Local structure of DNA toroids reveals curvature-dependent intermolecular forces

The structure and intermolecular forces of DNA condensates

Spontaneous assembly of DNA molecules into compact structures is ubiquitous in biological systems. Experiment has shown that polycations can turn electrostatic self-repulsion of DNA into attraction, yet the physical mechanism of DNA condensation has remained elusive. Here, we report the results of atomistic molecular dynamics simulations that elucidated the microscopic structure of dense DNA as...

Supplemental Material: The structure and intermolecular forces of DNA condensates

Intermolecular forces.

The nature of molecular interactions is examined. Intermolecular forces are divided into long-range and short-range components; the former operate at distances where the effects of electron exchange are negligible and decrease as an inverse power of the separation. The long-range interactions may be subdividied into electrostatic, induction and dispersion contributions, where the electrostatic ...

DNA toroids: stages in condensation.

The effects of polylysine (PLL) and PLL-asialoorosomucoid (AsOR) on DNA condensation have been analyzed by AFM. Different types of condensed DNA structures were observed, which show a sequence of conformational changes as circular plasmid DNA molecules condense progressively. The structures range from circular molecules with the length of the plasmid DNA to small toroids and short rods with app...

Multi-curvature liquid meniscus in a nanochannel: evidence of interplay between intermolecular and surface forces.

We examined the formation of a multiply curved meniscus inside rectangular nanochannels, whose width ranges from 50 to 800 nm at a constant height of 200 nm. When the channel width is smaller than approximately 400 nm under partial wetting conditions, a distinct multi-curvature meniscus was observed at the advancing front with an edge disjoined from the wall. In contrast, a typical pre-wetting ...