Existence of the B-Form DNA helix in nanoDNA liquid crystals and its variation due to aggregate assembly*

We show using diffraction of a synchrotron X-ray microbeam that liquid crystalline aggregates of 12mer nanoDNA, such as the Drew-Dickerson Dodecamer (DD), demonstrate a marked B-form DNA double-helix with only marginally less order than seen in longer DNA, such as the calf-thymus DNA used by Rosalind Franklin to produce the historic Photo 51. This finding is significant because it shows that B-form helical order persists in liquid crystals of DD even though the backbone of the column contains a double-strand break at every twelfth position and the DD segments are not held rigidly in place as part of a crystal. The coherence of the B-form helix is influenced by the mode of aggregate self-assembly, where aggregates assembled by a base-paired sticky-end produce much longer helical correlation lengths than those formed by hydrophobic blunt-ends. Finally, we found that aggregates of blunt-end 4mer oligomers shorter than half of a single B-form helical turn no longer display the B-form helical diffraction pattern but order with a different structure. This study gives fundamental insight into the extent to which the classical DNA helix is affected by discontinuity in the polymer backbone.