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arXiv · 1204.0985

Self-assembly of short DNA duplexes: from a coarse-grained model to experiments through a theoretical link

Cristiano De Michele·Lorenzo Rovigatti·Tommaso Bellini·Francesco Sciortino
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Abstract

Short blunt-ended DNA duplexes comprising 6 to 20 base pairs self-assemble into polydisperse semi-flexible chains due to hydrophobic stacking interactions between terminal base pairs. Above a critical concentration, which depends on temperature and duplex length, such chains order into liquid crystal phases. Here, we investigate the self-assembly of such double-helical duplexes with a combined numerical and theoretical approach. We simulate the bulk system employing the coarse-grained DNA model recently proposed by Ouldridge et al. [ J. Chem. Phys. 134, 08501 (2011) ]. Then we evaluate the input quantities for the theoretical framework directly from the DNA model. The resulting parameter-free theoretical predictions provide an accurate description of the simulation results in the isotropic phase. In addition, the theoretical isotropic-nematic phase boundaries are in line with experimental findings, providing a route to estimate the stacking free energy.

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Cristiano De Michele, Lorenzo Rovigatti, Tommaso Bellini, Francesco Sciortino. 2012-04-04. Self-assembly of short DNA duplexes: from a coarse-grained model to experiments through a theoretical link. https://doi.org/10.1039/c2sm25845e

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