Fig. 1.
The principle of DNA mutual alignment (taken from the supplementary material of ref. 38). The azimuthal orientation of each molecule Φv is shown by a bold arrow in its top cross-section (drawn from the axis to the middle of the minor groove of the molecule). The alignment with strands of one molecule facing the grooves of the other one (A) leads to intermolecular attraction (or reduced repulsion) compared with relative orientations with strand-to-strand alignment (B). To realize the corresponding energy gain of favorable juxtaposition, the strands must stay in register with the grooves over the whole juxtaposition length. Sequence-dependent variations in the local helical pitch H will disrupt such register in juxtaposition of molecules with different sequences but not in juxtaposition of molecules with the same sequences as illustrated in Fig. 2.