Liquid crystal self-assembly of random-sequence DNA oligomers

Abstract

In biological systems and nanoscale assemblies, the self-association of DNA is typically studied and applied in the context of the evolved or directed design of base sequences that give complementary pairing, duplex formation, and specific structural motifs. Here we consider the collective behavior of DNA solutions in the distinctly different regime where DNA base sequences are chosen at random or with varying degrees of randomness. We show that in solutions of completely random sequences, corresponding to a remarkably large number of different molecules, e.g., approximately 10 12 for random 20-mers, complementary still emerges and, for a narrow range of oligomer lengths, produces a subtle hierarchical sequence of structured self-assembly and organization into liquid crystal (LC) phases. This ordering follows from the kinetic arrest of oligomer association into long-lived partially paired double helices, followed by reversible association of these pairs into linear aggregates that in turn condense into LC domains.T he selectivity and reversibility of DNA and RNA association enables crucial biological functions in which oligomers selectively pair to target sequences even within large amounts of nucleic acid chains. Selectivity is decisive, for example, in the microRNA-mRNA interactions, crucial in the regulation of gene expression. Similar high levels of selectivity are exploited in genomic PCR, relying on the capacity of primers to target their complementary sequence within a full genome. Selective interactions of DNA oligomers have been exploited in the past years in a variety of strategies for the construction of designed self-assembled nanostructures (1-4). Selectivity combines with self-assembly in the recent observation that short oligomers of nucleic acids having complementary sequences exhibit liquid crystal (LC) ordering (5-7). In this article, we report LC ordering in solutions of DNA oligomers with random sequences where the large body of different competing sequences effectively reduces the selectivity of the interactions. With these results, we show that the phenomenology of the self-assembly of nucleic acid oligomers is actually much richer than previously recognized, involving self-selection, linear aggregation, and ordering of fully random chains. Our results strengthen the notion that DNA and RNA have unequaled capacity of self-structuring and unavoidably suggests self-assembly as the possible key factor for the emergence of nucleic acids from the prebiotic molecular clutter as the coding molecules of life. LC Ordering of Complementary DNA SequencesThe first observations of LC ordering of oligonucleotides were performed in solutions of 6-to 20-base-pair DNA oligomers (6 bp ≤ N B ≤ 20 bp) whose sequences promoted the formation of fully paired duplexes (example 1 in Fig. 1A). These were found to order into the chiral nematic (N Ã ) LC phase in concentration (c DNA ) ranges depending on the oligomer length and sequence. At larger c DNA , the solutions transform into the columnar (COL) phase and, at ...

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