Self-assembly of mesogenic bent-core DNA nanoduplexes. Issue 15 (20th March 2015)

• Record Type: Journal Article
• Authors: Nguyen, Khanh Thuy; Battisti, Anna; Ancora, Daniele; Sciortino, Francesco; De Michele, Cristiano
• Is Part Of: Soft matter. Volume 11:Issue 15(2015)
• Page Start: 2934
• Page End: 2944
• Publication Date: 2015-03-20
• Subjects: Soft condensed matter -- Periodicals; 530.413
• DOI: 10.1039/c4sm01571a
• Languages: English
• ISSNs: 1744-683X

Abstract

Abstract : Modelling DNA nanoduplexes as bent-core mesogens explains the sequence dependence of the isotropic–nematic phase boundary. Abstract : Short cylinder-like DNA duplexes, comprising 6 to 20 base pairs, self-assemble into semi-flexible chains, due to coaxial stacking interactions between their blunt ends. The mutual alignment of these chains gives rise to macroscopically orientationally ordered liquid crystal phases. Interestingly, experiments show that the isotropic–nematic phase boundary is sequence-dependent. We perform all-atom simulations of several sequences to gain insights into the structural properties of the duplex and correlate the resulting geometric properties with the observed location of the isotropic–nematic phase boundary. We identify in the duplex bending the key parameter for explaining the sequence dependence, suggesting that DNA duplexes can be assimilated to bent-core mesogens. We also develop a coarse-grained model for the different DNA duplexes to evaluate in detail how bending affects the persistence length and excluded volume of the aggregates. This information is fed into a recently developed formalism to predict the isotropic–nematic phase boundary for bent-core mesogens. The theoretical results agree with the experimental observations.