Liquid crystalline phases in oligonucleotide solutions

In this thesis, we investigate the behavior of short complementary B-form DNA oligomers, 6 to 20 base pairs in length, exhibiting chiral nematic and columnar liquid crystal phases, even though such duplexes lack the shape anisotropy required for liquid crystal ordering. Structural characterization reveals that these phases are produced by the end-to-end stacking of the duplex oligomers into polydisperse anisotropic rod-shaped aggregates, which can order into liquid crystals. By use of polarized optical microscopy, X-ray micro-di raction and optical interferometry, we determine the phase diagram of DNA oligomers and we estimate the stacking energy to be 4-6 KBT. We also nd that upon cooling mixed solutions of short DNA oligomers, in which only a small fraction of the present DNA is complementary, the duplex-forming oligomers phase-separate into liquid crystal droplets, leaving the unpaired single strands in isotropic solution. This spontaneous partitioning is the combined result of the free energy gain from the end-to-end stacking and LC ordering of duplexes and of depletion-type interactions favoring the segregation of the more rigid duplexes from the flexible single strands. In a chemical environment where oligomer ligation is possible, such ordering and condensation would provide an autocatalytic link whereby complementarity promotes the extended polymerization of complementary oligomers. The possible relevance of these observations for prebiotic synthesis of nucleic acids is discussed.