Topological Defects and the Optimum Size of DNA Condensates

130

Section: Resultsmentioning

confidence: 99%

Solid-to-fluid–like DNA transition in viruses facilitates infection

Liu

Sae-Ueng

et al. 2014

130

“…Several theories have been put forth as attempts to explain why toroids and other DNA condensate morphologies grow to a particular size (19,21,22,24,37). A common target of these theories has been to determine the origin of a limitation on DNA bundle size, or thickness͞number of windings in the case of toroids.…”

Section: Mgcl2 Causes a Greater Increase In Toroid Diameter Thanmentioning

confidence: 99%

“…These theories include growth limits based on the build-up of uncompensated electrostatic repulsions, the accumulation of packing defects, and kinetic barriers to DNA strand association in solution (19)(20)(21)(22)(23)(24)(25). All of these theoretical studies agree that DNA toroids should favor a particular size.…”

mentioning

confidence: 93%

Controlling the size of nanoscale toroidal DNA condensates with static curvature and ionic strength

Conwell

Vilfan

Hud

2003

203

190

The process of DNA condensation into nanometer-scale particles has direct relevance to several fields, including cell biology, virology, and gene delivery for therapeutic purposes. DNA condensation has also attracted the attention of polymer physicists, as the collapse of DNA molecules from solution into well defined particles represents an exquisite example of a polymer phase transition.Here we present a quantitative study of DNA toroids formed by condensation of 3 kb DNA with hexammine cobalt (III). The presence or absence of static loops within this DNA molecule demonstrates the effect of nucleation loop size on toroid dimensions and that nucleation is principally decoupled from toroid growth. A comparison of DNA condensates formed at low ionic strength with those formed in the presence of additional salts (NaCl or MgCl2) shows that toroid thickness is a salt-dependant phenomenon. Together, these results have allowed the development of models for DNA toroid formation in which the size of the nucleation loop directly influences the diameter of the fully formed toroid, whereas solution conditions govern toroid thickness. The data presented illustrate the potential that exists for controlling DNA toroid dimensions. Furthermore, this study provides a set of data that should prove useful as a test for theoretical models of DNA condensation.DNA ͉ gene delivery ͉ packaging ͉ condensation W ithin living cells, DNA is highly condensed as compared with free DNA in solution (1). In sperm cells and viruses, where gene transcription is inactive, DNA condensation approaches the limits of molecular compaction (2, 3). The condensation of free DNA in vitro has long been of interest as a potential model for DNA condensation in vivo, particularly as a model of DNA packaging in viruses (4-6). More recently, DNA condensation has attracted much attention for its direct relevance to the preparation of DNA for delivery as a part of gene therapies (7-10).More than 25 years ago it was discovered that multivalent cations cause DNA to collapse from solution into toroid-shaped condensates (11). These structures have typically been reported to measure Ϸ100 nm in outside diameter with a 30-nm hole; however, the generation of substantially larger toroids has also been reported (12, 13). Toroidal DNA condensates have been reported to be the morphology of DNA packaged within some bacterial phages and vertebrate sperm cells (4,5,(14)(15)(16). Thus, the DNA toroid is a morphology used by nature for the high-density packing of genomes. The condensation of DNA for artificial gene delivery has also used toroids (17, 18). However, researchers have yet to develop a method to package DNA that produces particles as homogeneous, both in terms of size and shape, as is achieved by natural packing systems.A considerable number of theoretical studies have sought to explain why DNA toroids and other condensate morphologies (e.g., rods) favor a particular size. These theories include growth limits based on the build-up of uncompensated electrostatic repulsio...

“…Basically, two theoretical approaches have been pursued to address this issue. In the first, the finite size of a toroid is argued to be the thermodynamically stable state of circumferentially wound DNA, reflecting the competition between the bending energy of the DNA chains and their mutual attraction in the presence of topologically unavoidable defects (24). Here it is predicted that the free energy density of a toroid begins to increase at a certain volume threshold that happens to correspond to a few tens of thousands of base pairs.…”

Section: Discussionmentioning

confidence: 99%

DNA delivery by phage as a strategy for encapsulating toroidal condensates of arbitrary size into liposomes

Lambert

Letellìer

Gelbart

et al. 2000

Self Cite

We report a strategy for encapsulating and condensing DNA. When T5 phage binds to its membrane protein receptor, FhuA, its double stranded DNA (120,000 bp) is progressively released base pair after base pair in the surrounding medium. Using cryoelectron microscopy, we have visualized the structures formed after T5 phage DNA is released into neutral unilamellar proteoliposomes reconstituted with the receptor FhuA. In the presence of spermine, toroidal condensates of circumferentially wrapped DNA were formed. Most significantly, the sizes of these toroids were shown to vary, from 90 to 200 nm in their outer diameters, depending on the number of DNA stands transferred. We have also analyzed T5 DNA release in bulk solution containing the detergent-solubilized FhuA receptor. After DNA release in a spermine containing solution, huge DNA condensates with a diameter of about 300 nm were formed containing the DNAs from as many as 10 -20 capsids. At alkaline pH, the condensates appeared as large hollow cylinders with a diameter of 200 nm and a height of 100 -200 nm. Overall, the striking feature of our experiments is that, because of the progressive release of DNA from the phage capsid, the mechanism of toroid formation is fundamentally different from that in the classical studies in which highly dilute, ''naked'' DNA is condensed by direct addition of polyvalent cations; as a consequence, our method leads to toroids of arbitrary size.polyamines ͉ condensation ͉ FhuA ͉ toroids T he condensation of DNA, i.e., the collapse of an extended worm-like random coil DNA molecule into a compact ordered state, has received considerable attention in diverse areas of science (1-3). In biology, it represents a process by which genetic information is packaged and protected. In medicine, it provides a promising means for gene therapy applications through new forms of condensed genes to be delivered to target cells. In polymer and condensed matter physics, DNA condensation is an example of a coil-globule transition or of a selfassembly process in which aggregation of two or more DNA molecules are involved.In vitro condensation of DNA by different chemical agents has provided useful insights into the physical factors governing folding and packaging of DNA. Among these condensing agents, much interest has focused on polycations that modify electrostatic interactions between DNA segments through neutralization of their charges (4) and͞or mediation of attractive forces between them (5). These agents, which induce collapse, aggregation, or complexation by interacting directly with DNA molecules, include small ions (polyamines, cobalt hexamine), cationic polypeptides (polylysine, polyhistidine), or proteins (histones) (6-11).When condensation is induced by addition of polyamines (spermine, spermidine) to very dilute aqueous solution of DNA, striking toroidal structures are the most common morphologies observed by electron microscopy (12-14). Here DNA is circumferentially wrapped as a toroid with a well defined hole in the middle and an outer di...