DNA Toroids:  Stages in Condensation

Abstract

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 approximately 1/6 to 1/8 the contour length of the uncondensed circular DNA. Single plasmid molecules of 6800 base pairs (bp) condense into single toroids of approximately 110 nm diameter, measured center-to-center. The results are consistent with a model for DNA condensation in which circular DNA molecules fold several times into progressively shorter rods. Structures intermediate between toroids and rods suggest that at least some toroids may form by the opening up of rods as proposed by Dunlap et al. [(1997) Nucleic Acids Res. 25, 3095]. Toroids and rods formed at lysine:nucleotide ratios of 5:1 and 6:1. This high lysine:nucleotide ratio is discussed in relation to entropic considerations and the overcharging of macroions. PLL-AsOR is much more effective than PLL alone for condensing DNA, because several PLL molecules are attached to a single AsOR molecule, resulting in an increased cation density.

Phase diagram of the ground states of DNA condensates

“…For x = 0.5, the transition line would become independent of L, but for this limiting case, both the toroid phase and the rod-like phase disappear (see below). Coexisting toroidal and rod-like condensates of similar volume and dimensions have been observed in experiments [14,15] suggesting that those condensates were close to a phase transition between the two kinds of structures. Fig.…”

“…This condensation phenomenon serves as an example of high polymer density packing in biology and of polymer phase transitions and phase separations in general, being relevant also for artificial gene delivery [12,13]. Several distinct morphologies of the DNA condensates have been observed including a toroid, a spheroid as well as a rodlike configuration [10,[14][15][16]. Our principal goal is to explore the rich interplay between the strong tendency for compactness, arising from the presence of multivalent cations or osmolytes in the solution, and the intrinsic stiffness of the DNA molecule promoting the chain to be locally straight.…”

Physical Morphology and Surface Properties of Unsaturated Pseudomonas putida Biofilms

“…For molecules of known molecular mass, molecular volumes measured by AFM correlate well with calculated molecular volumes (18,45,51). We measured diameters of extracellular structures but not volumes, because the height of these crowded structures is unknown.…”

Morphological variation in a toroid generated from a single polymer chain

“…When we consider the kinetics of the folding process of a polymer, other structures such as a rod will appear with the same property parameters 23,24 . …”