Semiflexible Polymer Confined in Closed Spaces

Sakaue, Takahiro

doi:10.1021/ma070594r

Cited by 67 publications

(99 citation statements)

References 27 publications

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“…Beyond having relevance to viral packaging, the behavior of polymers in confined geometries has long been a topic of fundamental interest in polymer physics (39)(40)(41) and, more recently, has attracted attention due to emerging applications of nanofabricated devices for DNA manipulation in biotechnology (42). Confinement of single DNA molecules in nanofabricated slits and channels has been extensively studied and shown to increase the molecular relaxation time due to reductions in conformational entropy and hydrodynamic interactions with the confining walls (42)(43)(44).…”

Section: Discussionmentioning

confidence: 99%

Nonequilibrium dynamics and ultraslow relaxation of confined DNA during viral packaging

Berndsen

Keller²,

Grimes

et al. 2014

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

101

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Many viruses use molecular motors that generate large forces to package DNA to near-crystalline densities inside preformed viral proheads. Besides being a key step in viral assembly, this process is of interest as a model for understanding the physics of charged polymers under tight 3D confinement. A large number of theoretical studies have modeled DNA packaging, and the nature of the molecular dynamics and the forces resisting the tight confinement is a subject of wide debate. Here, we directly measure the packaging of single DNA molecules in bacteriophage phi29 with optical tweezers. Using a new technique in which we stall the motor and restart it after increasing waiting periods, we show that the DNA undergoes nonequilibrium conformational dynamics during packaging. We show that the relaxation time of the confined DNA is >10 min, which is longer than the time to package the viral genome and 60,000 times longer than that of the unconfined DNA in solution. Thus, the confined DNA molecule becomes kinetically constrained on the timescale of packaging, exhibiting glassy dynamics, which slows the motor, causes significant heterogeneity in packaging rates of individual viruses, and explains the frequent pausing observed in DNA translocation. These results support several recent hypotheses proposed based on polymer dynamics simulations and show that packaging cannot be fully understood by quasistatic thermodynamic models.soft matter | virology | DNA condensation D NA packaging is both a critical step in viral assembly and a unique model for understanding the physics of polymers under strong confinement. Before packaging, the DNA (∼6-60 μm long) forms a loose random coil of diameter ∼1-3 μm. After translocation into the viral prohead (∼50-100 nm in diameter), a ∼10,000-fold volume compaction is achieved. Packaging is driven by a powerful molecular motor that must work against the large forces resisting confinement arising from DNA bending, repulsion between DNA segments, and entropy loss (1-8).DNA packaging in bacteriophages phi29, lambda, and T4 has been directly measured via single-molecule manipulation with optical tweezers and the packaging motors have been shown to generate forces of >60 pN, among the highest known for biomotors, while translocating DNA at rates ranging from ∼100 bp (for phage phi29, which packages a 19.3-kbp genome into a 42 × 54-nm prohead shell) up to as high as ∼2,000 bp/s (for phage T4, which packages a 171-kbp genome into a 120 × 86-nm prohead) (9-15). The force resisting packaging rises steeply with prohead filling and has been proposed to play an important role in driving viral DNA ejection (16).Recently, a variety of theoretical models for viral DNA packaging have been proposed (3)(4)(5)(17)(18)(19)(20)(21). The simplest treat DNA as an elastic rod with repulsive self-interactions and assume that packaging is a quasistatic thermodynamic process, i.e., that the DNA is able to continuously relax to a free-energy minimum state (3)(4)(5)(19)(20)(21). The DNA arrangement is generally assumed ...

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Section: Discussionmentioning

confidence: 99%

Nonequilibrium dynamics and ultraslow relaxation of confined DNA during viral packaging

Berndsen

Keller²,

Grimes

et al. 2014

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

101

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“…A nonlinear dependence on the chain length: ∆F ∼ N 9/4 0 for a chain with ν = 3/5 (in good solvent) and ∆F ∼ N 3 0 with ν = 1/2 (in θ solvent) is a characteristic of the SC regime [13,14]. By noting the velocity gradient ∇v ξ (t)/ξ(t), the overall dissipation is evaluated as…”

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confidence: 99%

“…In the former case, the entire chain cannot respond to the ejection force acting on a particular monomer residing at the pore immediately, and the highly nonequilibrium process of the front evolution associated with the tension propagation along the chain would occur [21], while in the latter, the pressure drop is transmitted not along the chain, but radially from the pore. These differences in the underlying physics are indeed a consequence of the different confinement regimes [13,14]. (II) The current description based on the analogy with the semidilute solution cannot be applied to the very dense system with φ…”

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confidence: 99%

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Dynamics of Polymer Decompression: Expansion, Unfolding, and Ejection

Sakaue

Yoshinaga

2009

Phys. Rev. Lett.

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The dynamics of polymer decompression from a compact state to swollen conformation can be formally described as nonlinear diffusion. We discuss two basic examples: (i) the expansion, or unfolding from a compact state, and (ii) the ejection of a compressed polymer through a pore. The problem can be solved exactly for case (i), but not for case (ii). Even in such situations, a scheme called uniform approximation is shown to be useful to get a physical insight involved. Its application to the case (ii) is able to account for conflicting numerical data in a consistent way.

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“…14 Slight changes in the pH value or the presence of certain chemical agents may trigger the release for drug delivery in medical applications. 15,16 While the problem of a single semiflexible macromolecule confined inside a sphere has received a lot of attention in the literature, [17][18][19][20][21][22][23][24][25][26][27][28][29][30] addressing issues such as ds DNA packaging in bacteriophage capsids, we here focus on systems containing always many confined chain molecules. Understanding the properties of biomolecules confined inside cells is a problem with many challenging aspects, 31 and a theoretical modeling of such systems in chemical detail would be a premature attempt in view of the large linear dimensions involved.…”

Section: Introductionmentioning

confidence: 99%

Conformations and orientational ordering of semiflexible polymers in spherical confinement

Milchev

Егоров

Nikoubashman

et al. 2017

The Journal of Chemical Physics

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Semiflexible polymers in lyotropic solution confined inside spherical nanoscopic "containers" with repulsive walls are studied by molecular dynamics simulations and density functional theory, as a first step to model confinement effects on stiff polymers inside of miniemulsions, vesicles, and cells. It is shown that the depletion effects caused by the monomer-wall repulsion depend distinctly on the radius R of the sphere. Further, nontrivial orientational effects occur when R, the persistence length p , and the contour length L of the polymers are of similar magnitude. At intermediate densities, a "shell" of wallattached chains is forming, such that the monomers belonging to those chains are in a layer at about the distance of one monomer from the container wall. At the same time, the density of the centers of mass of these chains is peaked somewhat further inside, but still near the wall. However, the arrangement of chains is such that the total monomer density is almost uniform in the sphere, apart from a small layering peak at the wall. It is shown that excluded volume effects among the monomers are crucial to account for this behavior, although they are negligible for comparable isolated single semiflexible chains of the same length. Published by AIP Publishing. [http://dx

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Semiflexible Polymer Confined in Closed Spaces

Cited by 67 publications

References 27 publications

Nonequilibrium dynamics and ultraslow relaxation of confined DNA during viral packaging

Nonequilibrium dynamics and ultraslow relaxation of confined DNA during viral packaging

Dynamics of Polymer Decompression: Expansion, Unfolding, and Ejection

Conformations and orientational ordering of semiflexible polymers in spherical confinement

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