Liquid crystalline phases of ultra-short DNA and RNA sequences
 

The ability of long, hydrated, double-stranded DNA to form liquid crystal phases has been known for more than 50 years and played a key role in the initial deciphering of its structure. However, according to the Onsager theory and further refinements of these ideas, strands of DNA with fewer than ~30 base pairs should be too short to form LC phases. Recent collaborative work between the Boulder group and the Complex Fluids and Molecular Biophysics group of the University of Milan has shown that self-pairing, or complementary, DNA oligomers as short as six base pairs can exhibit chiral nematic and columnar LC phases (Figure 1)1. Such phases are produced, in concentrated aqueous solutions, by the end-to-end adhesion – due to hydrophobic and p-stacking interactions – and consequent stacking of the duplex oligomers into polydisperse, anisotropic, rod-shaped aggregates, which can order into liquid crystal phases (Figure 2a).

Furthermore, if various sequences are present in the solution, the complementary ones, forming helices, phase-separate from the unpaired sequences into LC domains of double-stranded aggregates which coexist with an isotropic phase of single-stranded DNA2. Such behavior is thought to be produced by the entropy-driven demixing of rigid helices from flexible, unpaired strands, but a key role is also played by the templating effect of stacking and LC ordering.

 

Figure 1. Polarized microscopy images of LC phases of ultra-short DNA strands. (a) Chiral nematic phase of CGCAATTGCG: the colored textures reveal a sub-micrometer pitch, increasing from left to right along the concentration gradient. (b) Domains of hexagonal columnar phase. Scale bar is 50 µm.

 

DNA assembly

Figure 2. Sketch of the self-assembly process leading to the LC alignment of well-paired, short DNA duplexes. (a) Complementary sequences pair into helices, idealized as hydrophilic cylinders with hydrophobic ends capable of end-to-end adhesion and stacking (b) into units sufficiently anisotropic to orientationally and positionally order into LC phases (c), either chiral nematic( N*) or hexagonal columnar (COL). (d) Upon cooling, an isotropic mixture of single-stranded nano-DNAs, the complementary oligomers (yellow–orange and yellow–green) form duplexes and phase separate into LC domains.

The same staged self-assembly acts in RNA short strands3, an interesting fact since RNA is thought to be an earlier form of nucleic acid than DNA. The connection between nucleic acid duplexing and LC formation suggests that LC ordering may be autocatalytic for the growth of longer, complementary duplex NA in mixtures in which both complementary and non-complementary short strands are present. Such LC-enhanced assembly could have been a mechanism for the pre-biotic appearance of DNA-like molecules on primordial Earth.

References

[[1] M. Nakata, G. Zanchetta, B.D. Chapman, C.D. Jones, J.O. Cross, R. Pindak, T. Bellini, and N.A. Clark, “End-to-end stacking and liquid crystal condensation of 6-to-20-base pair DNA duplexes,” Science 318, 1276 (2007).
[2] G. Zanchetta, M. Nakata, M. Buscaglia, T. Bellini, and N.A. Clark, “Phase separation and liquid crystallization of complementary sequences in mixtures of nanoDNA oligomers,” Proceedings of the National Academy of Sciences USA 105, 1111 (2008).
[3] G. Zanchetta, T. Bellini, M.Nakata, and N.A. Clark, “Physical Polymerization and Liquid Crystallization of RNA Oligomers,” Journal of the American Chemical Society 130, 12864 (2008).

Text and images contributed by Giuliano Zanchetta and Michi Nakata.