Coexistence of coil and globule domains within a single confined DNA chain

Local structure of DNA toroids reveals curvature-dependent intermolecular forces

In viruses and cells, DNA is closely packed and tightly curved thanks to polyvalent cations inducing an effective attraction between its negatively charged filaments. Our understanding of this effective attraction remains very incomplete, partly because experimental data is limited to bulk measurements on large samples of mostly uncurved DNA helices. Here we use cryo electron microscopy to shed light on the interaction between highly curved helices. We find that the spacing between DNA helices in spermine-induced DNA toroidal condensates depends on their location within the torus, consistent with a mathematical model based on the competition between electrostatic interactions and the bending rigidity of DNA. We use our model to infer the characteristics of the interaction potential, and find that its equilibrium spacing strongly depends on the curvature of the filaments. In addition, the interaction is much softer than previously reported in bulk samples using different salt conditions. Beyond viruses and cells, our characterization of the interactions governing DNA-based dense structures could help develop robust designs in DNA nanotechnologies.

Agglomeration structure of superparamagnetic nanoparticles in a nematic liquid crystal medium: Image analysis datasets based on cryo-electron microscopy and polarised optical microscopy techniques

This dataset shows the agglomerate dimension and structure of oleic acid-coated superparamagnetic nanoparticles (SPIONs), which are dispersed in the nematic fluid of a thermotropic liquid crystal (LC), 4-cyano-4′-pentylbiphenyl (5CB). The analysed datasets were acquired from the raw images of the SPION-5CB mixtures obtained using cryogenic transmission electron microscopy (cryo-TEM) and polarised optical microscopy. The image data were quantitatively analysed to extract statistical information on the sizes of SPIONs and their agglomerates and the inter-particle spacing of the agglomerated SPIONs. This dataset supports the fundamental understanding on how colloidal nanospheres behave in an anisotropic fluid, and has a potential to be used as a part of database for automated design of new hybrid materials.

Manipulation of Confined Polyelectrolyte Conformations through Dielectric Mismatch

We demonstrate that a highly charged polyelectrolyte confined in a spherical cavity undergoes reversible transformations between amorphous conformations and a four-fold symmetry morphology as a function of dielectric mismatch between the media inside and outside the cavity. Surface polarization due to dielectric mismatch exhibits an extra "confinement" effect, which is most pronounced within a certain range of the cavity radius and the electrostatic strength between the monomers and counterions and multivalent counterions. For cavities with a charged surface, surface polarization leads to an increased amount of counterions adsorbed in the outer side, further compressing the confined polyelectrolyte into a four-fold symmetry morphology. The equilibrium conformation of the chain is dependent upon several key factors including the relative permittivities of the media inside and outside the cavity, multivalent counterion concentration, cavity radius relative to the chain length, and interface charge density. Our findings offer insights into the effects of dielectric mismatch in packaging and delivery of polyelectrolytes across media with different relative permittivities. Moreover, the reversible transformation of the polyelectrolyte conformations in response to environmental permittivity allows for potential applications in biosensing and medical monitoring.

DNA size in confined environments

For short DNA molecules in crowded environments, we evaluate macroscopic parameters such as the average end-to-end distance and the twist conformation by tuning the strength of the site specific confinement driven by the crowders.