Crowding‐induced organization in cells: spontaneous alignment and sorting of filaments with physiological control points

Herzfeld, Judith

doi:10.1002/jmr.703

Cited by 34 publications

(33 citation statements)

References 42 publications

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“…These forces are considered to be responsible for various mechanisms of self-assembly and spatial organization in living cells (1). Indeed, mismatch in flexibility and tendency to aggregate into elongated chains are exactly the key properties of the nDNA system.…”

Section: Entropy and Energy Combine To Drive The Ndna Phase Separationmentioning

confidence: 99%

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Phase separation and liquid crystallization of complementary sequences in mixtures of nanoDNA oligomers

Zanchetta

Nakata

Buscaglia

et al. 2008

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

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Using optical microscopy, we have studied the phase behavior of mixtures of 12-to 22-bp-long nanoDNA oligomers. The mixtures are chosen such that only a fraction of the sample is composed of mutually complementary sequences, and hence the solutions are effectively mixtures of single-stranded and double-stranded (duplex) oligomers. When the concentrations are large enough, such mixtures phase-separate via the nucleation of duplex-rich liquid crystalline domains from an isotropic background rich in single strands. We find that the phase separation is approximately complete, thus corresponding to a spontaneous purification of duplexes from the single-strand oligos. We interpret this behavior as the combined result of the energy gain from the end-to-end stacking of duplexes and of depletion-type attractive interactions favoring the segregation of the more rigid duplexes from the flexible single strands. This form of spontaneous partitioning of complementary nDNA offers a route to purification of short duplex oligomers and, if in the presence of ligation, could provide a mode of positive feedback for the preferential synthesis of longer complementary oligomers, a mechanism of possible relevance in prebiotic environments.condensation ͉ nucleation ͉ depletion ͉ prebiotic ͉ PEG M olecular crowding of cellular interior is known to play a role in the spontaneous organization of biological macromolecules (1). Several biochemical and physiological processes are found to be influenced by strong packing constraints (2, 3), and complex ordered arrangements, such as liquid-crystalline mesophases, have been shown to arise from highly packed biomolecules (4). Of particular interest is the ordering of highly concentrated DNA in cell nuclei, which can lead to a variety of mesophases in vivo (5). However, whether such ordering caused by packing constraints had represented an evolutionary advantage remains an open question.Concentrated solutions of fully hybridized nanoDNA (nDNA) exhibit various liquid crystalline forms of supramolecular ordering, promoted by end-to-end adhesion of the paired bases at the terminals of the duplexes. This behavior has been reported recently for a wide set of self-complementary (SC) 6-to 20-bp nDNA sequences and for mutually complementary sequences in the same length range (6). Here we explore the phase behavior of mixtures of nDNA in which only some of the sequences are complementary, thus able to pair in double strands (DSs), and part of the sequences are not, and thus always remain in the solution as single strands (SSs). We have found that in concentrated mixtures of duplex and SS nDNA, the system phaseseparates into duplex-rich liquid crystal (LC) domains coexisting with a duplex-poor isotropic phase, leading to the physical segregation of 4-to 6-nm-long complementary chains from noncomplementary ones. This phase separation is a collective effect of the duplex and SS nDNA because the duplexes alone would not form LCs in such solutions, their concentration being well below that required for LC forma...

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Section: Entropy and Energy Combine To Drive The Ndna Phase Separationmentioning

confidence: 99%

“…role in the spontaneous organization of biological macromolecules (1). Several biochemical and physiological processes are found to be influenced by strong packing constraints (2,3), and complex ordered arrangements, such as liquid-crystalline mesophases, have been shown to arise from highly packed biomolecules (4).…”

mentioning

confidence: 99%

Phase separation and liquid crystallization of complementary sequences in mixtures of nanoDNA oligomers

Zanchetta

Nakata

Buscaglia

et al. 2008

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

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“…Onsager first demonstrated that hard core steric interactions suffice to order rods in thermal equilibrium [1]. Above a critical concentration, orientational entropy is sacrificed for gains in translational entropy; therefore, crowding alone induces a temperature-independent isotropic-nematic (I-N) transition [2]. In this entropically driven transition, the kinetic motion of the rods serves as a mechanism for adequately sampling phase space.…”

