaton. As before, DNA breathing within the premelton takes place, followed by chains "snapping back" to form pairs of single-stranded "bubble-like" protrusions on opposite chains. As pairs of protrusions move apart, Z- DNA forms within. The molecular boundaries that allow the helix to "swing left" capitalize on the additional flexibility and length provided by the single-stranded DNA regions on opposite DNA chains. B - Z boundaries form simultaneously on both ends in a concerted 2-fold symmetric process. This is a direct consequence of the nonlinearity that ties the process together.
Due to its extreme complexity, it is not possible to say anything more about the stereochemistry of the junction. A fundamental prediction of the model, however, is the appearance of single-stranded DNA regions juxtaposed to beta-DNA regions within each B-Z junction. The model predicts S1 nuclease sensitive sites to lie within these junctions, and predicts high cooperativity to accompany ethidium binding, leading to increasing lengths of beta-DNA "pinned" by ethidium at the expense of Z-DNA. Both predictions have been supported by existing experimental evidence.
An analogous model can be used to understand the A- to Z- RNA transition, which makes similar predictions.