Detailed calculations have shown that there is little or no base pair unstacking in the first half of the B- to beta-DNA (and the A- to beta-DNA) transitions. The combination of unwinding DNA counterbalanced by right-handed superhelical writhing is achieved almost entirely by modulating alternate sugar pucker geometries. As one passes over the energy barrier separating C2' endo from C3' endo sugar conformations, however, there is a more rapid onset of partial base pair unstacking to relieve strain energies in the sugar-phosphate chain that would otherwise develop.
Furthermore, we have observed that it is necessary to relax the exact requirement that only alternate sugars are involved in the transition. To get over the energy barriers in the centers of these transitions, it is necessary to "rock" the other sugar residue "backwards", towards the C2' exo conformation (in the B- to beta- pathway), or towards the C3' exo conformation (in the A- to beta- pathway). This maneuver readily allows passage through these barriers.