mentioning

confidence: 99%

Spontaneous Patterning of Confined Granular Rods

et al. 2006

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Vertically vibrated rod-shaped granular materials confined to quasi-2D containers self organize into distinct patterns. We find, consistent with theory and simulation, a density dependent isotropicnematic transition. Along the walls, rods interact sterically to form a wetting layer. For high rod densities, complex patterns emerge as a result of competition between bulk and boundary alignment. A continuum elastic energy accounting for nematic distortion and local wall anchoring reproduces the structures seen experimentally.PACS numbers: 45.70.Qj, 61.30.Eb, 61.30.Hn From nanometer sized molecules forming liquid crystals to timber floating down a river, rod shaped materials pervade our everyday existence. Onsager first demonstrated that hard core steric interactions suffice to order rods in thermal equilibrium [1]. Above a critical concentration, orientational entropy is sacrificed for gains in translational entropy; therefore, crowding alone induces a temperature-independent isotropic-nematic (I-N) transition [2]. In this entropically driven transition, the kinetic motion of the rods serves as a mechanism for adequately sampling phase space. While thermal excitation mixes microscopic particles, macroscopic rods require an externally applied energy for randomization. For both vertical and horizontal vibrations, a density dependent nematic to smectic-like transition was previously observed for granular rods [3]. Such driven dissipative systems, however, are far from equilibrium and need not evolve to states of maximal configurational entropy. For example, prior studies utilizing macroscopic rods focused on jammed or other metastable states [3,4].Here, we report on finite-sized driven dissipative granular systems of rods in steady-state that share many properties of lyotropic liquid crystals at equilibrium. We find that short ranged hard core interactions determine the arrangement of the moving rods for all densities. A phase transition from a disordered isotropic state to a nematiclike state occurs as a function of rod density and rod aspect (length-to-diameter) ratio, L/D. By using excluded volume scaling predicted by mean field theories for liquid crystals, our data give a single normalized transition density for all rod L/D and densities tested.However, excluded volume interactions in the bulk cannot explain all rod behavior because confining boundaries also strongly influence rod ordering. For relatively low rod densities, experimental results for rod alignment and density profiles with respect to the wall strikingly resemble theoretical predictions [5], indicating that rods interact via hard core steric repulsions with the surrounding boundaries. As the rods become dense, rod ordering in the bulk nematic competes with rod ordering along the surrounding walls. This frustration creates distinct yet easily reproduced patterns. We account for observed structures by modeling the system as a liquid crystal undergoing the elastic deformations of splay and bend subject to a simple wall interaction [6,7]. Moreover, w...

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“…Here too, a decrease in free volume drives these processes. 9,22 The crucial difference of course is that in our case free volume is primarily linked with the volume the particles themselves take up, whereas in the more conventional case it is caused by the mutual excluded volume of groups of particles.…”

Section: Summary and Discussionmentioning

confidence: 92%

“…20 Indeed, in an increasing number of experiments, crowding agents are added or the experiments are carried out in living cells to address crowding-related effects, e.g., in complexation and folding. 21 While our understanding of how crowding induces phase separation in multi-component systems is relatively advanced, [22][23][24] much less is known about how self-crowding affects protein phase behaviour in the liquid phase. Here, we study theoretically how a combination of volume exclusion and attractive interactions influences the switching between two conformational states of a model protein and through that its solution phase behaviour.…”

Section: Introductionmentioning

confidence: 99%

Self-crowding induced phase separation in protein dispersions

Stegen

Schoot

2015

The Journal of Chemical Physics

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The coupling between protein conformation, molecular volume, and solution phase behaviour is studied theoretically for a two-state, coarse-grained protein model in which protein molecules can reversibly switch between a native and a non-native excited state. In the model, native and non-native conformers are represented by perfect spheres with different hard-core diameters. We presume the larger, non-native species to attract each other through some unspecified potential. We find that at low concentrations the native state is stabilised energetically and that at high concentrations the native state is again stabilised but this time by self-crowding, i.e., a lack of free volume. These two regimes are separated by two first-order transitions from a region where the non-native conformational state is prevalent, stabilised by attractive interactions between the proteins. The calculated phase diagram is very sensitive to even quite small differences in particle volumes and has unusual features, including the loss of a critical point if the size difference is sufficiently large. C 2015 AIP Publishing LLC. [http://dx

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Crowding‐induced organization in cells: spontaneous alignment and sorting of filaments with physiological control points

Cited by 34 publications

References 42 publications

Phase separation and liquid crystallization of complementary sequences in mixtures of nanoDNA oligomers

Phase separation and liquid crystallization of complementary sequences in mixtures of nanoDNA oligomers

Spontaneous Patterning of Confined Granular Rods

Self-crowding induced phase separation in protein dispersions

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