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

Conwell, Christine C.; Vilfan, Igor D.; Hud, Nicholas V.

doi:10.1073/pnas.1533135100

Cited by 203 publications

(204 citation statements)

References 36 publications

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“…The structures of the cation-MT bundle phases are not sensitive to the concentration of condensing cation when all MTs are in the bundle phase, unlike what has been recently observed for DNA with low ionic strength (31). However, the addition of monovalent salt dramatically affects the MT bundles and causes the MT-MT spacing to swell (Fig.…”

Section: Resultsmentioning

confidence: 68%

Higher-order assembly of microtubules by counterions: From hexagonal bundles to living necklaces

Needleman

Ojeda-López²,

Raviv³

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

167

204

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Cellular factors tightly regulate the architecture of bundles of filamentous cytoskeletal proteins, giving rise to assemblies with distinct morphologies and physical properties, and a similar control of the supramolecular organization of nanotubes and nanorods in synthetic materials is highly desirable. However, it is unknown what principles determine how macromolecular interactions lead to assemblies with defined morphologies. In particular, electrostatic interactions between highly charged polyelectrolytes, which are ubiquitous in biological and synthetic self-assembled structures, are poorly understood. We have used a model system consisting of microtubules (MTs) and multivalent cations to examine how microscopic interactions can give rise to distinct bundle phases in biological polyelectrolytes. The structure of these supramolecular assemblies was elucidated on length scales from subnanometer to micrometer with synchrotron x-ray diffraction, transmission electron microscopy, and differential interference contrast microscopy. Tightly packed hexagonal bundles with controllable diameters were observed for large trivalent, tetravalent, and pentavalent counterions. Unexpectedly, in the presence of small divalent cations, we have discovered a living necklace bundle phase, comprised of 2D dynamic assemblies of MTs with linear, branched, and loop topologies. This new bundle phase is an experimental example of nematic membranes. The morphologically distinct MT assemblies give insight into general features of bundle formation and may be used as templates for miniaturized materials with applications in nanotechnology and biotechnology.cation ͉ like-charge attraction ͉ x-ray I n this article, we present our findings on the assembly behavior of microtubules (MTs), a model nanoscale tubule. MTs are hollow, cylindrical protein polymers, with inner and outer diameters of Ϸ15 and 25 nm, respectively, involved in a variety of cellular functions, including cell division, intracellular transport, and cell morphology. MTs often assemble into arrays and bundles as in axostyles in protozoa, the cortical array in plants, the mitotic spindle, and neuronal processes (1). MT-associated proteins (MAPs) regulate the interactions between MTs, giving rise to MT bundles with various degrees of order and different MT-MT spacings, both in native biological structures such as axons and dentrites and in in vivo overexpression experiments (2). In vitro experiments show that subtle mutations in MAPs can lead to bundles with radically different structures, converting hexagonally packed bundles into linear chains of MTs (3). However, it is unclear how MAP-controlled, MT-MT interactions lead to bundles with the observed architectures.Understanding the fundamental mechanisms underlying the nature of the self-assembly of nanometer-scale tubules and rods is also important from a technological perspective. Nanotubes are currently being developed as miniaturized materials with applications as circuitry components, templates for nanosized wires and optic...

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Section: Resultsmentioning

confidence: 68%

Higher-order assembly of microtubules by counterions: From hexagonal bundles to living necklaces

Needleman

Ojeda-López²,

Raviv³

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

167

204

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“…Toroids of size larger than ∼200 nm have been observed. In a detailed study [17], the toroid mean diameter was found to vary between 30 and 100 nm depending on the solution conditions, while the toroid thickness was in the range from 10 to 70 nm. The geometry of a toroid can be characterized by the ratio between its thickness and its diameter.…”

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confidence: 99%

“…5, we show some experimental data for the maximum thickness to diameter ratio (data extracted from Ref. [17]) under var- [17]. For a given condensation condition (see legend), we take only the point with the maximum thickness to diameter ratio.…”

