Liquid Crystal Ordering in DNA Double Helices with Backbone Discontinuities

Short DNA double helices in highly concentrated solutions self-assemble into long noncovalent polymers and globally order as liquid crystals. What level of helical defect is compatible with this collective ordering is still unclear. In this work, we show that a series of 20 bp-long DNA double helices with different structural defects such as nicks and gaps still retain their capability to transition into liquid crystalline solutions despite the increased flexibility of their structure. These results expand our understanding of the space of hybridization motifs leading to linear physical polymerization and liquid crystal ordering. Moreover, by studying liquid-crystalline solutions made of 20 bp-long duplexes with a central dinucleotidic gap, we find that regardless of the highly crowded state of the system, guanosine monophosphate molecules can diffuse in-between the DNA polymers and effectively fill the gap. This finding enables formulation of a prebiotic scenario where fragmented DNA double helices, held together by self-interactions and supramolecular ordering, form a matrix rich in substrates for ligation, gap-filling, and primer extension reactions.