As described earlier, premeltons within B-DNA structure contain central beta-DNA core regions connected to B-DNA on either side through kink and antikink boundaries. We have investigated the molecular nature of these boundaries by nonlinear least squares methods. These studies show that it is possible to form premelton structures within B-DNA and within A-DNA (i.e., B-B premeltons, and A-A premeltons), as well as hybrid structures that connect the two (i.e., B-A premeltons and A-B premeltons). Such hybrid premeltons are easily constructed by connecting the central beta-DNA core with either type of kink-antikink boundary. It is important to note that, whereas B-B and A-A premeltons are nontopological, B-A and A-B premeltons are topological.

The B to A structural phase transition can now be understood in the following way. In the presence of suitable thermodynamic conditions (i.e., those that create a bias that favors the formation of A-DNA), kink and antikink within premeltons in B-DNA structure (B-B premeltons) begin to move apart to form larger and larger core regions, whose centers modulate into A-DNA structure. This necessarily involves the formation of B-A premeltons and A-B premeltons, which act as phase boundaries that continue to move apart, leaving A-DNA to form within. Finally, long regions of A-DNA appear, containing A-A premeltons embedded within.

Such a mechanism is reversible, and illustrates how a bifurcation within the central core region of this low energy kink-antikink bound state structure gives rise to the B- to A- DNA structural phase transition.