Liquid Crystal ordering of DNA Dickerson Dodecamer duplexes with different 5’- Phosphate terminations

Abstract

The onset of liquid crystal (LC) phases in concentrated aqueous solutions of DNA oligomers crucially depends on the end-to-end interaction between the DNA duplexes, which can be provided by the aromatic stacking of the terminal base-pairs or by the pairing of complementary dangling-ends. Here we investigated the LC behavior of three blunt-end 12-base-long DNA duplexes synthesized with hydroxyl, phosphate and triphosphate 5’-termini. We experimentally characterized the concentration-temperature phase diagrams and we quantitatively estimated the end-to-end stacking free energy, by comparing the empirical data with the predictions of coarse-grained linear aggregation models.

The preservation of LC ordering, even in presence of the bulky and highly charged triphosphate group, indicates that attractive stacking interactions are still present and capable of induce linear aggregation of the DNA duplexes. This finding strengthens the potential role of chromonic like self-assembly for the prebiotic formation of linear polymeric nucleic acids.

Acknowledgement

We are indebted to Tommaso Bellini and Noel A. Clark for having incited this work, for their useful support for the calculation of the phase boundaries from the model and, most importantly, for having introduced us to the fascinating world of DNA liquid crystals. M.T. acknowledges the support of the Invernizzi Fundation.

M.T., G.P.S. and T.P.F. conceived the experiments; M.T. and G.P.S. performed the DNA synthesis; M.T., G.P.S. and T.P.F. performed the experiments; M.T. and T.P.F. analyzed the data; T.P.F. wrote the manuscript.

The authors declare that they have no competing interests.