Prof. Cristiano De Michele:

Liquid Crystal Ordering by Short DNA Duplexes Self-Assembly

Abstract:

Concentrated solutions of short blunt-ended DNA duplexes, as short as 6 base pairs, are known to order into the nematic liquid crystal phase. This self-assembly is due to the stacking interactions between duplex terminals, which promotes their aggregation into polydisperse chains with a significant persistence length. Experiments show that liquid crystal phases form above a critical volume fraction  depending on the duplex length. We investigate two coarse-grained models of DNA double-helical duplexes by means of numerical simulations and a recently proposed theoretical framework [1]. In the first model (SQ) the DNA duplex is represented as an hard quasi-cylinder whose bases are decorated with two identical reactive sites and the stacking interaction between terminal sites is modeled via a short-range square-well potential. In the second model (RB) [2,3], which is less minimalist, nucleotides are represented as rigid bodies with three interaction sites. We compare numerical results with theoretical predictions and find a satisfactory quantitative matching of the system structure in the isotropic phase for both models. For the SQ model we also find an acceptable agreement between theoretical and numerical results for the isotropic-nematic phase boundaries. Finally the comparison of critical concentrations calculated theoretically for both models with experimental findings enables us to provide an estimate of the coaxial stacking energy in line with experimental expectations.

References:

[1] C. De Michele, T. Bellini and F. Sciortino, Macromolecules 45, 1090 (2012).

[2] C. De Michele, L. Rovigatti and F. Sciortino, in preparation.

[3] T. E. Ouldridge, A. A. Louis and J. P. K. Doye , J. Chem. Phys. 134, 085101 (2011).

[4] V. A. Vasiliskov, D. V. Prokopenko, and A. D. Mirzabekov, Nucleic Acids Res. 29, 2303 (2001). [5] P. Yakovchuk, E. Protozanova, and M. D. Frank-Kamenetskii, Nucleic Acids Res. 34, 564 (2006).