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confidence: 99%

Phase diagram of the ground states of DNA condensates

et al. 2015

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Phase diagram of the ground states of DNA in a bad solvent is studied for a semi-flexible polymer model with a generalized local elastic bending potential characterized by a nonlinearity parameter x and effective self-attraction promoting compaction. x = 1 corresponds to the worm-like chain model. Surprisingly, the phase diagram as well as the transition lines between the ground states are found to be a function of x. The model provides a simple explanation for the results of prior experimental and computational studies and makes predictions for the specific geometries of the ground states. The results underscore the impact of the form of the microscopic bending energy at macroscopic observable scales.The non-linear elasticity of DNA at short length scales, probed by non-equilibrium DNA cyclization experiments [1,2], AFM imaging on surfaces [3], as well as by equilibrium mechanically constrained DNA experiments [4][5][6], is still not well understood. While the conclusions regarding the first two methods for probing non-linear ds-DNA elasticity have been criticized [7], the experiments on stressed DNA ring molecules are performed by a different methodology based on thermodynamic methods via DNA high-curvature states through partial hybridization of a ss-DNA loop with a linear complementary strand [6]. This methodology does not depend on thermal fluctuations to realize high-curvature states and thus appears to have a far better accuracy and reliability. The non-linearity in this latter case is clearly present and is captured in a single parameter describing the onset of DNA kink formation. This clearly exhibited elastic nonlinearity is taken as the motivation for the present study that attempts to derive the macroscopic consequences of this interesting microscopic elastic behavior of DNA.Another interesting facet of DNA behavior is that under specific solution conditions, it condenses into highly compact structures with pronounced symmetry [8][9][10][11]. 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. In the absence of stiffness, one would expect the chain to adopt a densely compact spheroidal globule configuration. The key issue is to understand how local stiffness and the detailed way it enters the elastic energy result in the spheroidal configuration becoming unstable w.r.t. other lower energy configurations. In particular, one would like to map out a phase diagram and understand the different condensate geometries.The topolog...

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“…[8][9][10][11][12][13] A few recent experiments concentrated on the kinetics of DNA compaction. They showed that DNA condenses continuously and linearly with time once the compaction process begins.…”

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confidence: 99%

Compaction Dynamics of Single DNA Molecules under Tension

Wang

Zhang

et al. 2006

J. Am. Chem. Soc.

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The compaction of DNA by multivalent cations has been the subject of many investigations, not only because it is biologically important, but also because it poses a fascinating challenge to our understanding of semiflexible polymers. [1][2][3][4][5] Polyelectrolyte theory has figured out that the attractive potential that leads to DNA compaction originates from correlated fluctuation of counterions shared between DNA segments. 6 Experimental observations have revealed that DNA condensates have generally a toroidal geometry with a typical size of ∼100 nm in diameter. It is generally believed that DNA within a toroid is organized in a hexagonal close-packed lattice, 7 but how such a structure is formed is still not fully understood.Single-molecule measurements have proven helpful to understanding the nucleation and growth of DNA condensates. [8][9][10][11][12][13] A few recent experiments concentrated on the kinetics of DNA compaction. They showed that DNA condenses continuously and linearly with time once the compaction process begins. [14][15][16][17] The results seemed to support the widely accepted opinion that the toroid is formed by continuously absorbing DNA to a primary loop randomly nucleated on DNA. The temporal resolution of the experiments was, however, relatively low. They might not be able to resolve the time trajectories of the DNA compaction.Exerting forces on DNA is a useful way to study processes relevant to DNA. 18 The force may slow down the dynamical process so that details can be observed using an apparatus of finite temporal resolution. Here we report single-molecule studies on the dynamics of hexaammine cobalt chloride-induced DNA compaction under tension. It turns out that the compaction process is more sophisticated than the static structural model has suggested. DNA condenses into toroid in a quantized manner.The measurements were performed using transverse magnetic tweezers similar to the one recently developed by Yan and Marko. 19 Two micrometer-sized beads are tethered to the two ends of a λ-phage DNA (16.4 µm). One bead is fixed in space by a micropipette, and the other is free in solution. A magnetic rod is inserted into the solution to generate a constant force to the free magnetic bead. The experiments were done in phosphate-buffered saline (10 mM PBS, 5 mM NaCl, pH ) 7.4). After adjusting the force on DNA, 10 µL of 10 mM hexaammine cobalt chloride solution was added into the sample cell. The final concentration of the trivalent cations was 100 µM. Figure 1a shows the time course of DNA compaction at a force F ) 0.5 pN. Time courses measured at other concentrations of the trivalent cations (from 35 to 200 µM) are quite similar. After addition of the cations, a long induction period was observed before the compaction started. The induction time becomes longer when a less concentrated solution of trivalent cations is added. The compaction is discontinuous and stepwise. The two big steps in Figure 1a consist of multiple small steps. Such discontinuous compactions were also observed...

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

Cited by 203 publications

References 36 publications

Higher-order assembly of microtubules by counterions: From hexagonal bundles to living necklaces

Higher-order assembly of microtubules by counterions: From hexagonal bundles to living necklaces

Phase diagram of the ground states of DNA condensates

Compaction Dynamics of Single DNA Molecules under Tension

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